1
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Vögele M, Köfinger J, Hummer G. Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS APPLIED BIO MATERIALS 2024; 7:528-534. [PMID: 36070609 PMCID: PMC10880049 DOI: 10.1021/acsabm.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
Nanofiltration technology faces the competing challenges of achieving high fluid flux through uniformly narrow pores of a mechanically and chemically stable filter. Supported dense-packed 2D-crystals of single-walled carbon nanotube (CNT) porins with ∼1 nm wide pores could, in principle, meet these challenges. However, such CNT membranes cannot currently be synthesized at high pore density. Here, we use computer simulations to explore lipid-mediated self-assembly as a route toward densely packed CNT membranes, motivated by the analogy to membrane-protein 2D crystallization. In large-scale coarse-grained molecular dynamics (MD) simulations, we find that CNTs in lipid membranes readily self-assemble into large clusters. Lipids trapped between the CNTs lubricate CNT repacking upon collisions of diffusing clusters, thereby facilitating the formation of large ordered structures. Cluster diffusion follows the Saffman-Delbrück law and its generalization by Hughes, Pailthorpe, and White. On longer time scales, we expect the formation of close-packed CNT structures by depletion of the intervening shared annular lipid shell, depending on the relative strength of CNT-CNT and CNT-lipid interactions. Our simulations identify CNT length, diameter, and end functionalization as major factors for the self-assembly of CNT membranes.
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Affiliation(s)
- Martin Vögele
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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2
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Palkar V, Thakar D, Kuksenok O. Nanogel Degradation at Soft Interfaces and in Bulk: Tracking Shape Changes and Interfacial Spreading. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Vaibhav Palkar
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Devanshu Thakar
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
- Department of Chemical Engineering, Indian Institute of Technology, Gandhinagar 382055, India
| | - Olga Kuksenok
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
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3
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Mesoscale Modeling of Agglomeration of Molecular Bottlebrushes: Focus on Conformations and Clustering Criteria. Polymers (Basel) 2022; 14:polym14122339. [PMID: 35745920 PMCID: PMC9227207 DOI: 10.3390/polym14122339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
Using dissipative particle dynamics, we characterize dynamics of aggregation of molecular bottlebrushes in solvents of various qualities by tracking the number of clusters, the size of the largest cluster, and an average aggregation number. We focus on a low volume fraction of bottlebrushes in a range of solvents and probe three different cutoff criteria to identify bottlebrushes belonging to the same cluster. We demonstrate that the cutoff criteria which depend on both the coordination number and the length of the side chain allows one to correlate the agglomeration status with the structural characteristics of bottlebrushes in solvents of various qualities. We characterize conformational changes of the bottlebrush within the agglomerates with respect to those of an isolated bottlebrush in the same solvents. The characterization of bottlebrush conformations within the agglomerates is an important step in understanding the relationship between the bottlebrush architecture and material properties. An analysis of three distinct cutoff criteria to identify bottlebrushes belonging to the same cluster introduces a framework to identify both short-lived transient and long-lived agglomerates; the same approach could be further extended to characterize agglomerates of various macromolecules with complex architectures beyond the specific bottlebrush architecture considered herein.
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4
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Palkar V, Kuksenok O. Controlling Degradation and Erosion of Polymer Networks: Insights from Mesoscale Modeling. J Phys Chem B 2021; 126:336-346. [PMID: 34964629 DOI: 10.1021/acs.jpcb.1c09570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding and controlling degradation of polymer networks on the mesoscale is critical for a range of applications. We utilize dissipative particle dynamics to capture photocontrolled degradation and erosion processes in hydrogels formed by end-linking of four-arm polyethylene glycol precursors. We demonstrate that the polydispersity and the fraction of broken-off fragments scale with the relative extent of reaction. The reverse gel point measured is close to the value predicted by the bond percolation theory on a diamond lattice. We characterize the erosion process via tracking the mass loss that accounts for the fragments remaining in contact with the percolated network. We quantify the dependence of the mass loss on the extent of reaction and on the properties of the film prior to degradation. These results elucidate the main features of degradation and erosion on the mesoscale and could provide guidelines for future design of degrading materials with dynamically controlled properties.
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Affiliation(s)
- Vaibhav Palkar
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Olga Kuksenok
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
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5
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Banerjee A, Lu CY, Dutt M. A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides. Phys Chem Chem Phys 2021; 24:1553-1568. [PMID: 34940778 DOI: 10.1039/d1cp04205j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reconstituted photosynthetic proteins which are activated upon exposure to solar energy hold enormous potential for powering future solid state devices and solar cells. The functionality and integration of these proteins into such devices has been successfully enabled by lipid-like peptides. Yet, a fundamental understanding of the organization of these peptides with respect to the photosynthetic proteins and themselves remains unknown and is critical for guiding the design of such light-activated devices. This study investigates the relative organization of one such peptide sequence V6K2 (V: valine and K: lysine) within assemblies. Given the expansive spatiotemporal scales associated with this study, a hybrid coarse-grained (CG) model which captures the structure, conformation and aggregation of the peptide is adopted. The CG model uses a combination of iterative Boltzmann inversion and force matching to provide insight into the relative organization of V6K2 in assemblies. The CG model reproduces the structure of a V6K2 peptide sequence along with its all atom (AA) solvation structure. The relative organization of multiple peptides in an assembly, as captured by CG simulations, is in agreement with corresponding results from AA simulations. Also, a backmapping procedure reintroduces the AA details of the peptides within the aggregates captured by the CG model to demonstrate the relative organization of the peptides. Furthermore, a large number of peptides self-assemble into an elongated micelle in the CG simulation, which is consistent with experimental findings. The coarse-graining procedure is tested for transferability to longer peptide sequences, and hence can be extended to other amphiphilic peptide sequences.
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Affiliation(s)
- Akash Banerjee
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
| | - Chien Yu Lu
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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6
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Ifra, Singh A, Saha S. High Adsorption of α-Glucosidase on Polymer Brush-Modified Anisotropic Particles Acquired by Electrospraying-A Combined Experimental and Simulation Study. ACS APPLIED BIO MATERIALS 2021; 4:7431-7444. [PMID: 35006717 DOI: 10.1021/acsabm.1c00682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this particular contribution, we aim to immobilize a model enzyme such as α-glucosidase onto poly(DMAEMA) [poly(2-dimethyl amino ethyl methacrylate)] brush-modified anisotropic (cup- and disc-shaped) biocompatible polymeric particles. The anisotropic particles comprising a blend of PLA [poly(lactide)] and poly(MMA-co-BEMA) [poly((methyl methacrylate)-co-(2-(2-bromopropionyloxy) ethyl methacrylate)] were acquired by electrospraying, a scalable and convenient technique. We have also demonstrated the role of a swollen polymer brush grafted on the surface of cup-/disc-shaped particles via surface-initiated atom transfer radical polymerization in immobilizing an unprecedentedly high loading of enzyme [441 mg/g (cup)-589 mg/g (disc) of particles, 15-20 times higher than that of the literature-reported system] as compared to non-brush-modified particles. Circular dichroism spectroscopy was used to predict the structural changes of the enzyme upon immobilization onto the carrier particles. An enormously high amount of enzymes with preserved activity (∼85 ± 13% for cups and ∼78 ± 15% for discs) was found to adhere onto brush-modified particles at pH 7 via electrostatic adsorption. These findings were further explored at the atomistic level using a coarse-grained dissipative particle dynamics simulation approach, which exhibited excellent correlation with experimental results. In addition, accelerated particle separation was also achieved via magnetic force-induced aggregation within 20 min (without a centrifuge) by incorporating magnetic nanoparticles into disc-shaped particles while electrojetting. This further strengthens the technical feasibility of the process, which holds immense potential to be applied for various enzymes intended for several applications.
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Affiliation(s)
- Ifra
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Awaneesh Singh
- Department of Physics, Indian Institute of Technology (BHU), Varanasi 221005, India
| | - Sampa Saha
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
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7
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Choudhury CK, Kuksenok O. Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding. J Phys Chem B 2020; 124:11379-11386. [PMID: 33270459 DOI: 10.1021/acs.jpcb.0c08603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We developed a dissipative particle dynamics (DPD) approach that captures polyalanine folding into a stable helical conformation. Within the proposed native-based approach, the DPD parameters are derived based on the contact map constructed from the molecular dynamics (MD) simulations. We show that the proposed approach reproduces the folding of polypeptides of various lengths, including bundle formation for sufficiently long polypeptides. The proposed approach also allows one to capture the folding of the helical segments of the lysozyme. With further development of computationally efficient native-based DPD approaches for folding, modeling of a range of biomaterials incorporating α-helical segments could be extended to time and length scales far beyond those accessible in molecular dynamics simulations.
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Affiliation(s)
- Chandan Kumar Choudhury
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Olga Kuksenok
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
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8
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Jing H, Wang Y, Desai PR, Ramamurthi KS, Das S. Formation and Properties of a Self-Assembled Nanoparticle-Supported Lipid Bilayer Probed through Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5524-5533. [PMID: 32362127 PMCID: PMC7494177 DOI: 10.1021/acs.langmuir.0c00593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We have carried out coarse-grained molecular dynamics (MD) simulations to study the self-assembly procedure of a system of randomly placed lipid molecules, water beads, and a nanoparticle (NP). The self-assembly results in the formation of the nanoparticle-supported lipid bilayer (NPSLBL), with the self-assembly mechanism being driven by events such as the formation of small lipid clusters, merging of the lipid clusters in the vicinity of the NP to form NP-embedded vesicle with a pore, and collapsing of that pore to eventually form the equilibrated NPSLBL system overcoming a large free-energy barrier. Subsequently, we quantify the properties and the configurations of this NPSLBL system. We reveal that unlike our proposition of an equal number of lipid molecules occupying the inner and outer leaflets in a recent report studying the properties of a preassembled lipid bilayer, the equilibrated self-assembled NPSLBL system demonstrates a much larger number of lipid molecules occupying the outer leaflet as compared to the inner leaflet. Second, the thickness of the water layer entrapped between the NP and the inner leaflet shows similar values as predicted by experiments and our previous study. Finally, we reveal that, similar to our previous study, the diffusivity of the lipid molecules in the outer leaflet is larger than that in the inner leaflet but, due to higher temperature employed during our simulations, are even larger than that predicted by our previous study.
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Affiliation(s)
- Haoyuan Jing
- Department of Mechanical Engineering, University of Maryland, 4298 Campus Drive, College Park, MD 20742
| | - Yanbin Wang
- Department of Mechanical Engineering, University of Maryland, 4298 Campus Drive, College Park, MD 20742
| | - Parth Rakesh Desai
- Department of Mechanical Engineering, University of Maryland, 4298 Campus Drive, College Park, MD 20742
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, 4298 Campus Drive, College Park, MD 20742
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9
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Wang S, Guo H, Li Y, Li X. Penetration of nanoparticles across a lipid bilayer: effects of particle stiffness and surface hydrophobicity. NANOSCALE 2019; 11:4025-4034. [PMID: 30768108 DOI: 10.1039/c8nr09381d] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The cellular uptake of nanoparticles (NPs) has drawn significant attention due to their great importance and potential in drug delivery, bioimaging, and specific targeting. Here, we conduct a computational study on the translocation process of soft nanoparticles with different elasticities and surface hydrophobicities through a lipid bilayer membrane. It is shown that the translocation abilities of hydrophilic NPs can be enhanced by increasing their stiffness, while the penetrability of hydrophobic NPs is weakened by increasing the particle stiffness. The free energy analysis indicates that rigid hydrophilic NPs and soft hydrophobic NPs encounter lower energy barriers during penetration. In direct translocation, different deformation modes are observed for NPs with different surface hydrophobicities during cellular internalization. Further, deformation analysis demonstrates that hydrophilic NPs are flattened in the membrane plane, while hydrophobic NPs are elongated along the membrane norm during penetration. We conclude that the elasticity of NPs has an obvious impact on their ability to penetrate across the lipid bilayer membrane through different morphological responses of hydrophilic and hydrophobic NPs. These results shed light on the coupled effects of particle elasticity and surface hydrophobicity on the cellular uptake of elastic NPs, which may provide useful guidelines for designing effective nanocarrier systems for drug delivery.
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Affiliation(s)
- Shuo Wang
- Department of Engineering Mechanics, School of Naval Architecture, Ocean and Civil Engineering (State Key Laboratory of Ocean Engineering, MOE Key Laboratory of Hydrodynamics), Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
| | - Hui Guo
- Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yinfeng Li
- Department of Engineering Mechanics, School of Naval Architecture, Ocean and Civil Engineering (State Key Laboratory of Ocean Engineering, MOE Key Laboratory of Hydrodynamics), Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
| | - Xuejin Li
- Department of Engineering Mechanics and Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou 310027, P. R. China.
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10
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Water permeation in polymeric membranes: Mechanism and synthetic strategy for water-inhibiting functional polymers. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2018.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Lv K, Li Y. Indentation of Graphene-Covered Atomic Force Microscopy Probe Across a Lipid Bilayer Membrane: Effect of Tip Shape, Size, and Surface Hydrophobicity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7681-7689. [PMID: 29860845 DOI: 10.1021/acs.langmuir.8b01262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the interaction of graphene with cell membranes is crucial to the development of graphene-based biological applications and the management of graphene safety issues. To help reveal the key factors controlling the interaction between graphene and cell membranes, here we adopt the dissipative particle dynamics method to analyze the evolution of interaction force and free energy as the graphene-covered atomic force microscopy (AFM) probe indents across a lipid bilayer. The simulation results show that the graphene-covered AFM probe can cause severe deformation of the cell membrane which drives the lipid molecule to adsorb and diffuse at the surface of graphene. The breakthrough force and free energy are calculated to study the effects of the tip shape, size, and surface hydrophobicity on the piercing behaviors of graphene-covered AFM. In addition, the deformation of cell membrane can decrease the dependency of the breakthrough force on the tip shape. The analysis of surface functionalization suggests that the horizontal patterns on graphene can change the preferred orientation in the penetration process, but the vertical patterns on graphene may disrupt the cell membrane. What's more, the bending stiffness of graphene has little influence on the penetration process as graphene pierces into the cell membrane. These results provide useful guidelines for the molecular design of graphene materials with controllable cell penetrability.
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Affiliation(s)
- Kang Lv
- Collaborative Innovation Center for Advanced Ship and Deep-Sea Exploration , Shanghai 200240 , China
| | - Yinfeng Li
- Collaborative Innovation Center for Advanced Ship and Deep-Sea Exploration , Shanghai 200240 , China
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12
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Vögele M, Köfinger J, Hummer G. Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discuss 2018; 209:341-358. [DOI: 10.1039/c8fd00011e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Carbon nanotube porins embedded in lipid membranes are studied by molecular dynamics simulations.
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Affiliation(s)
- Martin Vögele
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
- Institute for Biophysics
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13
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Xu Y, Luo Z, Li S, Li W, Zhang X, Zuo YY, Huang F, Yue T. Perturbation of the pulmonary surfactant monolayer by single-walled carbon nanotubes: a molecular dynamics study. NANOSCALE 2017; 9:10193-10204. [PMID: 28485435 DOI: 10.1039/c7nr00890b] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) are at present synthesized on a large scale with a variety of applications. The increasing likelihood of exposure to SWCNTs, however, puts human health at a high risk. As the front line of the innate host defense system, the pulmonary surfactant monolayer (PSM) at the air-water interface of the lungs interacts with the inhaled SWCNTs, which in turn inevitably perturb the ultrastructure of the PSM and affect its biophysical functions. Here, using molecular dynamics simulations, we demonstrate how the diameter and length of SWCNTs critically regulate their interactions with the PSM. Compared to their diameters, the inhalation toxicity of SWCNTs was found to be largely affected by their lengths. Short SWCNTs with lengths comparable to the monolayer thickness are found to vertically insert into the PSM with no indication of translocation, possibly leading to accumulation of SWCNTs in the PSM with prolonged retention and increased inflammation potentials. The perturbation also comes from the forming water pores across the PSM. Longer SWCNTs are found to horizontally insert into the PSM during inspiration, and they can be wrapped by the PSM during deep expiration via a tube diameter-dependent self-rotation. The potential toxicity of longer SWCNTs comes from severe lipid depletion and the PSM-rigidifying effect. Our findings could help reveal the inhalation toxicity of SWCNTs, and pave the way for the safe use of SWCNTs as vehicles for pulmonary drug delivery.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Zhen Luo
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Weiguo Li
- College of Science, China University of Petroleum (East China), Qingdao 266580, China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yi Y Zuo
- Department of Mechanical Engineering, University of Hawaii at Monoa, Honolulu, Hawaii 96822, USA
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
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14
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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] [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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15
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Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G. Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS NANO 2017; 11:1273-1280. [PMID: 28103440 DOI: 10.1021/acsnano.6b05434] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets. As the CNT moves away from the symmetry axis connecting the vesicle centers, the inner leaflets merge, forming a pore that completes fusion. The distinct mechanism of CNT-mediated membrane fusion may be transferable, providing guidance in the development of fusion agents, e.g., for the targeted delivery of drugs or nucleic acids.
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Affiliation(s)
- Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Stephanie M Linker
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Martin Vögele
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt , 60438 Frankfurt am Main, Germany
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16
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Chu X, Aydin F, Dutt M. Modeling Interactions between Multicomponent Vesicles and Antimicrobial Peptide-Inspired Nanoparticles. ACS NANO 2016; 10:7351-7361. [PMID: 27434532 DOI: 10.1021/acsnano.5b08133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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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17
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Aydin F, Dutt M. Surface Reconfiguration of Binary Lipid Vesicles via Electrostatically Induced Nanoparticle Adsorption. J Phys Chem B 2016; 120:6646-56. [DOI: 10.1021/acs.jpcb.6b02334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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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18
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Harnessing steric hindrance to control interfacial adsorption of patchy nanoparticles onto hairy vesicles. Colloids Surf B Biointerfaces 2016; 141:458-466. [DOI: 10.1016/j.colsurfb.2016.01.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/25/2016] [Accepted: 01/31/2016] [Indexed: 11/22/2022]
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19
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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] [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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20
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Li NK, Fuss WH, Tang L, Gu R, Chilkoti A, Zauscher S, Yingling YG. Prediction of solvent-induced morphological changes of polyelectrolyte diblock copolymer micelles. SOFT MATTER 2015; 11:8236-8245. [PMID: 26315065 DOI: 10.1039/c5sm01742d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Self-assembly processes of polyelectrolyte block copolymers are ubiquitous in industrial and biological processes; understanding their physical properties can also provide insights into the design of polyelectrolyte materials with novel and tailored properties. Here, we report systematic analysis on how the ionic strength of the solvent and the length of the polyelectrolyte block affect the self-assembly and morphology of the polyelectrolyte block copolymer materials by constructing a salt-dependent morphological phase diagram using an implicit solvent ionic strength (ISIS) method for dissipative particle dynamics (DPD) simulations. This diagram permits the determination of the conditions for the morphological transition into a specific shape, namely vesicles or lamellar aggregates, wormlike/cylindrical micelles, and spherical micelles. The scaling behavior for the size of spherical micelles is predicted, in terms of radius of gyration (R(g,m)) and thickness of corona (Hcorona), as a function of solvent ionic strength (c(s)) and polyelectrolyte length (NA), which are R(g,m) ∼ c(s)(-0.06)N(A)(0.54) and Hcorona ∼ c(s)(-0.11)N(A)(0.75). The simulation results were corroborated through AFM and static light scattering measurements on the example of the self-assembly of monodisperse, single-stranded DNA block-copolynucleotides (polyT50-b-F-dUTP). Overall, we were able to predict the salt-responsive morphology of polyelectrolyte materials in aqueous solution and show that a spherical-cylindrical-lamellar change in morphology can be obtained through an increase in solvent ionic strength or a decrease of polyelectrolyte length.
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Affiliation(s)
- Nan K Li
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA.
| | - William H Fuss
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA.
| | - Lei Tang
- Department of Mechanical Engineering and Materials Science, Duke University, 144 Hudson Hall, Durham, NC 27708, USA
| | - Renpeng Gu
- Department of Mechanical Engineering and Materials Science, Duke University, 144 Hudson Hall, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall, Durham, NC 27708, USA
| | - Stefan Zauscher
- Department of Mechanical Engineering and Materials Science, Duke University, 144 Hudson Hall, Durham, NC 27708, USA
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA.
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21
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Moreno N, Nunes SP, Peinemann KV, Calo VM. Topology and Shape Control for Assemblies of Block Copolymer Blends in Solution. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01891] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Nicolas Moreno
- Biological and Environmental Science and Engineering Division, ‡Center for Numerical Porous Media, §Advanced Membranes and Porous Material Center, and ∥Earth Science & Engineering and Applied Mathematics & Computational Science, King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia 23955-6900
| | - Suzana P. Nunes
- Biological and Environmental Science and Engineering Division, ‡Center for Numerical Porous Media, §Advanced Membranes and Porous Material Center, and ∥Earth Science & Engineering and Applied Mathematics & Computational Science, King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia 23955-6900
| | - Klaus-Viktor Peinemann
- Biological and Environmental Science and Engineering Division, ‡Center for Numerical Porous Media, §Advanced Membranes and Porous Material Center, and ∥Earth Science & Engineering and Applied Mathematics & Computational Science, King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia 23955-6900
| | - Victor M. Calo
- Biological and Environmental Science and Engineering Division, ‡Center for Numerical Porous Media, §Advanced Membranes and Porous Material Center, and ∥Earth Science & Engineering and Applied Mathematics & Computational Science, King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia 23955-6900
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22
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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] [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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23
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The design of shape-tunable hairy vesicles. Colloids Surf B Biointerfaces 2015; 128:268-275. [DOI: 10.1016/j.colsurfb.2015.01.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 01/10/2015] [Accepted: 01/28/2015] [Indexed: 11/20/2022]
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24
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Yue T, Zhang X, Huang F. Molecular modeling of membrane responses to the adsorption of rotating nanoparticles: promoted cell uptake and mechanical membrane rupture. SOFT MATTER 2015; 11:456-465. [PMID: 25388826 DOI: 10.1039/c4sm01760a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recently, a unique dynamic magnetic field was developed to induce the rotational movement of superparamagnetic iron oxide nanoparticles. This technique has been applied to remotely control both cellular internalization and apoptosis. Therefore, a thorough understanding of how a lipid membrane responds to the introduction of rotating NPs is quite important to promote the applications of this technique in a variety of biomedical area. Here, we performed Dissipative Particle Dynamics (DPD) simulations to systematically investigate the interaction mechanism between lipid membranes and rotating NPs. Two kinds of membrane responses are observed. One is the promoted cell uptake and the other is the mechanical membrane rupture. The promoting effect of NP rotation on the cell uptake is ascribed to the enhanced membrane monolayer protrusion, which can wrap the NP from the top side. Meanwhile, the rotating NP exerts a shearing force on the membrane. Accordingly, the membrane undergoes a local distortion around the NP. If the shearing force exceeds a critical value, the local membrane distortion develops into a mechanical rupture. A number of factors, like NP size, NP shape, ligand density and rotation speed, are critical in both of the above membrane responses.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China.
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25
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Yue T, Wang X, Zhang X, Huang F. Molecular modeling of interaction between lipid monolayer and graphene nanosheets: implications for pulmonary nanotoxicity and pulmonary drug delivery. RSC Adv 2015. [DOI: 10.1039/c5ra04922a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding how nanoparticles interact with the pulmonary surfactant monolayer (PSM) is of great importance for safe applications in biomedicine and for evaluation of both health and environment impacts.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- People's Republic of China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- People's Republic of China
| | - Xianren Zhang
- State Key Laboratory of Organic–Inorganic Composites
- Beijing University of Chemical Technology
- Beijing
- People's Republic of China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- People's Republic of China
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26
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Kacar G, Peters EAJF, van der Ven LGJ, de With G. Hierarchical multi-scale simulations of adhesion at polymer–metal interfaces: dry and wet conditions. Phys Chem Chem Phys 2015; 17:8935-44. [DOI: 10.1039/c5cp00343a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multi-scale simulations are performed to study the adhesion properties of different polymer–metal interfaces in the absence and presence of water.
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Affiliation(s)
- Gokhan Kacar
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
| | - Elias A. J. F. Peters
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
| | - Leendert G. J. van der Ven
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
| | - Gijsbertus de With
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
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27
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Lewis DD, Villarreal FD, Wu F, Tan C. Synthetic biology outside the cell: linking computational tools to cell-free systems. Front Bioeng Biotechnol 2014; 2:66. [PMID: 25538941 PMCID: PMC4260521 DOI: 10.3389/fbioe.2014.00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/23/2014] [Indexed: 12/22/2022] Open
Abstract
As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.
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Affiliation(s)
- Daniel D. Lewis
- Integrative Genetics and Genomics, University of California Davis, Davis, CA, USA
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | | | - Fan Wu
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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28
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Kobryn AE, Nikolić D, Lyubimova O, Gusarov S, Kovalenko A. Dissipative Particle Dynamics with an Effective Pair Potential from Integral Equation Theory of Molecular Liquids. J Phys Chem B 2014; 118:12034-49. [DOI: 10.1021/jp503981p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Alexander E. Kobryn
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Dragan Nikolić
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
| | - Olga Lyubimova
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
| | - Sergey Gusarov
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Andriy Kovalenko
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
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29
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Aydin F, Ludford P, Dutt M. Phase segregation in bio-inspired multi-component vesicles encompassing double tail phospholipid species. SOFT MATTER 2014; 10:6096-6108. [PMID: 25008809 DOI: 10.1039/c4sm00998c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Our aim is to investigate the phase segregation and the structure of multi-component bio-inspired phospholipid vesicles via dissipative particle dynamics. The chemical distinction in the phospholipid species arises due to different head and tail group moieties, and molecular stiffness of the hydrocarbon tails. The individual amphiphilic phospholipid molecular species are represented by a hydrophilic head group and two hydrophobic tails. The distinct chemical nature of the moieties is modeled effectively via soft repulsive interaction parameters, and the molecular rigidity is tuned via suitable three-body potential constants. We demonstrate the formation of a stable hybrid vesicle through the self-assembly of the amphiphilic phospholipid molecules in the presence of a hydrophilic solvent. We investigate and characterize the phase segregation and the structure of the binary vesicles for different phospholipid mixtures. Our results demonstrate macroscopic phase separation for phospholipid mixtures composed of species with different hydrocarbon tail groups. We also investigate the relationship between the phase segregation and thermodynamic variables such as interfacial line tension and surface tension, and obtain correspondence between existing theory and experiments, and our simulation results. We report variations in the molecular chain stiffness to have negligible contributions to the phase segregation in the mixed bilayer, and to demonstrate shape transformations of the hybrid vesicle. Our results can be used to design novel bio-inspired hybrid vehicles for potential applications in biomedicine, sensing, imaging and sustainability.
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Affiliation(s)
- Fikret Aydin
- Department of Chemical Engineering, Rutgers The State University of New Jersey, Piscataway, NJ 08854, USA.
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30
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Dallavalle M, Leonzio M, Calvaresi M, Zerbetto F. Explaining Fullerene Dispersion by using Micellar Solutions. Chemphyschem 2014; 15:2998-3005. [DOI: 10.1002/cphc.201402282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 11/11/2022]
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31
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Zhang Z, Li T, Nies E. Mesoscale Simulations of Cylindrical Nanoparticle-Driven Assembly of Diblock Copolymers in Concentrated Solutions. Macromolecules 2014. [DOI: 10.1021/ma500690g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zunmin Zhang
- Division of Polymer Chemistry
and Materials, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| | - Ting Li
- Division of Polymer Chemistry
and Materials, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| | - Erik Nies
- Division of Polymer Chemistry
and Materials, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
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32
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Aydin F, Dutt M. Bioinspired Vesicles Encompassing Two-Tail Phospholipids: Self-Assembly and Phase Segregation via Implicit Solvent Coarse-Grained Molecular Dynamics. J Phys Chem B 2014; 118:8614-23. [DOI: 10.1021/jp503376r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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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33
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34
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Yong X, Crabb EJ, Moellers NM, Balazs AC. Self-healing vesicles deposit lipid-coated Janus particles into nanoscopic trenches. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:16066-16074. [PMID: 24325317 DOI: 10.1021/la4039182] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Using dissipative particle dynamics (DPD) simulations, we model the interaction between nanoscopic lipid vesicles and Janus nanoparticles localized on an adhesive substrate in the presence of an imposed flow. The system is immersed in a hydrophilic solution, and the hydrophilic substrate contains nanoscopic trenches, which are either step- or wedge-shaped. The fluid-driven vesicle successfully picks up Janus particles on the substrate, transports these particles as cargo along the surface, and then drops off the particles into the trenches. For Janus particles with a relatively large hydrophobic region, lipids from the bilayer membrane become detached from the vesicle and bound to the hydrophobic domain of the deposited particle. While the detachment of these lipids rips the vesicle, it provides a coating that effectively shields the hydrophobic portion of the nanoparticle from the outer solution. After the particle has been dropped off, the torn vesicle undergoes structural rearrangement, reforming into a closed structure that resembles its original shape. In effect, the vesicle displays pronounced adaptive behavior, shedding lipids to form a protective coating around the particle and undergoing a self-healing process after the particle has been deposited. This responsive, adaptive behavior is observed in cases involving both the step- and wedge-shaped trenches, but the step trench is more effective at inducing particle drop off. The results reveal that the introduction of grooves or trenches into a hydrophilic surface can facilitate the targeted delivery of amphiphilic particles by self-healing vesicles, which could be used for successive delivery events.
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Affiliation(s)
- Xin Yong
- Chemical Engineering Department, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
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35
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Dutt M, Kuksenok O, Balazs AC. Nano-pipette directed transport of nanotube transmembrane channels and hybrid vesicles. NANOSCALE 2013; 5:9773-9784. [PMID: 23963614 DOI: 10.1039/c3nr33991b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Using computational modeling, we simulate the interactions between a nanopipette and transmembrane, end-functionalized nanotubes that are localized within flat bilayers or nanoscopic vesicles. The functional groups (hairs) provide a "handle" for the moving pipette to controllably pick up and move the nanotubes to specific locations in the flat membrane, or the hybrid vesicle to specified regions on a surface. The ability to localize these hybrid vesicles on surfaces paves the way for creating nanoreactor arrays in fluidic devices.
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Affiliation(s)
- Meenakshi Dutt
- Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854, USA
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36
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Kamalasanan K, Gottardi R, Tan S, Chen Y, Godugu B, Rothstein S, Balazs AC, Star A, Little SR. "Zero-dimensional" single-walled carbon nanotubes. Angew Chem Int Ed Engl 2013; 52:11308-12. [PMID: 24038731 DOI: 10.1002/anie.201305526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 11/08/2022]
Abstract
The shorter, the more dispersible: An iterative, emulsion-based shortening technique has been used to reduce the length of single-walled carbon nanotubes (SWNTs) to the same order of magnitude as their diameter (ca. 1 nm), thus achieving an effectively "zero-dimensional" structure with improved dispersibility and, after hydroxylation, long-term water solubility. Finally, zero-dimensional SWNTs were positively identified using mass spectrometry for the first time.
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Affiliation(s)
- Kaladhar Kamalasanan
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15261 (USA) http://littlelab.pitt.edu
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37
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Kamalasanan K, Gottardi R, Tan S, Chen Y, Godugu B, Rothstein S, Balazs AC, Star A, Little SR. “Zero-Dimensional” Single-Walled Carbon Nanotubes. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Chaban VV, Verspeek B, Khandelia H. Novel Ultrathin Membranes Composed of Organic Ions. J Phys Chem Lett 2013; 4:1216-1220. [PMID: 26282045 DOI: 10.1021/jz400424f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Until recently, construction of bilayers was an exclusive mission of nature. It requires careful choice of compounds, whose delicate interplay between head group attraction and chain repulsion engenders a truly unique balance over a narrow temperature range. We report the investigation of artificial bilayers composed of long-chained organic ions, such as dodecyltrimethylammonium (DMA(+)) and perfluorooctaonate (PFO(-)). Various ratios of DMA/PFO surfactants result in bilayers of different stability, thickness, area per molecule, and density profiles. In our quest for water filtration, we incorporated aquaporin protein into the DMA/PFO bilayer but did not observe sufficient stability of the system. We discuss further steps to utilize these surfactant bilayers as highly selective, salt-impermeable membranes.
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Affiliation(s)
- Vitaly V Chaban
- †MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M. 5230, Denmark
| | - Bram Verspeek
- ‡Department of Biomedical Engineering, University of Technology Eindhoven, The Netherlands
| | - Himanshu Khandelia
- †MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M. 5230, Denmark
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Salib I, Yong X, Crabb EJ, Moellers NM, McFarlin GT, Kuksenok O, Balazs AC. Harnessing fluid-driven vesicles to pick up and drop off Janus particles. ACS NANO 2013; 7:1224-1238. [PMID: 23363323 DOI: 10.1021/nn304622f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Using dissipative particle dynamics (DPD) simulations, we model the interaction between nanoscopic lipid vesicles and Janus nanoparticles in the presence of an imposed flow. Both the vesicle and Janus nanoparticles are localized on a hydrophilic substrate and immersed in a hydrophilic solution. The fluid-driven vesicle successfully picks up Janus particles on the substrate and transports these particles as cargo along the surface. The vesicle can carry up to four particles as its payload. Hence, the vesicles can act as nanoscopic "vacuum cleaners", collecting nanoscopic debris localized on the floors of the fluidic devices. Importantly, these studies reveal how an imposed flow can facilitate the incorporation of nanoparticles into nanoscale vesicles. With the introduction of a "sticky" domain on the substrate, the vesicles can also robustly drop off and deposit the particles on the surface. The controlled pickup and delivery of nanoparticles via lipid vesicles can play an important step in the bottom-up assembly of these nanoparticles within small-scale fluidic devices.
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Affiliation(s)
- Isaac Salib
- Chemical Engineering Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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Dürr UH, Soong R, Ramamoorthy A. When detergent meets bilayer: birth and coming of age of lipid bicelles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:1-22. [PMID: 23465641 PMCID: PMC3741677 DOI: 10.1016/j.pnmrs.2013.01.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/30/2012] [Indexed: 05/12/2023]
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Vishnyakov A, Talaga DS, Neimark AV. DPD Simulation of Protein Conformations: From α-Helices to β-Structures. J Phys Chem Lett 2012; 3:3081-3087. [PMID: 26296009 DOI: 10.1021/jz301277b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We suggest a coarse-grained model for DPD simulations of polypeptides in solutions. The model mimics hydrogen bonding that stabilizes α-helical and β-structures using dissociable Morse bonds between quasiparticles representing the peptide groups amenable to hydrogen bonding. We demonstrate the capabilities of the model by simulating transitions between coil-like, globular, α-helical, and β-hairpin configurations of model peptides, varying Morse potential parameters, the hydrophobicities of residue side chains, and pH, which determines the charges of residue side chains. We construct a model triblock polypeptide mimicking the sequence of residues α-synuclein at two different pHs. The conformations of this model polypeptide depend on pH similarly to the behavior observed experimentally. The suggested approach to accounting for hydrogen bond formation within the general DPD framework may make the DPD method a competitive alternative to CGMD for modeling equilibrium and dynamic properties of proteins and polypeptides, especially during their transport in confined environments.
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Affiliation(s)
| | - David S Talaga
- ‡Chemistry and Biochemistry, Montclair State University, New Jersey
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Li Y, Li X, Li Z, Gao H. Surface-structure-regulated penetration of nanoparticles across a cell membrane. NANOSCALE 2012; 4:3768-75. [PMID: 22609866 DOI: 10.1039/c2nr30379e] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The cell uptake rate of nanoparticles (NPs) coated with mixed hydrophilic/hydrophobic ligands is known to be strongly influenced by the ligand pattern on the nanoparticle surface. To help reveal the physical mechanism behind this intriguing phenomenon, here we perform dissipative particle dynamics simulations to analyze the evolution of free energy as the ligand-coated NPs pierce through a lipid bilayer. Four characteristic ligand patterns are considered: striated NPs with alternating hydrophilic and hydrophobic groups compared to NPs with randomly mixed ligands at the same hydrophilic to hydrophobic ratio, as well as NPs coated with homogeneous hydrophilic or hydrophobic ligands. The free energy analysis indicates that among the four ligand patterns under study, the striated NP encounters the lowest energy barrier during translocation across the membrane. Further analysis reveals that the translocation of the striated NP is facilitated by the constraint of its rotational degree of freedom by the anisotropic ligand pattern, which prevented the free energy of the system from sinking to a deeper valley as the NP passes through the hydrophobic core of the bilayer. Finally, the critical forces required for almost instant penetration of these patterned NPs across the bilayer are calculated and shown to be consistent with the free energy analysis. These findings provide useful guidelines for the molecular design of patterned NPs for controllable cell penetrability.
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Affiliation(s)
- Yinfeng Li
- Department of Engineering Mechanics, Shanghai Jiao Tong University, Shanghai 200240, China
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Arai N, Yasuoka K, Zeng XC. Nanochannel with uniform and Janus surfaces: shear thinning and thickening in surfactant solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2866-72. [PMID: 22204605 DOI: 10.1021/la2034643] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
On basis of molecular simulation of confined surfactant solutions, we show that by adding chemical patterns on the inner surface of nanochannels dynamical properties of the confined surfactant solutions could be modified from shear thinning to shear thickening. To this end, we select uniformly hydrophobic and hydrophilic surfaces as well as a stripe-patterned Janus surface as three prototype confining surfaces of nanochannels. In all three nanochannels, when the surfactant solution is under relatively low shear rates, it shears thin. Under moderate shear rates, a sharp decrease in the shear viscosity could occur due to surfactant morphology transition. Under relatively high shear rates, a shear-thinning-to-thickening transition can emerge due to the tendency of stratification normal to the confining surface. Our simulation study offers a guide to steering dynamic properties of surfactant fluids in nanofluidic devices through engineering surfaces of nanochannels by design.
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Affiliation(s)
- Noriyoshi Arai
- Department of Mechanical Engineering and Intelligent Systems, University of Electro-Communications, Tokyo 182-8585, Japan
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Masoud H, Alexeev A. Controlled release of nanoparticles and macromolecules from responsive microgel capsules. ACS NANO 2012; 6:212-219. [PMID: 22176274 DOI: 10.1021/nn2043143] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Using a mesoscale computational model, we probe the release of nanoparticles and linear macromolecules from hollow microgel capsules that swell and deswell in response to external stimuli. Our simulations reveal that responsive microcapsules can be effectively utilized for steady and pulsatile release of encapsulated solutes. Swollen gel capsules allow steady, diffusive release of nanoparticles and polymer chains, whereas gel deswelling causes burst-like discharge of solutes driven by an outward flow of the solvent enclosed within a shrinking capsule. We demonstrate that this hydrodynamic release can be regulated by introducing rigid microscopic rods in the capsule interior. Thus, our findings disclose an efficient approach for controlled release from stimuli-responsive microcarriers that could be useful for designing advanced drug delivery systems.
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Affiliation(s)
- Hassan Masoud
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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