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Shrestha R, Carpenter TS, Van QN, Agamasu C, Tonelli M, Aydin F, Chen D, Gulten G, Glosli JN, López CA, Oppelstrup T, Neale C, Gnanakaran S, Gillette WK, Ingólfsson HI, Lightstone FC, Stephen AG, Streitz FH, Nissley DV, Turbyville TJ. Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane. Commun Biol 2024; 7:242. [PMID: 38418613 PMCID: PMC10902389 DOI: 10.1038/s42003-024-05916-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.
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Affiliation(s)
- Rebika Shrestha
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Que N Van
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Constance Agamasu
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Fikret Aydin
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - De Chen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Gulcin Gulten
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - James N Glosli
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Tomas Oppelstrup
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - William K Gillette
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Felice C Lightstone
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Andrew G Stephen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Frederick H Streitz
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Dwight V Nissley
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA
| | - Thomas J Turbyville
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA.
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Bhatia H, Aydin F, Carpenter TS, Lightstone FC, Bremer PT, Ingólfsson HI, Nissley DV, Streitz FH. The confluence of machine learning and multiscale simulations. Curr Opin Struct Biol 2023; 80:102569. [PMID: 36966691 DOI: 10.1016/j.sbi.2023.102569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 06/04/2023]
Abstract
Multiscale modeling has a long history of use in structural biology, as computational biologists strive to overcome the time- and length-scale limits of atomistic molecular dynamics. Contemporary machine learning techniques, such as deep learning, have promoted advances in virtually every field of science and engineering and are revitalizing the traditional notions of multiscale modeling. Deep learning has found success in various approaches for distilling information from fine-scale models, such as building surrogate models and guiding the development of coarse-grained potentials. However, perhaps its most powerful use in multiscale modeling is in defining latent spaces that enable efficient exploration of conformational space. This confluence of machine learning and multiscale simulation with modern high-performance computing promises a new era of discovery and innovation in structural biology.
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Affiliation(s)
- Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA. https://twitter.com/@harshbhatia85
| | - Fikret Aydin
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Felice C Lightstone
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Peer-Timo Bremer
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Dwight V Nissley
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD, 21701, USA.
| | - Frederick H Streitz
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
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3
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Ingólfsson HI, Bhatia H, Aydin F, Oppelstrup T, López CA, Stanton LG, Carpenter TS, Wong S, Di Natale F, Zhang X, Moon JY, Stanley CB, Chavez JR, Nguyen K, Dharuman G, Burns V, Shrestha R, Goswami D, Gulten G, Van QN, Ramanathan A, Van Essen B, Hengartner NW, Stephen AG, Turbyville T, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, Nissley DV, Streitz FH. Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure. J Chem Theory Comput 2023; 19:2658-2675. [PMID: 37075065 PMCID: PMC10173464 DOI: 10.1021/acs.jctc.2c01018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Interdependence across time and length scales is common in biology, where atomic interactions can impact larger-scale phenomenon. Such dependence is especially true for a well-known cancer signaling pathway, where the membrane-bound RAS protein binds an effector protein called RAF. To capture the driving forces that bring RAS and RAF (represented as two domains, RBD and CRD) together on the plasma membrane, simulations with the ability to calculate atomic detail while having long time and large length- scales are needed. The Multiscale Machine-Learned Modeling Infrastructure (MuMMI) is able to resolve RAS/RAF protein-membrane interactions that identify specific lipid-protein fingerprints that enhance protein orientations viable for effector binding. MuMMI is a fully automated, ensemble-based multiscale approach connecting three resolution scales: (1) the coarsest scale is a continuum model able to simulate milliseconds of time for a 1 μm2 membrane, (2) the middle scale is a coarse-grained (CG) Martini bead model to explore protein-lipid interactions, and (3) the finest scale is an all-atom (AA) model capturing specific interactions between lipids and proteins. MuMMI dynamically couples adjacent scales in a pairwise manner using machine learning (ML). The dynamic coupling allows for better sampling of the refined scale from the adjacent coarse scale (forward) and on-the-fly feedback to improve the fidelity of the coarser scale from the adjacent refined scale (backward). MuMMI operates efficiently at any scale, from a few compute nodes to the largest supercomputers in the world, and is generalizable to simulate different systems. As computing resources continue to increase and multiscale methods continue to advance, fully automated multiscale simulations (like MuMMI) will be commonly used to address complex science questions.
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Affiliation(s)
- Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Tomas Oppelstrup
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Liam G Stanton
- Department of Mathematics and Statistics, San José State University, San José, California 95192, United States
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sergio Wong
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Xiaohua Zhang
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Joseph Y Moon
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Joseph R Chavez
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Gautham Dharuman
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Rebika Shrestha
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland 21701, United States
| | - Debanjan Goswami
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland 21701, United States
| | - Gulcin Gulten
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland 21701, United States
| | - Que N Van
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland 21701, United States
| | - Arvind Ramanathan
- Computing, Environment & Life Sciences (CELS) Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Brian Van Essen
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Andrew G Stephen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland 21701, United States
| | - Thomas Turbyville
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland 21701, United States
| | - Peer-Timo Bremer
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - James N Glosli
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Felice C Lightstone
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Dwight V Nissley
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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4
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Aydin F, Andrade MFC, Stinson RS, Zagalskaya A, Schwalbe-Koda D, Chen Z, Sharma S, Maiti A, Esposito DV, Ardo S, Pham TA, Ogitsu T. Mechanistic Insights on Permeation of Water over Iron Cations in Nanoporous Silicon Oxide Films for Selective H 2 and O 2 Evolution. ACS Appl Mater Interfaces 2023; 15:17814-17824. [PMID: 36975208 DOI: 10.1021/acsami.2c22865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Electrocatalysts encapsulated by an ultrathin and semipermeable oxide layer offer a promising avenue for efficient, selective, and cost-effective production of hydrogen through photoelectrochemical water splitting. This architecture is especially attractive for Z-scheme water splitting, for which a nanoporous oxide film can be leveraged to mitigate undesired, yet kinetically facile, reactions involving redox shuttles, such as aqueous iron cations, by limiting transport of these species to catalytically active sites. In this work, molecular dynamics simulations were combined with electrochemical measurements to provide a mechanistic understanding of permeation of water and Fe(III)/Fe(II) redox shuttles through nanoporous SiO2 films. It is shown that even for SiO2 pores with a width as small as 0.8 nm, water does not experience any energy barrier for permeating into the pores due to a favorable interaction with hydrophilic silanol groups on the oxide surface. In contrast, permeation of Fe(III) and Fe(II) into microporous SiO2 pores is limited due to high energy barriers, which stem from a combination of distortion and dehydration of the second and third ion solvation shells. Our simulations and experimental results show that SiO2 coatings can effectively mitigate undesired Fe(III)/Fe(II) redox reactions at underlying electrodes by attenuating permeation of iron cations, while allowing water to permeate and thus participate in water splitting reactions. In a broader context, our study demonstrates that selectivity of solvated cations can be manipulated by controlling the pore size and surface chemistry of oxide films.
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Affiliation(s)
- Fikret Aydin
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Marcos F Calegari Andrade
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Robert S Stinson
- Chemical Engineering Department, Columbia Electrochemical Energy Center, Columbia University, New York, New York 10027, United States
| | - Alexandra Zagalskaya
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel Schwalbe-Koda
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Zejie Chen
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Shubham Sharma
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Amitesh Maiti
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel V Esposito
- Chemical Engineering Department, Columbia Electrochemical Energy Center, Columbia University, New York, New York 10027, United States
| | - Shane Ardo
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Tuan Anh Pham
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Tadashi Ogitsu
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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5
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Aluru NR, Aydin F, Bazant MZ, Blankschtein D, Brozena AH, de Souza JP, Elimelech M, Faucher S, Fourkas JT, Koman VB, Kuehne M, Kulik HJ, Li HK, Li Y, Li Z, Majumdar A, Martis J, Misra RP, Noy A, Pham TA, Qu H, Rayabharam A, Reed MA, Ritt CL, Schwegler E, Siwy Z, Strano MS, Wang Y, Yao YC, Zhan C, Zhang Z. Fluids and Electrolytes under Confinement in Single-Digit Nanopores. Chem Rev 2023; 123:2737-2831. [PMID: 36898130 PMCID: PMC10037271 DOI: 10.1021/acs.chemrev.2c00155] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification to new gas permeable materials for water electrolyzers and energy-storage devices. SDNs also present unique opportunities to achieve ultrasensitive and selective chemical sensing at the single-ion and single-molecule limit. In this review article, we summarize the progress on nanofluidics of SDNs, with a focus on the confinement effects that arise in these extremely narrow nanopores. The recent development of precision model systems, transformative experimental tools, and multiscale theories that have played enabling roles in advancing this frontier are reviewed. We also identify new knowledge gaps in our understanding of nanofluidic transport and provide an outlook for the future challenges and opportunities at this rapidly advancing frontier.
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Affiliation(s)
- Narayana R Aluru
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Fikret Aydin
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Daniel Blankschtein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Alexandra H Brozena
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Samuel Faucher
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - John T Fourkas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Hao-Kun Li
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Yuhao Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zhongwu Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Arun Majumdar
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Joel Martis
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Rahul Prasanna Misra
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Tuan Anh Pham
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Haoran Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - Archith Rayabharam
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Mark A Reed
- Department of Electrical Engineering, Yale University, 15 Prospect Street, New Haven, Connecticut06520, United States
| | - Cody L Ritt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Eric Schwegler
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zuzanna Siwy
- Department of Physics and Astronomy, Department of Chemistry, Department of Biomedical Engineering, University of California, Irvine, Irvine92697, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Yun-Chiao Yao
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Cheng Zhan
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Ze Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
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6
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Aydin F, Georgouli K, Dharuman G, Glosli JN, Carpenter TS, Lightstone FC, Ingolfsson H, Bremer PT, Bhatia H. Predicting membrane orientational states of RAS and RAS-RAF based on the lipid environment using deep learning. Biophys J 2023; 122:506a. [PMID: 36784613 DOI: 10.1016/j.bpj.2022.11.2697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Fikret Aydin
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | | | - James N Glosli
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Felice C Lightstone
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | | | - Harsh Bhatia
- Lawrence Livermore National Laboratory, Livermore, CA, USA
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7
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López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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8
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Abstract
Nanopores lined with hydrophobic groups function as switches for water and all dissolved species, such that transport is allowed only when applying a sufficiently high transmembrane pressure difference or voltage. Here we show a hydrophobic nanopore system whose wetting and ability to transport water and ions is rectified and can be controlled with salt concentration. The nanopore we study contains a junction between a hydrophobic zone and a positively charged hydrophilic zone. The nanopore is closed for transport at low salt concentrations and exhibits finite current only when the concentration reaches a threshold value that is dependent on the pore opening diameter, voltage polarity and magnitude, and type of electrolyte. The smallest nanopore studied here had a 4 nm diameter and did not open for transport in any concentration of KCl or KI examined. A 12 nm nanopore was closed for all KCl solutions but conducted current in KI at concentrations above 100 mM for negative voltages and opened for both voltage polarities at 500 mM KI. Nanopores with a hydrophobic/hydrophilic junction can thus function as diodes, such that one can identify a range of salt concentrations where the pores transport water and ions for only one voltage polarity. Molecular dynamics simulations together with continuum models provided a multiscale explanation of the observed phenomena and linked the salt concentration dependence of wetting with an electrowetting model. Results presented are crucial for designing next-generation chemical and ionic separation devices as well as understanding fundamental properties of hydrophobic interfaces under nanoconfinement.
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Affiliation(s)
- Jake W Polster
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Fikret Aydin
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Tuan Anh Pham
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Zuzanna S Siwy
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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9
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Sandikci F, Kokurcan A, Guler Çimen S, Çimen S, Taşkın Türkmenoğlu T, Aydin F, İmamoğlu M. The effect of everolimus on ureteral anastomosis and renal ischemia reperfusion injury. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)01166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Buchsbaum SF, Jue ML, Sawvel AM, Chen C, Meshot ER, Jin Park S, Wood M, Jen Wu K, Bilodeau CL, Aydin F, Anh Pham T, Lau EY, Fornasiero F. Fast diffusive transport through carbon nanotube pores. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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11
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Aydin F, Durumeric AEP, da Hora GCA, Nguyen JDM, Oh MI, Swanson JMJ. Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables. J Chem Phys 2021; 155:045101. [PMID: 34340389 DOI: 10.1063/5.0055489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Understanding the permeation of biomolecules through cellular membranes is critical for many biotechnological applications, including targeted drug delivery, pathogen detection, and the development of new antibiotics. To this end, computer simulations are routinely used to probe the underlying mechanisms of membrane permeation. Despite great progress and continued development, permeation simulations of realistic systems (e.g., more complex drug molecules or biologics through heterogeneous membranes) remain extremely challenging if not intractable. In this work, we combine molecular dynamics simulations with transition-tempered metadynamics and techniques from the variational approach to conformational dynamics to study the permeation mechanism of a drug molecule, trimethoprim, through a multicomponent membrane. We show that collective variables (CVs) obtained from an unsupervised machine learning algorithm called time-structure based Independent Component Analysis (tICA) improve performance and substantially accelerate convergence of permeation potential of mean force (PMF) calculations. The addition of cholesterol to the lipid bilayer is shown to increase both the width and height of the free energy barrier due to a condensing effect (lower area per lipid) and increase bilayer thickness. Additionally, the tICA CVs reveal a subtle effect of cholesterol increasing the resistance to permeation in the lipid head group region, which is not observed when canonical CVs are used. We conclude that the use of tICA CVs can enable more efficient PMF calculations with additional insight into the permeation mechanism.
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Affiliation(s)
- Fikret Aydin
- Quantum Simulation Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | | | - Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - John D M Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Myong In Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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12
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Zhan C, Sun Y, Aydin F, Wang YM, Pham TA. Erratum: "Confinement effects on the solvation structure of solvated alkaline metal cations in a single-digit 1T-MoS 2 nanochannel: A first-principles study" [J. Chem. Phys. 154, 164706 (2021)]. J Chem Phys 2021; 154:209903. [PMID: 34241184 DOI: 10.1063/5.0056265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Cheng Zhan
- Material Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Yangyunli Sun
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Fikret Aydin
- Material Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Y Morris Wang
- Department of Materials Science and Engineering, University of California, Los Angeles, California 90095, USA
| | - Tuan Anh Pham
- Material Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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13
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Oyarzun DI, Zhan C, Hawks SA, Cerón MR, Kuo HA, Loeb CK, Aydin F, Pham TA, Stadermann M, Campbell PG. Unraveling the Ion Adsorption Kinetics in Microporous Carbon Electrodes: A Multiscale Quantum-Continuum Simulation and Experimental Approach. ACS Appl Mater Interfaces 2021; 13:23567-23574. [PMID: 33979129 DOI: 10.1021/acsami.1c01640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding sorption in porous carbon electrodes is crucial to many environmental and energy technologies, such as capacitive deionization (CDI), supercapacitor energy storage, and activated carbon filters. In each of these examples, a practical model that can describe ion electrosorption kinetics is highly desirable for accelerating material design. Here, we proposed a multiscale model to study the ion electrosorption kinetics in porous carbon electrodes by combining quantum mechanical simulations with continuum approaches. Our model integrates the Butler-Volmer (BV) equation for sorption kinetics and a continuously stirred tank reactor (CSTR) formulation with atomistic calculations of ion hydration and ion-pore interactions based on density functional theory (DFT). We validated our model experimentally by using ion mixtures in a flow-through electrode CDI device and developed an in-line UV absorption system to provide unprecedented resolution of individual ions in the separation process. We showed that the multiscale model captures unexpected experimental phenomena that cannot be explained by the traditional ion electrosorption theory. The proposed multiscale framework provides a viable approach for modeling separation processes in systems where pore sizes and ion hydration effects strongly influence the sorption kinetics, which can be leveraged to explore possible strategies for improving carbon-based and, more broadly, pore-based technologies.
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Affiliation(s)
- Diego I Oyarzun
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Cheng Zhan
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Steven A Hawks
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Maira R Cerón
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Helen A Kuo
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Colin K Loeb
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Fikret Aydin
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Tuan Anh Pham
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Michael Stadermann
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Patrick G Campbell
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
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14
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Zhan C, Sun Y, Aydin F, Wang YM, Pham TA. Confinement effects on the solvation structure of solvated alkaline metal cations in a single-digit 1T-MoS 2 nanochannel: A first-principles study. J Chem Phys 2021; 154:164706. [PMID: 33940836 DOI: 10.1063/5.0047554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Confinement plays an important role in determining ion transport in porous materials, which, in turn, may influence the performance of many energy storage and desalination devices. In this work, we combined density functional theory (DFT) with an implicit solvation model and ab initio molecular dynamics (AIMD) to investigate the effects of nanoconfinement on several solvated alkaline metal cations in a single-digit 1T-MoS2 nanochannel. Our DFT calculations with a solvation model indicated that cations with stronger hydration energy introduce a higher number of co-intercalated water molecules into the channel, consistent with early experimental observation obtained for MXene (2D transition metal carbide) channels. The predicted optimal water numbers for the cations were then used for AIMD simulations that explicitly include the effects of the solvent. When compared with the cations in bulk solution, our simulations showed that the hydration structure and coordination number (CN) of the solvated cations confined in the MoS2 channel can be significantly altered. We found that larger cations with weaker hydration energy (K+, Rb+, and Cs+) exhibited a distinctive CN decrease under confinement, while smaller cations (Li+ and Na+) retained a similar hydration shell as in the bulk solution. More specifically, the hydration shell of large cations (K+, Rb+, and Cs+) in MoS2 showed similar features of the coordination angle to the bulk, which suggests the partially broken hydration shell with no geometry change under confinement. Our simulations provided insights into the change of the hydration structure of alkaline metal cations under confinement, which may have important implications on their transport in the 1T-MoS2 channel.
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Affiliation(s)
- Cheng Zhan
- Material Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Yangyunli Sun
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Fikret Aydin
- Material Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Y Morris Wang
- Department of Materials Science and Engineering, University of California, Log Angeles, California 90095, USA
| | - Tuan Anh Pham
- Material Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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15
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Sakci Z, Aydin F, Ceylan O, Ogul H. Sinonasal teratocarcinosarcoma mimicking chronic invasive fungal disease of paranasal sinuses. Ann R Coll Surg Engl 2021; 103:e193-e195. [PMID: 33852367 DOI: 10.1308/rcsann.2020.7088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Sinonasal teratoid carcinosarcoma or teratocarcinoma is an extremely rare aggressive tumour. It usually arises in the nasal cavity and paranasal sinuses. In this study, the authors described magnetic resonance imaging and computed tomography findings from a patient with sinonasal teratocarcinoma. Computed tomography of the sinonasal teratoid carcinosarcoma can mimic paranasal fungal infections. Magnetic resonance imaging is a very useful tool for making a differential diagnosis between the sinonasal teratoid carcinosarcoma and paranasal sinusitis.
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Affiliation(s)
- Z Sakci
- Umraniye Training and Research Hospital, Istanbul, Turkey
| | - F Aydin
- Ataturk University, Erzurum, Turkey
| | - O Ceylan
- Umraniye Training and Research Hospital, Istanbul, Turkey
| | - H Ogul
- Umraniye Training and Research Hospital, Istanbul, Turkey
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16
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Aydin F, Moradzadeh A, Bilodeau CL, Lau EY, Schwegler E, Aluru NR, Pham TA. Ion Solvation and Transport in Narrow Carbon Nanotubes: Effects of Polarizability, Cation-π Interaction, and Confinement. J Chem Theory Comput 2021; 17:1596-1605. [PMID: 33625224 DOI: 10.1021/acs.jctc.0c00827] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding ion solvation and transport under confinement is critical for a wide range of emerging technologies, including water desalination and energy storage. While molecular dynamics (MD) simulations have been widely used to study the behavior of confined ions, considerable deviations between simulation results depending on the specific treatment of intermolecular interactions remain. In the following, we present a systematic investigation of the structure and dynamics of two representative solutions, that is, KCl and LiCl, confined in narrow carbon nanotubes (CNTs) with a diameter of 1.1 and 1.5 nm, using a combination of first-principles and classical MD simulations. Our simulations show that the inclusion of both polarization and cation-π interactions is essential for the description of ion solvation under confinement, particularly for large ions with weak hydration energies. Beyond the variation in ion solvation, we find that cation-π interactions can significantly influence the transport properties of ions in CNTs, particularly for KCl, where our simulations point to a strong correlation between ion dehydration and diffusion. Our study highlights the complex interplay between nanoconfinement and specific intermolecular interactions that strongly control the solvation and transport properties of ions.
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Affiliation(s)
- Fikret Aydin
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
| | - Alireza Moradzadeh
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Camille L Bilodeau
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Edmond Y Lau
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
| | - Eric Schwegler
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tuan Anh Pham
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, California 94550, United States
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17
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Buchsbaum SF, Jue ML, Sawvel AM, Chen C, Meshot ER, Park SJ, Wood M, Wu KJ, Bilodeau CL, Aydin F, Pham TA, Lau EY, Fornasiero F. Fast Permeation of Small Ions in Carbon Nanotubes. Adv Sci (Weinh) 2021; 8:2001802. [PMID: 33552850 PMCID: PMC7856893 DOI: 10.1002/advs.202001802] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Simulations and experiments have revealed enormous transport rates through carbon nanotube (CNT) channels when a pressure gradient drives fluid flow, but comparatively little attention has been given to concentration-driven transport despite its importance in many fields. Here, membranes are fabricated with a known number of single-walled CNTs as fluid transport pathways to precisely quantify the diffusive flow through CNTs. Contrary to early experimental studies that assumed bulk or hindered diffusion, measurements in this work indicate that the permeability of small ions through single-walled CNT channels is more than an order of magnitude higher than through the bulk. This flow enhancement scales with the ion free energy of transfer from bulk solutions to a nanoconfined, lower-dielectric environment. Reported results suggest that CNT membranes can unlock dialysis processes with unprecedented efficiency.
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Affiliation(s)
- Steven F. Buchsbaum
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Melinda L. Jue
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - April M. Sawvel
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Chiatai Chen
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Eric R. Meshot
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Sei Jin Park
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Marissa Wood
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Kuang Jen Wu
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Camille L. Bilodeau
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic InstituteTroyNY12180USA
| | - Fikret Aydin
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Tuan Anh Pham
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Edmond Y. Lau
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Francesco Fornasiero
- Physical and Life SciencesLawrence Livermore National LaboratoryLivermoreCA94550USA
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18
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Deaton TA, Aydin F, Li NK, Chu X, Dutt M, Yingling YG. Dissipative Particle Dynamics Approaches to Modeling the Self-Assembly and Morphology of Neutral and Ionic Block Copolymers in Solution. Foundations of Molecular Modeling and Simulation 2021. [DOI: 10.1007/978-981-33-6639-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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19
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Aydin F, Cerón MR, Hawks SA, Oyarzun DI, Zhan C, Pham TA, Stadermann M, Campbell PG. Selectivity of nitrate and chloride ions in microporous carbons: the role of anisotropic hydration and applied potentials. Nanoscale 2020; 12:20292-20299. [PMID: 33001104 DOI: 10.1039/d0nr04496b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding ion transport in porous carbons is critical for a wide range of technologies, including supercapacitors and capacitive deionization for water desalination, yet many details remain poorly understood. For instance, an atomistic understanding of how ion selectivity is influenced by the molecular shape of ions, morphology of the micropores and applied voltages is largely lacking. In this work, we combined molecular dynamics simulations with enhanced sampling methods to elucidate the mechanism of nitrate and chloride selectivity in subnanometer graphene slit-pores. We show that nitrate is preferentially adsorbed over chloride in the slit-like micropores. This preferential adsorption was found to stem from the weaker hydration energy and unique anisotropy of the ion solvation of nitrate. Beside the effects of ion dehydration, we found that applied potential plays an important role in determining the ion selectivity, leading to a lower selectivity of nitrate over chloride at a high applied potential. We conclude that the measured ion selectivity results from a complex interplay between voltage, confinement, and specific ion effects-including ion shape and local hydration structure.
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Affiliation(s)
- Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Maira R Cerón
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Steven A Hawks
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Diego I Oyarzun
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Cheng Zhan
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Tuan Anh Pham
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Michael Stadermann
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Patrick G Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
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20
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Cerón MR, Aydin F, Hawks SA, Oyarzun DI, Loeb CK, Deinhart A, Zhan C, Pham TA, Stadermann M, Campbell PG. Cation Selectivity in Capacitive Deionization: Elucidating the Role of Pore Size, Electrode Potential, and Ion Dehydration. ACS Appl Mater Interfaces 2020; 12:42644-42652. [PMID: 32869974 DOI: 10.1021/acsami.0c07903] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Capacitive deionization (CDI) is a promising water desalination technology that is applicable to the treatment of low-salinity brackish waters and the selective removal of ionic contaminants. In this work, we show that by making a small change in the synthetic procedure of hierarchical carbon aerogel monolith (HCAM) electrodes, we can adjust the pore-size distribution and tailor the selectivity, effectively switching between selective adsorption of calcium or sodium ions. Ion selectivity was measured for a mixture of 5 mM NaCl and 2.5 mM CaCl2. For the low activated flow-through CDI (fteCDI) cell, we observed extremely high sodium selectivity over calcium (SNa/Ca ≫ 10, no Ca2+ adsorbed) at all of the applied potentials, while for the highly activated fteCDI cell, we observed a selectivity value of 6.6 ± 0.8 at 0.6 V for calcium over sodium that decreased to 2.2 ± 0.03 at 1.2 V. Molecular dynamics simulations indicated that the loss in Ca2+ selectivity over Na+ at high applied voltages could be due to a competition between ion-pore electrostatic interactions and volume exclusion ("crowding") effects. Interestingly, we also find with these simulations that the relative sizes of the ions change due to changes in hydration at a higher voltage.
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Affiliation(s)
- Maira R Cerón
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Fikret Aydin
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Steven A Hawks
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Diego I Oyarzun
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Colin K Loeb
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Amanda Deinhart
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Cheng Zhan
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Tuan Anh Pham
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Michael Stadermann
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Patrick G Campbell
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
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21
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Li Y, Li Z, Aydin F, Quan J, Chen X, Yao YC, Zhan C, Chen Y, Pham TA, Noy A. Water-ion permselectivity of narrow-diameter carbon nanotubes. Sci Adv 2020; 6:6/38/eaba9966. [PMID: 32938679 PMCID: PMC7494338 DOI: 10.1126/sciadv.aba9966] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Carbon nanotube (CNT) pores, which mimic the structure of the aquaporin channels, support extremely high water transport rates that make them strong candidates for building artificial water channels and high-performance membranes. Here, we measure water and ion permeation through 0.8-nm-diameter CNT porins (CNTPs)-short CNT segments embedded in lipid membranes-under optimized experimental conditions. Measured activation energy of water transport through the CNTPs agrees with the barrier values typical for single-file water transport. Well-tempered metadynamics simulations of water transport in CNTPs also report similar activation energy values and provide molecular-scale details of the mechanism for water entry into these channels. CNTPs strongly reject chloride ions and show water-salt permselectivity values comparable to those of commercial desalination membranes.
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Affiliation(s)
- Yuhao Li
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Zhongwu Li
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Fikret Aydin
- Quantum Simulations Group, Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Jana Quan
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Xi Chen
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA 94343, USA
| | - Yun-Chiao Yao
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA 94343, USA
| | - Cheng Zhan
- Quantum Simulations Group, Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Tuan Anh Pham
- Quantum Simulations Group, Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
- School of Natural Sciences, University of California Merced, Merced, CA 94343, USA
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22
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Aydin F, Abay M, Şahin O, Abay S, Karakaya E, Müştak İB, Müştak HK, Gümüşsoy KS, Kayman T. Species distribution, genetic diversity and antimicrobial susceptibility of Campylobacter isolates recovered from the preputial cavity of healthy rams in Turkey. J Appl Microbiol 2020; 129:1173-1184. [PMID: 32416023 DOI: 10.1111/jam.14703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 11/30/2022]
Abstract
AIMS Campylobacter sp. are important causes of reproductive disease in ruminants worldwide. Although healthy bulls are well-known carriers for infection of cows, the role of rams as a potential source for infecting ewes is unclear. This study aimed to determine prevalence, species distribution, genetic diversity and antimicrobial susceptibility profiles of Campylobacter sp. isolated from the preputial cavity of healthy rams. METHODS AND RESULTS The material of this prospective study comprised 191 swab samples taken from the preputial cavity of healthy rams. Enrichment and membrane filtration were employed for the isolation of Campylobacter. Presumptive isolates were confirmed as Campylobacter by phenotypic and molecular tests. 16S rRNA gene sequence analysis was used for the definitive identification of the isolates at species level, and genotyping was performed using pulsed-field gel electrophoresis (PFGE). The susceptibility of the Campylobacter sp. isolates to various antibiotics was determined by the disk diffusion test. In all, 27 of the 191 (14·13%) swab samples were found to be positive for Campylobacter sp. (28 isolates were recovered in total). Per phenotypic and genotypic analyses, one isolate was identified as Campylobacter mucosalis and the remaining 27 isolates were identified as Campylobacter sputorum bv. faecalis. The PFGE analysis of the C. sputorum biovar faecalis isolates produced 17 clusters and 24 different pulsotypes, indicating high genetic heterogeneity. All 28 isolates were found to be susceptible to all of the antibiotics tested. CONCLUSIONS Healthy rams may be an important reservoir of different Campylobacter species in the preputium. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrated for the first time that healthy rams can carry different Campylobacter sp. including genetically diverse C. sputorum bv. faecalis and C. mucosalis in the preputial cavity. Further investigation on the potential implication of this finding on sheep reproductive health (e.g. infectious infertility, and abortion) and overall epidemiology of Campylobacter may be warranted.
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Affiliation(s)
- F Aydin
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - M Abay
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - O Şahin
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
| | - S Abay
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - E Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - İ B Müştak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - H K Müştak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - K S Gümüşsoy
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - T Kayman
- Medical Microbiology Clinic, Şişli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
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23
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Li Z, Li Y, Yao YC, Aydin F, Zhan C, Chen Y, Elimelech M, Pham TA, Noy A. Strong Differential Monovalent Anion Selectivity in Narrow Diameter Carbon Nanotube Porins. ACS Nano 2020; 14:6269-6275. [PMID: 32347708 DOI: 10.1021/acsnano.0c02423] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inner pores of carbon nanotubes combine extremely fast water transport and ion selectivity that could potentially be useful for high-performance water desalination and separation applications. We used dye-quenching halide assays and stopped-flow spectrometry to determine intrinsic permeability of three small monovalent halide anions (chloride, bromide, iodide) and one pseudohalide anion (thiocyanate) through narrow 0.8 nm diameter carbon nanotube porins (CNTPs). These measurements revealed unexpectedly strong differential ion selectivity with permeabilities of different ions varying by up to 2 orders of magnitude. Removal of the negative charge from the nanotube entrance increased anion permeability by only a relatively small factor, indicating that electrostatic repulsion was not a major determinant of CNTP selectivity. First principle molecular dynamics simulations revealed that the origin of this strong differential ion selectivity is partial dehydration of anions upon entry into the narrow CNTP channels.
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Affiliation(s)
- Zhongwu Li
- Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yuhao Li
- Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Yun-Chiao Yao
- Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
- School of Natural Sciences, University of California Merced, Merced, California 94343, United States
| | - Fikret Aydin
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Cheng Zhan
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Tuan Anh Pham
- Quantum Simulations Group, Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Aleksandr Noy
- Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
- School of Natural Sciences, University of California Merced, Merced, California 94343, United States
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24
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Bilgic A, Aydin F, Sumer P, Keskiner I, Koc S, Bozkurt S, Mumcu G, Alpsoy E, Uzun S, Akman-Karakas A. Oral health related qualıty of lıfe and dısease severıty ın autoımmune bullous dıseases. Niger J Clin Pract 2020; 23:159-164. [PMID: 32031089 DOI: 10.4103/njcp.njcp_216_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background There is an increased risk of long-term dental and periodontal disease in autoimmune bullous diseases (AIBD). Aims In this cross-sectional study, we aimed to determine whether the oral health-related quality of life status (OHRQoL) was associated with disease severity and activity in patients with AIBD. Subjects and Methods 67 patients with AIBD were enrolled in this study. Autoimmune Bullous Skin Disorder Intensity Score (ABSIS) was used to evaluate the disease severity. The score was categorized as a significant course (≥17) and moderate course (<17). Oral health impact profile-14 (OHIP-14) questionnaire was filled to assess the OHRQoL. Self-reported oral health status and oral lesion related pain score were also evaluated in the study group. Results OHIP-14 score was significantly higher in active patients (42.28 ± 13.66) than inactive patients (29.08 ± 12.25) (P = 0.004) and it was correlated with the pain score (6.33 ± 2.78; r = 0.409, P = 0.013). Furthermore, OHIP-14 score was higher in patients with a significant disease course (45.18 ± 15.08) (P = 0.010) than in patients with a moderate course (36.09 ± 9.73). Conclusions OHRQoL may be useful in the disease management and treatment. Since it can be affected by both presence of oral erosions and disease severity, a collaboration between dermatologists and dentists could be crucial to the disease management in AIBD.
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Affiliation(s)
- A Bilgic
- Seydisehir State Hospital, Dermatology Clinic, Seydisehir, Konya, Turkey
| | - F Aydin
- Ondokuz Mayis University, Faculty of Medicine, Department of Dermatology, Samsun, Antalya, Turkey
| | - P Sumer
- Ondokuz Mayis University, Faculty of Dentistry, Department of Dentomaxillofacial Radyology, Samsun, Antalya, Turkey
| | - I Keskiner
- Ondokuz Mayis University, Faculty of Dentistry, Department of Periodontology, Samsun, Antalya, Turkey
| | - S Koc
- Kepez State Hospital, Dermatology Clinic, Antalya, Turkey
| | - S Bozkurt
- Akdeniz University, Faculty of Medicine, Biostatistics and Medical Informatics Department, Antalya, Turkey
| | - G Mumcu
- Department of Health Management, Marmara University Faculty of Health Sciences, İstanbul, Turkey
| | - E Alpsoy
- Akdeniz University, Faculty of Medicine, Department of Dermatology and Venereology, Antalya, Turkey
| | - S Uzun
- Akdeniz University, Faculty of Medicine, Department of Dermatology and Venereology, Antalya, Turkey
| | - A Akman-Karakas
- Akdeniz University, Faculty of Medicine, Department of Dermatology and Venereology, Antalya, Turkey
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25
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Abstract
Understanding ion transport in nanoporous materials is critical to a wide variety of energy and environmental technologies, ranging from ion-selective membranes, drug delivery, and biosensing, to ion batteries and supercapacitors. While nanoscale transport is often described by continuum models that rely on a point charge description for ions and a homogeneous dielectric medium for the solvent, here, we show that transport of aqueous solutions at a hydrophobic interface can be highly dependent on the size and hydration strength of the solvated ions. Specifically, measurements of ion current through single silicon nitride nanopores that contain a hydrophobic-hydrophilic junction show that transport properties are dependent not only on applied voltage but also on the type of anion. We find that in Cl--containing solutions the nanopores only conducted ionic current above a negative voltage threshold. On the other hand, introduction of large polarizable anions, such as Br- and I-, facilitated the pore wetting, making the pore conductive at all examined voltages. Molecular dynamics simulations revealed that the large anions, Br- and I-, have a weaker solvation shell compared to that of Cl- and consequently were prone to migrate from the aqueous solution to the hydrophobic surface, leading to the anion accumulation responsible for pore wetting. The results are essential for designing nanoporous systems that are selective to ions of the same charge, for realization of ion-induced wetting in hydrophobic pores, as well as for a fundamental understanding on the role of ion hydration shell on the properties of solid/liquid interfaces.
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Affiliation(s)
- Jake W Polster
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Elif Turker Acar
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Chemistry, Faculty of Engineering, Istanbul University - Cerrahpasa, Avcılar, 34320 Istanbul, Turkey
| | - Fikret Aydin
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Cheng Zhan
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Tuan Anh Pham
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Zuzanna S Siwy
- Department of Chemistry, University of California, Irvine, California 92697, United States
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26
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Aydin F, Zhan C, Ritt C, Epsztein R, Elimelech M, Schwegler E, Pham TA. Similarities and differences between potassium and ammonium ions in liquid water: a first-principles study. Phys Chem Chem Phys 2020; 22:2540-2548. [DOI: 10.1039/c9cp06163k] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding ion solvation in liquid water is critical in optimizing materials for a wide variety of emerging technologies, including water desalination and purification.
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Affiliation(s)
- Fikret Aydin
- Lawrence Livermore National Laboratory
- Livermore
- USA
| | - Cheng Zhan
- Lawrence Livermore National Laboratory
- Livermore
- USA
| | - Cody Ritt
- Department of Chemical and Environmental Engineering
- Yale University
- New Haven
- USA
| | - Razi Epsztein
- Department of Chemical and Environmental Engineering
- Yale University
- New Haven
- USA
- Faculty of Civil and Environmental Engineering
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering
- Yale University
- New Haven
- USA
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27
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Genc S, Ademoglu E, Aydin F, Omer B. The performance evaluation of Snibe Maglumi 4000P for hormone assays. Clin Chim Acta 2019. [DOI: 10.1016/j.cca.2019.03.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Aydin F, Sun R, Swanson JMJ. Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations. Biophys J 2019; 117:87-98. [PMID: 31174850 DOI: 10.1016/j.bpj.2019.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023] Open
Abstract
Mycolactone, a cytotoxic and immunosuppressive macrolide produced by Mycobacterium ulcerans, is the central virulent factor in the skin disease Buruli ulcer. This multifunctional cytotoxin affects fundamental cellular processes such as cell adhesion, immune response, and cell death by targeting various cellular structures. Developing effective diagnostics that target mycolactone has been challenging, potentially because of suspected interactions with lipophilic architectures, including membranes. To better understand the pathogenesis of Buruli ulcer disease, aid in the development of diagnostics, and learn how amphiphiles in general use lipid trafficking to navigate the host environment, we seek to understand the nature of mycolactone-membrane interactions. Herein, we characterize how the two dominant isomers of mycolactone (A and B) interact with and permeate DPPC membranes with all-atom molecular dynamics simulations employing transition-tempered metadynamics and compare these results to those obtained by MARTINI coarse-grained simulations. Our all-atom simulations reveal that both isomers have a strong preference to associate with the membrane, although their mechanisms and energetics of membrane permeation differ slightly. Water molecules are found to play an important role in the permeation process. Although the MARTINI coarse-grained simulations give the correct free energy of membrane association, they fail to capture the mechanism of permeation and role of water during permeation as seen in all-atom simulations.
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Affiliation(s)
- Fikret Aydin
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois
| | - Rui Sun
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois
| | - Jessica M J Swanson
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois.
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29
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Harker AJ, Katkar HH, Bidone TC, Aydin F, Voth GA, Applewhite DA, Kovar DR. Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia cross-linker fascin. Mol Biol Cell 2019; 30:851-862. [PMID: 30601697 PMCID: PMC6589784 DOI: 10.1091/mbc.e18-08-0500] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ena/VASP tetramers are processive actin elongation factors that localize to diverse F-actin networks composed of filaments bundled by different cross-linking proteins, such as filopodia (fascin), lamellipodia (fimbrin), and stress fibers (α-actinin). Previously, we found that Ena takes approximately threefold longer processive runs on trailing barbed ends of fascin-bundled F-actin. Here, we used single-molecule TIRFM (total internal reflection fluorescence microscopy) and developed a kinetic model to further dissect Ena/VASP’s processive mechanism on bundled filaments. We discovered that Ena’s enhanced processivity on trailing barbed ends is specific to fascin bundles, with no enhancement on fimbrin or α-actinin bundles. Notably, Ena/VASP’s processive run length increases with the number of both fascin-bundled filaments and Ena “arms,” revealing avidity facilitates enhanced processivity. Consistently, Ena tetramers form more filopodia than mutant dimer and trimers in Drosophila culture cells. Moreover, enhanced processivity on trailing barbed ends of fascin-bundled filaments is an evolutionarily conserved property of Ena/VASP homologues, including human VASP and Caenorhabditis elegans UNC-34. These results demonstrate that Ena tetramers are tailored for enhanced processivity on fascin bundles and that avidity of multiple arms associating with multiple filaments is critical for this process. Furthermore, we discovered a novel regulatory process whereby bundle size and bundling protein specificity control activities of a processive assembly factor.
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Affiliation(s)
- Alyssa J Harker
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Harshwardhan H Katkar
- Department of Chemistry, cThe James Franck Institute, and dInstitute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637.,Department of Biology, Reed College, Portland, OR 97202
| | - Tamara C Bidone
- Department of Chemistry, cThe James Franck Institute, and dInstitute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637.,Department of Biology, Reed College, Portland, OR 97202
| | - Fikret Aydin
- Department of Chemistry, cThe James Franck Institute, and dInstitute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637.,Department of Biology, Reed College, Portland, OR 97202
| | - Gregory A Voth
- Department of Chemistry, cThe James Franck Institute, and dInstitute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637.,Department of Biology, Reed College, Portland, OR 97202
| | | | - David R Kovar
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637.,Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
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30
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Aydin F, Katkar HH, Voth GA. Multiscale simulation of actin filaments and actin-associated proteins. Biophys Rev 2018; 10:1521-1535. [PMID: 30382557 PMCID: PMC6297090 DOI: 10.1007/s12551-018-0474-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/21/2018] [Indexed: 02/04/2023] Open
Abstract
Actin is an important cytoskeletal protein that serves as a building block to form filament networks that span across the cell. These networks are orchestrated by a myriad of other cytoskeletal entities including the unbranched filament-forming protein formin and branched network-forming protein complex Arp2/3. Computational models have been able to provide insights into many important structural transitions that are involved in forming these networks, and into the nature of interactions essential for actin filament formation and for regulating the behavior of actin-associated proteins. In this review, we summarize a subset of such models that focus on the atomistic features and those that can integrate atomistic features into a larger picture in a multiscale fashion.
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Affiliation(s)
- Fikret Aydin
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Harshwardhan H Katkar
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA
| | - Gregory A Voth
- Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA.
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31
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Ciftci HS, Demir E, Karadeniz MS, Tefik T, Nane I, Oguz FS, Aydin F, Turkmen A. Influence of uridine diphosphate-glucuronosyltransferases (1A9) polymorphisms on mycophenolic acid pharmacokinetics in patients with renal transplant. Ren Fail 2018; 40:395-402. [PMID: 30012031 PMCID: PMC6052413 DOI: 10.1080/0886022x.2018.1489285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: There are differences in pharmacokinetic of mycophenolic acid among individuals. The UGT1A9 enzyme is of special interest since it is the main enzyme involved in the glucuronidation of MPA. Single nucleotide polymorphisms in the UGT1A9 gene may be responsible for individual differences in the pharmacokinetics of MPA. The aim of this study was to explain MPA pharmacokinetics in UGT1A9 1399 C > T polymorphisms in Turkish renal transplant patients. Patients and methods: One hundred and twenty-five living-donor transplant recipients and 100 healthy control subjects underwent UGT1A9 1399 C > T genotyping using polymerase chain reaction–restriction fragment length polymorphism. Concentrations of MPA were determined with Cloned Enzyme Donor Immunoassay (CEDIA). Besides that, all the patients were monitored for acute rejection and graft function during the study period. Results: The UGT1A9 1399 C > T CC, CT, and TT genotype frequencies among patients were, respectively, 68.0%, 23.2%, and 8.8%. The CC, CT, and TT genotype frequencies among controls were, respectively, 63.0%, 23.0%, and 14.0%. There was no significant difference between patients and controls (p = .480, p = .999, p = .286, respectively). At first month, respectively, through blood concentrations of MPA were significantly higher in UGT1A9 1399 C > T TT carriers than in CT and CC carriers (p = .046). The doses for these patients were lower at first month (p = .021). Acute rejection episodes were not associated with the CC vs CT or TT genotypes (p = .064). Conclusions: Our results demonstrated a correlation between the UGT1A9 1399 C > T polymorphism and MPA pharmacokinetics among renal transplant patients. Determination of UGT1A9 polymorphism may help to achieve target of MPA blood concentrations.
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Affiliation(s)
- H S Ciftci
- a Department of Medical Biology, Istanbul Faculty of Medicine , Istanbul University , Istanbul , Turkey
| | - E Demir
- b Department of Nephrology , Istanbul Faculty of Medicine, Istanbul University , Istanbul , Turkey
| | - M S Karadeniz
- c Department of Anesthesia , Istanbul Faculty of Medicine, Istanbul University , Istanbul , Turkey
| | - T Tefik
- d Department of Urology , Istanbul Faculty of Medicine, Istanbul University , Istanbul , Turkey
| | - I Nane
- d Department of Urology , Istanbul Faculty of Medicine, Istanbul University , Istanbul , Turkey
| | - F S Oguz
- a Department of Medical Biology, Istanbul Faculty of Medicine , Istanbul University , Istanbul , Turkey
| | - F Aydin
- e Department of Medical Biology and Genetics , Faculty of Medicine, Istanbul Bilim University , Istanbul , Turkey
| | - A Turkmen
- b Department of Nephrology , Istanbul Faculty of Medicine, Istanbul University , Istanbul , Turkey
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32
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Abstract
Formins play an important role in the polymerization of unbranched actin filaments, and particular formins slow elongation by 5–95%. We studied the interactions between actin and the FH2 domains of formins Cdc12, Bni1 and mDia1 to understand the factors underlying their different rates of polymerization. All-atom molecular dynamics simulations revealed two factors that influence actin filament elongation and correlate with the rates of elongation. First, FH2 domains can sterically block the addition of new actin subunits. Second, FH2 domains flatten the helical twist of the terminal actin subunits, making the end less favorable for subunit addition. Coarse-grained simulations over longer time scales support these conclusions. The simulations show that filaments spend time in states that either allow or block elongation. The rate of elongation is a time-average of the degree to which the formin compromises subunit addition rather than the formin-actin complex literally being in ‘open’ or ‘closed’ states.
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Affiliation(s)
- Fikret Aydin
- Department of Chemistry, The University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States.,James Franck Institute, The University of Chicago, Chicago, United States
| | - Naomi Courtemanche
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Thomas D Pollard
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States.,James Franck Institute, The University of Chicago, Chicago, United States
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33
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Turgay Yildirim O, Gonullu E, Aydin F, Aksit E, Huseyinoglu Aydin A, Dagtekin E. Nocturnal blood pressure dipping is similar in rheumatoid arthritis patients as compared to a normal population. Z Rheumatol 2018; 78:190-194. [PMID: 29651574 DOI: 10.1007/s00393-018-0451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Rheumatoid arthritis (RA) is a systemic autoimmune inflammatory disorder which further doubles the risk of developing cardiovascular disease. Some studies suggest that in RA patients, the prevalence of hypertension increases due to prednisolone use, clinical status, genetic factors, and physical inactivity. On the other hand, dipper and non-dipper status in RA patients compared to non-RA subjects has not been investigated to our knowledge. Purpose of the study is to investigate whether non-dipper status is more deteriorated in RA patients. METHODS Sixty-five RA patients and 61 age-sex-matched control patients were evaluated in this cross-sectional study. Patients were classified according to 24-h ambulatory blood pressure monitoring results. Patients with previous hypertension diagnosis, coronary artery disease, and abnormal kidney function were excluded. RESULTS Mean age of the study sample was 53.7 ± 12.3 years and 40.5% were male. There was no significant difference between groups in terms of basic demographic characteristics. Leukocyte counts (p = 0.001), neutrophil counts (p = 0.001), and red cell distribution width (p = 0.000) were significantly higher in the RA group. ABPM results indicate no significant difference between RA patients and the control group in terms of daytime systolic and diastolic blood pressure, nighttime systolic and diastolic blood pressure, and average systolic and diastolic blood pressure results (p > 0.05). There was no statistical difference regarding the non-dipper status of patient groups (p = 0.412). Nocturnal blood pressure dipping was significantly similar between groups (p = 0.980). CONCLUSION In conclusion, RA patients have similar values in terms of nocturnal blood pressure dipping and hypertension diagnosis as compared to normal population.
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Affiliation(s)
| | - E Gonullu
- Rheumatology Department, Eskişehir State Hospital, Eskişehir, Turkey
| | - F Aydin
- Cardiology Department, Eskişehir State Hospital, Eskişehir, Turkey
| | - E Aksit
- Cardiology Department, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - E Dagtekin
- Cardiology Department, Eskişehir State Hospital, Eskişehir, Turkey
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Chu X, Yu X, Greenstein J, Aydin F, Uppaladadium G, Dutt M. Flow-Induced Shape Reconfiguration, Phase Separation, and Rupture of Bio-Inspired Vesicles. ACS Nano 2017; 11:6661-6671. [PMID: 28582613 DOI: 10.1021/acsnano.7b00753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The structural integrity of red blood cells and drug delivery carriers through blood vessels is dependent upon their ability to adapt their shape during their transportation. Our goal is to examine the role of the composition of bio-inspired multicomponent and hairy vesicles on their shape during their transport through in a channel. Through the dissipative particle dynamics simulation technique, we apply Poiseuille flow in a cylindrical channel. We investigate the effect of flow conditions and concentration of key molecular components on the shape, phase separation, and structural integrity of the bio-inspired multicomponent and hairy vesicles. Our results show the Reynolds number and molecular composition of the vesicles impact their flow-induced deformation, phase separation on the outer monolayer due to the Marangoni effect, and rupture. The findings from this study could be used to enhance the design of drug delivery and tissue engineering systems.
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Affiliation(s)
- Xiaolei Chu
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Xiang Yu
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Joseph Greenstein
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Fikret Aydin
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Geetartha Uppaladadium
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Meenakshi Dutt
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
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Akgul SU, Ciftci HS, Temurhan S, Caliskan Y, Bayraktar A, Tefik T, Kaya IA, Canitez IO, Demir E, Yazici H, Bakkaloglu H, Aydin AE, Turkmen A, Nane I, Aydin F, Oguz FS. Association Between HLA Antibodies and Different Sensitization Events in Renal Transplant Candidates. Transplant Proc 2017; 49:425-429. [PMID: 28340805 DOI: 10.1016/j.transproceed.2017.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Human leukocyte antigen (HLA) allo-immunization is caused by various events such as blood transfusions, pregnancies, or organ transplantations, which can lead to sensitization. In this retrospective study, we evaluated different sensitization models and their effects on panel-reactive antibody (PRA) profiles of renal transplantation candidates. METHODS Anti-HLA class I/II antibody screening tests were performed in 906 renal transplantation candidates with the use of a microbead-based assay (Luminex). RESULTS Two hundred ninety-seven (32.8%) of the patients were determined as positive in terms of PRA, and 609 (67.2%) were negative. Sensitized and non-sensitized patients were compared separately in terms of each sensitization type. The anti-HLA class I, II, and I+II positivity rates in patients sensitized only by blood transfusion were 13.1%, 6.3%, and 14.1%, the rates with pregnancy sensitization were 35.5%, 29%, and 45.2%, and rates with previous transplantation sensitization were 15.6%, 34.4%, and 38.9%, respectively. Prevalence of PRA positivity was significantly higher in patients with previous pregnancy than with transplantation and transfusion (odds ratio, 1.003; 95% confidence interval, 0.441-2.281; P = .031). The risk of developing HLA class I antibodies was higher in pregnancies (P < .001), and the risk of developing anti-HLA class II antibodies was higher in patients who had undergone a previous transplantation (P < .001). The rate of developing HLA-B antibodies in patients sensitized by pregnancy were significantly higher compared with sensitization after transfusion (P = .015), as was the rate of developing HLA-DQ antibodies in patients sensitized by previous transplantation compared with sensitization through pregnancy (P = .042). CONCLUSIONS In patients who are waiting for kidney transplantation, sensitization by pregnancy and transplantation have a significant impact on development of HLA class I and class II antibodies.
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Affiliation(s)
- S U Akgul
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey.
| | - H S Ciftci
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - S Temurhan
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Y Caliskan
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A Bayraktar
- Department of General Surgery, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - T Tefik
- Department of Urology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - I A Kaya
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - I O Canitez
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - E Demir
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - H Yazici
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - H Bakkaloglu
- Department of General Surgery, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A E Aydin
- Department of General Surgery, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A Turkmen
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - I Nane
- Department of Urology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - F Aydin
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - F S Oguz
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
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Ciftci HS, Karadeniz MS, Tefik T, Caliskan Y, Yazıcı H, Demir E, Turkmen A, Nane I, Oguz FS, Aydin F. Influence of Proton Pump Inhibitors on Mycophenolic Acid Pharmacokinetics in Patients With Renal Transplantation and the Relationship With Cytochrome 2C19 Gene Polymorphism. Transplant Proc 2017; 49:490-496. [PMID: 28340819 DOI: 10.1016/j.transproceed.2017.01.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Most patients have serious digestive complications after renal transplantation. Therefore, it is important to protect gastrointestinal function to improve the survival rate of transplant patients. Proton pump inhibitors (PPIs) such as lansoprazole and rabeprazole are widely administered to renal transplant patients with mycophenolic acid (MPA) in the perioperative period. PPIs are metabolized by cytochrome (CYP) 2C19 enzymes. Mycophenolate sodium (MYF) and mycophenolate mofetil (MMF) have been used in immunosuppression. Clinically relevant drug-drug interactions have been described between immunosuppressive drugs. In the present study, we investigated the drug interaction between MPA and lansoparazole or rabeprazole and the impact of CYP2C19 polymorphisms on these drug interactions after renal transplantation. MATERIALS AND METHODS A total of 125 renal transplant patients taking MPA derivatives between 2012 and 2016 were included in this study. The 125 patients were divided into 6 groups: MMF/tacrolimus/steroid together with lansoprazole or rabeprazole; MYF/tacrolimus/steroid together with lansoprazole or rabeprazole and without PPI. The single nucleotide polymorphisms of CYP2C19 were determined by the polymerase chain reaction-restriction fragment length polymorphism. Plasma concentrations of MPA were measured by cloned enzyme donor immunoassay. Clinical parameters such as incidence of delayed graft function and acute rejection, the rate of change of serum creatinine, toxicity, and gastrointestinal adverse effects were analyzed retrospectively. RESULTS The mean concentrations of MPA in the MYF group were higher than those in the MMF group. The mean dose-adjusted blood concentration of MPA coadministered with lansoprazole was lower than that of MPA with rabeprazole or without PPI in MMF and MYF groups (P < .05). In patients with the CYP2C19*2/*2 genotype, the mean concentrations of MMF with lansoprazole were significantly lower than those with rabeprazole with MMF or without PPI (P < .05). Gastrointestinal side effects were significantly higher in MMF with lansoprazole group than in MYF with lansoprazole group (P < .05). However, no differences were found according to genotype distribution in all groups (P > .05). CONCLUSION Polymorphisms in CYP2C19 are related to the metabolic oxidation of drugs to varying degrees. Both genetic and clinical factors in pharmacokinetics may help to make further progress toward individualized therapy to yield maximum efficacy with minimal side effects.
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Affiliation(s)
- H S Ciftci
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey.
| | - M S Karadeniz
- Department of Anesthesiology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - T Tefik
- Department of Urology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Y Caliskan
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - H Yazıcı
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - E Demir
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A Turkmen
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - I Nane
- Department of Urology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - F S Oguz
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - F Aydin
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
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Karadeniz ST, Akgul SU, Ogret Y, Ciftci HS, Bayraktar A, Bakkaloglu H, Caliskan Y, Yelekci K, Turkmen A, Aydin AE, Oguz FS, Carin M, Aydin F. Corrected Panel-Reactive Antibody Positivity Rates for Hypersensitized Patients in Turkish Population With Calculated Panel-Reactive Antibody Software. Transplant Proc 2017; 49:445-447. [PMID: 28340809 DOI: 10.1016/j.transproceed.2017.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION High rates of panel-reactive antibody (PRA) may decrease the chance of kidney transplantation and may result in long waiting periods before transplantation. The calculated PRA (cPRA) is performed based on unacceptable HLA antigens. These antigens are identified by a program that was created based on the antibodies that developed against the HLA antigens circulating in serum and on the risk of binding of these antibodies to antigens. The antigen profile of the population and antigen frequencies can be measured, and more realistic cPRA positivity rates may be obtained using this method. MATERIALS AND METHODS We developed a program based on the HLA antigens of 494 blood donors in 2 European Federation for Immunogenetics-accredited Tissue Typing Laboratories in Turkey. Next-generation sequencing-based tissue typing (HLA-A, -B, -C, -DR, -DQ, 4 digits) of the samples was performed. The PRA screening test was performed on 380 patients who were waiting for organ transplant from a cadaver in Istanbul Faculty of Medicine. The single antigen bead assay testing was performed to identify the antibody profiles on 48 hypersensitized patients. RESULTS The PRA testing results using the current methods were 44.6% ± 18.5%, and the cPRA rate was 86.2% ± 5.1%. The mean PRA positivity of the sensitized patients using the current methods was 44.6%; however, the rate was 86.2% using the cPRA. DISCUSSION cPRA shows the rate of the rejected donors according to all unacceptable antigens. The need for a list of unacceptable antigens in place of the PRA positivity rate is a real change in the sensitization-dependent calculation as cPRA positivity rate. CONCLUSION In principal, implementation of cPRA will encourage many centers and laboratories to adopt a standard measurement of sensitization in Turkey. It will increase the chances of better donor match, particularly for hypersensitized patients, by the creation of an unacceptable mismatch program using cPRA software.
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Affiliation(s)
- S T Karadeniz
- Calculated Biology and Bioinformatics Program, Department of Bioinformatics and Genetics, Kadir Has University, Istanbul, Turkey.
| | - S U Akgul
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Y Ogret
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - H S Ciftci
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A Bayraktar
- Department of General Surgery, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - H Bakkaloglu
- Department of General Surgery, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Y Caliskan
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - K Yelekci
- Calculated Biology and Bioinformatics Program, Department of Bioinformatics and Genetics, Kadir Has University, Istanbul, Turkey
| | - A Turkmen
- Department of Nephrology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A E Aydin
- Department of General Surgery, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - F S Oguz
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - M Carin
- Tissue Typing Laboratories, Florence Nightingale Hospital, Istanbul, Turkey
| | - F Aydin
- Department of Medical Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
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Topcu T, Kavgaci H, Ozdemir F, Mentese A, Orem A, Aydin F. Plasma Malondialdehyde and Ischemia-modified Albumin levels in breast cancer patients before and after adjuvant chemotherapy. Breast 2017. [DOI: 10.1016/s0960-9776(17)30162-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Aydin F, Yurdakok Dikmen B, Kismali G. The potential cytotoxic effects of Valeriana officinalis extract on prostate cancer cell lines DU-145 and PC-3. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.2037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dikmen BY, Kuzukiran O, Tutun H, Sevin S, Aydin F, Filazi A. Antropogenic ecotoxicity evaluation in vitro and its relation to the occurrence of some persistent organic pollutants in water and sediment samples collected from Ankara River. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
We examine the interaction between peptide-inspired nanoparticles, or nanopins, and multicomponent vesicles using the dissipative particle dynamics simulation technique. We study the role of nanopin architecture and cholesterol concentration on the binding of the nanopins to the lipid bilayer, their insertion, and postembedding self-organization. We find the insertion to be triggered by enthalpically unfavorable interactions between the hydrophilic solvent and the lipophilic components of the nanopins. The nanopins are observed to form aggregates in solution, insert into the bilayer, and disassemble into the individual nanopins following the insertion process. We examine factors that influence the orientation of the nanopins in the host vesicle. We report the length of the hydrophilic segment of the nanopins to regulate their orientation within the clusters before the embedding process and in the bilayer, after the postinsertion disassembly of the aggregates. The orientation angle distribution for a given nanopin architecture is found to be driven by energy minimization. In addition, higher concentration of cholesterol is observed to constrain the orientation of the nanopins. We also report thermal fluctuations to induce transverse diffusion of nanopins with specific architectures. The incidence of transverse diffusion is observed to decrease with the concentration of cholesterol. Our results can provide guidelines for designing peptide-inspired nanoparticles or macromolecules that can interface with living cells to serve as sensors for applications in medicine, sustainability, and energy.
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Affiliation(s)
- Xiaolei Chu
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Fikret Aydin
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Meenakshi Dutt
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
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Affiliation(s)
- Fikret Aydin
- Department
of Chemical and
Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Meenakshi Dutt
- Department
of Chemical and
Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
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Aydin F, Chu X, Uppaladadium G, Devore D, Goyal R, Murthy NS, Zhang Z, Kohn J, Dutt M. Self-Assembly and Critical Aggregation Concentration Measurements of ABA Triblock Copolymers with Varying B Block Types: Model Development, Prediction, and Validation. J Phys Chem B 2016; 120:3666-76. [PMID: 27031284 DOI: 10.1021/acs.jpcb.5b12594] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The dissipative particle dynamics (DPD) simulation technique is a coarse-grained (CG) molecular dynamics-based approach that can effectively capture the hydrodynamics of complex systems while retaining essential information about the structural properties of the molecular species. An advantageous feature of DPD is that it utilizes soft repulsive interactions between the beads, which are CG representation of groups of atoms or molecules. In this study, we used the DPD simulation technique to study the aggregation characteristics of ABA triblock copolymers in aqueous medium. Pluronic polymers (PEG-PPO-PEG) were modeled as two segments of hydrophilic beads and one segment of hydrophobic beads. Tyrosine-derived PEG5K-b-oligo(desaminotyrosyl tyrosine octyl ester-suberate)-b-PEG5K (PEG5K-oligo(DTO-SA)-PEG5K) block copolymers possess alternate rigid and flexible components along the hydrophobic oligo(DTO-SA) chain, and were modeled as two segments of hydrophilic beads and one segment of hydrophobic, alternate soft and hard beads. The formation, structure, and morphology of the initial aggregation of the polymer molecules in aqueous medium were investigated by following the aggregation dynamics. The dimensions of the aggregates predicted by the computational approach were in good agreement with corresponding results from experiments, for the Pluronic and PEG5K-oligo(DTO-SA)-PEG5K block copolymers. In addition, DPD simulations were utilized to determine the critical aggregation concentration (CAC), which was compared with corresponding results from an experimental approach. For Pluronic polymers F68, F88, F108, and F127, the computational results agreed well with experimental measurements of the CAC measurements. For PEG5K-b-oligo(DTO-SA)-b-PEG5K block polymers, the complexity in polymer structure made it difficult to directly determine their CAC values via the CG scheme. Therefore, we determined CAC values of a series of triblock copolymers with 3-8 DTO-SA units using DPD simulations, and used these results to predict the CAC values of triblock copolymers with higher molecular weights by extrapolation. In parallel, a PEG5K-b-oligo(DTO-SA)-b-PEG5K block copolymer was synthesized, and the CAC value was determined experimentally using the pyrene method. The experimental CAC value agreed well with the CAC value predicted by simulation. These results validate our CG models, and demonstrate an avenue to simulate and predict aggregation characteristics of ABA amphiphilic triblock copolymers with complex structures.
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Affiliation(s)
- Fikret Aydin
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - Xiaolei Chu
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - Geetartha Uppaladadium
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - David Devore
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - Ritu Goyal
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - N Sanjeeva Murthy
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - Zheng Zhang
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - Joachim Kohn
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
| | - Meenakshi Dutt
- Department of Chemical Engineering and ‡New Jersey Center for Biomaterials, Rutgers, The State University of New Jersey , Piscataway 08854, New Jersey, United States
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Aksoy AN, Aydin F, Kucur SK, Gözükara I. Maternal and fetal Doppler velocimetry in women diagnosed with fear of childbirth. Niger J Clin Pract 2016; 19:632-5. [DOI: 10.4103/1119-3077.183238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Yildirim Y, Kara AV, Kilinç F, Aydin F, Aydin E, Yilmaz Z, Kadiroglu AK, Yilmaz ME. DETERMINATION OF VOLUME OVERLOAD BY BIOELECTRICAL IMPEDANCE ANALYSIS AND NT-PROBNP IN DIABETIC PRE-DIALYSIS PATIENTS. Acta Endocrinol (Buchar) 2016; 12:19-25. [PMID: 31258795 DOI: 10.4183/aeb.2016.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introduction Diabetic chronic kidney disease has more fatal clinical progresses and this situation can be related to volume overload, which is seen more commonly in diabetic chronic kidney disease patients than in non-diabetic chronic kidney disease patients. Therefore, we examined the effect of diabetes mellitus on volume overload in newly diagnosed stage 5 chronic kidney disease patients whose volume overloads were not showing signs of improvement from renal replacement therapy. Method One hundred and five patients (46 diabetic, 59 non-diabetic) with end-stage chronic kidney disease, who had glomerular filtration rate (GFR) under 15 mL/min for at least three months were enrolled in this prospective study. We determined the body volume overload and configuration using a bioimpedance device. NT-proBNP levels were recorded. Results There was a statistically significant difference between diabetic and non-diabetic groups according to overhydration (OH, p=0.003), extracellular water (ECW, p=0.045), intracellular water (ICW, p<0.001) and OH/ECW (p=0.003). In addition, there was a statistically significant difference between groups in terms of N-terminal Pro-brain Natriuretic Peptide (NT-proBNP levels, p=0.008). Discussion We compared diabetic and non-diabetic end-stage chronic kidney disease patients who were not in renal replacement therapy yet. We found more volume overload and extracellular fluid volume in the diabetic group.
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Affiliation(s)
- Y Yildirim
- Dicle University, Faculty of Medicine, Dept. of Nephrology, Diyarbakir, Turkey
| | - A V Kara
- Dicle University, Faculty of Medicine, Dept. of Nephrology, Diyarbakir, Turkey
| | - F Kilinç
- Dicle University, Faculty of Medicine, Dept. of Endocrinology, Diyarbakir, Turkey
| | - F Aydin
- Dicle University, Faculty of Medicine, Dept. of Internal Medicine, Diyarbakir, Turkey
| | - E Aydin
- Dicle University, Faculty of Medicine, Dept. of Internal Medicine, Diyarbakir, Turkey
| | - Z Yilmaz
- Dicle University, Faculty of Medicine, Dept. of Nephrology, Diyarbakir, Turkey
| | - A K Kadiroglu
- Dicle University, Faculty of Medicine, Dept. of Nephrology, Diyarbakir, Turkey
| | - M E Yilmaz
- Dicle University, Faculty of Medicine, Dept. of Nephrology, Diyarbakir, Turkey
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Chong L, Aydin F, Dutt M. Implicit solvent coarse-grained model of polyamidoamine dendrimers: Role of generation and pH. J Comput Chem 2015; 37:920-6. [PMID: 26676461 DOI: 10.1002/jcc.24277] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/24/2015] [Accepted: 11/08/2015] [Indexed: 01/18/2023]
Abstract
Highly branched polymers such as polyamidoamine (PAMAM) dendrimers are promising macromolecules in the realm of nanobiotechnology due to their high surface coverage of tunable functional groups. Modeling efforts of PAMAM can provide structural and morphological properties, but the inclusion of solvents and the exponential growth of atoms with generations make atomistic simulations computationally expensive. We apply an implicit solvent coarse-grained model, called the Dry Martini force field, to PAMAM dendrimers. The reduced number of particles and the absence of a solvent allow the capture of longer spatiotemporal scales. This study characterizes PAMAM dendrimers of generations one through seven in acidic, neutral, and basic pH environments. Comparison with existing literature, both experimental and theoretical, is done using measurements of the radius of gyration, moment of inertia, radial distributions, and scaling exponents. Additionally, ion coordination distributions are studied to provide insight into the effects of interior and exterior protonation on counter ions. This model serves as a starting point for future designs of larger functionalized dendrimers.
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Affiliation(s)
- Leebyn Chong
- Department of Chemical and Biochemical Engineering, Rutgers the State University of New Jersey, Piscataway, New Jersey, 08854
| | - Fikret Aydin
- Department of Chemical and Biochemical Engineering, Rutgers the State University of New Jersey, Piscataway, New Jersey, 08854
| | - Meenakshi Dutt
- Department of Chemical and Biochemical Engineering, Rutgers the State University of New Jersey, Piscataway, New Jersey, 08854
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Aydin F, Uppaladadium G, Dutt M. Harnessing Nanoscale Confinement to Design Sterically Stable Vesicles of Specific Shapes via Self-Assembly. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b02239] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fikret Aydin
- Department of Chemical and
Biochemical Engineering, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Geetartha Uppaladadium
- Department of Chemical and
Biochemical Engineering, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Meenakshi Dutt
- Department of Chemical and
Biochemical Engineering, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, United States
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Yukself EP, Aydin F, Senturk N, Ozden MG, Canturk T, Turanli AY. Dermatomyositis accompanying nasopharyngeal carcinoma in a Caucasion patient. GIORN ITAL DERMAT V 2015; 150:274-276. [PMID: 25876152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- E P Yukself
- Ondokuz Mayis University, Faculty of Medicine, Department of Dermatology, Samsun, Turkey -
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Seyhun Y, Ciftci HS, Kekik C, Karadeniz MS, Tefik T, Nane I, Turkmen A, Oguz FS, Aydin F. Genetic association of interleukin-2, interleukin-4, interleukin-6, transforming growth factor-β, tumour necrosis factor-α and blood concentrations of calcineurin inhibitors in Turkish renal transplant patients. Int J Immunogenet 2015; 42:147-60. [PMID: 25817300 DOI: 10.1111/iji.12192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 02/16/2015] [Accepted: 02/22/2015] [Indexed: 01/22/2023]
Abstract
Cytokines are essential for the control of the immune response as most of the immunosuppressive drugs target cytokine production or their action. The calcineurin inhibitors (CNIs) cyclosporine (CsA) and tacrolimus are immunosuppressive drugs widely used after renal transplantation to prevent allograft rejection. They are characterized by large interindividual variability in their pharmacokinetics; therefore, monitoring their blood concentrations is important to predict their optimal dosage following transplantation. Calcineurin inhibitors inhibit the phosphatase activity of calcineurin, thereby suppressing the production of other cytokines such as transforming growth factor (TGF-β), tumour necrosis factor-α (TNF-α), interleukin (IL)-6, IL-2, and IL-4. The aim of this study was to investigate the relationship between polymorphisms of cytokines and blood concentrations of CNIs in renal transplant patients. The study included 53 CsA-treated renal transplant patients and 37 tacrolimus-treated renal transplant patients. Cytokine polymorphisms were analysed using polymerase chain reaction (PCR) sequence-specific primers with the cytokine CTS-PCR-sequence-specific primers Tray Kit; University of Heidelberg. Blood concentrations of CNIs were determined with Cloned Enzyme Donor Immunoassay (CEDIA) method. Patients with TC genotype of TGF-β at codon 10 had lower CsA blood concentrations than the TT and CC genotypes (P = 0.005) at 1 month in CsA treatment group. The ratio of blood concentration/dose of CsA for patients with TGF-β1-codon 10 TC genotype was lower than for patients with TT, CC genotypes, and the dose given to these patients was higher in the first month (P = 0.046). The ratio of blood concentration/dose of CsA for patients with IL-2-330 GG genotype was higher than for patients with GT, TT genotypes, and the dose given to these patients was lower at first month and sixth months (P = 0.043, P = 0.035 respectively). The tacrolimus blood concentrations were significantly higher in patients with the genotype GG of IL-2-330 (P = 0.012) at the third month. Patients who had the TC genotype TGF-β codon 10 had lower CsA blood concentrations and this group had higher acute rejection (P = 0.033). These results suggest that the genotyping for TGF-β-codon 10, IL-2-330 and IL-6-174 polymorphisms may help individualized immunosuppressive dosage regiments.
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Affiliation(s)
- Y Seyhun
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - H S Ciftci
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - C Kekik
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - M S Karadeniz
- Department of Anesthesia, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - T Tefik
- Department of Urology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - I Nane
- Department of Urology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - A Turkmen
- Division of Nephrology, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - F S Oguz
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - F Aydin
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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Aydin F, Aykaç D, Burcu Arslan N, Kazak C. Synthesis, characterization, and crystal structure of bis[4-(3′-benzoyl)thiocarbamidophenyl]ether. CRYSTALLOGR REP+ 2014. [DOI: 10.1134/s1063774514070050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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