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Liu S, Chen S, Xiao L, Zhang K, Qi Y, Li H, Cheng Y, Hu Z, Lin C. Unraveling the motion and deformation characteristics of red blood cells in a deterministic lateral displacement device. Comput Biol Med 2024; 168:107712. [PMID: 38006825 DOI: 10.1016/j.compbiomed.2023.107712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/16/2023] [Accepted: 11/15/2023] [Indexed: 11/27/2023]
Abstract
Deterministic Lateral Displacement (DLD) device has gained widespread recognition and trusted for filtering blood cells. However, there remains a crucial need to explore the complex interplay between deformable cells and flow within the DLD device to improve its design. This paper presents an approach utilizing a mesoscopic cell-level numerical model based on dissipative particle dynamics to effectively capture this complex phenomenon. To establish the model's credibility, a series of numerical simulations were conducted and the numerical results were validated with nominal experimental data from the literature. These include single cell stretching experiment, comparisons of the morphological characteristics of cells in DLD, and comparison the specific row-shift fraction of DLD required to initiate the zigzag mode. Additionally, we investigate the effect of cell rigidity, which serves as an indicator of cell health, on average flow velocity, trajectory, and asphericity. Moreover, we extend the existing theory of predicting zigzag mode for solid spherical particles to encompass the behavior of red blood cells. To achieve this, we introduce a new concept of effective diameter and demonstrate its applicability in providing highly accurate predictions across a wide range of conditions.
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Affiliation(s)
- Shuai Liu
- School of Aerospace Engineering and Applied Mechanics, Tongji University, Shanghai, 200092, China
| | - Shuo Chen
- School of Aerospace Engineering and Applied Mechanics, Tongji University, Shanghai, 200092, China.
| | - Lanlan Xiao
- School of Mechanical and Automotive Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Kaixuan Zhang
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yuan Qi
- Artificial Intelligence Innovation and Incubation Institute, Fudan University, Shanghai, 200433, China
| | - Hao Li
- Artificial Intelligence Innovation and Incubation Institute, Fudan University, Shanghai, 200433, China
| | - Yuan Cheng
- Artificial Intelligence Innovation and Incubation Institute, Fudan University, Shanghai, 200433, China
| | - Zixin Hu
- Artificial Intelligence Innovation and Incubation Institute, Fudan University, Shanghai, 200433, China; Fudan Zhangjiang Institute, Shanghai, 201203, China; Shanghai Pudong Hospital, Shanghai, 201399, China
| | - Chensen Lin
- Artificial Intelligence Innovation and Incubation Institute, Fudan University, Shanghai, 200433, China; Fudan Zhangjiang Institute, Shanghai, 201203, China; Shanghai Pudong Hospital, Shanghai, 201399, China.
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2
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Michael C, Pancaldi F, Britton S, Kim OV, Peshkova AD, Vo K, Xu Z, Litvinov RI, Weisel JW, Alber M. Combined computational modeling and experimental study of the biomechanical mechanisms of platelet-driven contraction of fibrin clots. Commun Biol 2023; 6:869. [PMID: 37620422 PMCID: PMC10449797 DOI: 10.1038/s42003-023-05240-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
While blood clot formation has been relatively well studied, little is known about the mechanisms underlying the subsequent structural and mechanical clot remodeling called contraction or retraction. Impairment of the clot contraction process is associated with both life-threatening bleeding and thrombotic conditions, such as ischemic stroke, venous thromboembolism, and others. Recently, blood clot contraction was observed to be hindered in patients with COVID-19. A three-dimensional multiscale computational model is developed and used to quantify biomechanical mechanisms of the kinetics of clot contraction driven by platelet-fibrin pulling interactions. These results provide important biological insights into contraction of platelet filopodia, the mechanically active thin protrusions of the plasma membrane, described previously as performing mostly a sensory function. The biomechanical mechanisms and modeling approach described can potentially apply to studying other systems in which cells are embedded in a filamentous network and exert forces on the extracellular matrix modulated by the substrate stiffness.
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Affiliation(s)
- Christian Michael
- Department of Mathematics, University of California Riverside, Riverside, CA, 92521, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA, 92521, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Francesco Pancaldi
- Department of Mathematics, University of California Riverside, Riverside, CA, 92521, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Samuel Britton
- Department of Mathematics, University of California Riverside, Riverside, CA, 92521, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Oleg V Kim
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
- Department of Biomedical Engineering and Mechanics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Alina D Peshkova
- Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Khoi Vo
- Department of Mathematics, University of California Riverside, Riverside, CA, 92521, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Zhiliang Xu
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Rustem I Litvinov
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - John W Weisel
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA.
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA, 92521, USA.
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA, 92521, USA.
- Department of Bioengineering, University of California Riverside, Riverside, CA, 92521, USA.
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Xia Y, Rao Q, Hamed A, Kane J, Semeykina V, Zharov I, Deo M, Li Z. Flow Reduction in Pore Networks of Packed Silica Nanoparticles: Insights from Mesoscopic Fluid Models. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8135-8152. [PMID: 35731695 DOI: 10.1021/acs.langmuir.2c01038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A modified many-body dissipative particle dynamics (mDPD) model is rigorously calibrated to achieve realistic fluid-fluid/solid interphase properties and applied for mesoscale flow simulations to elucidate the transport mechanisms of heptane liquid and water, respectively, through pore networks formed by packed silica nanoparticles with a uniform diameter of 30 nm. Two million CPU core hours were used to complete the simulation studies. Results show reduction of permeability by 54-64% in heptane flow and by 88-91% in water flow, respectively, compared to the Kozeny-Carman equation. In these nanopores, a large portion of the fluids are in the near-wall regions and thus not mobile due to the confinement effect, resulting in reduced hydraulic conductivity. Moreover, intense oscillations in the calculated flow velocities also indicate the confinement effect that contests the external driven force to flow. The generic form of Darcy's law is considered valid for flow through homogeneous nanopore networks, while permeability depends collectively on pore size and surface wettability. This fluid-permeability dependency is unique to flow in nanopores. In addition, potential dependence of permeability on pore connectivity is observed when the porosity remains the same in different core specimens.
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Affiliation(s)
- Yidong Xia
- Energy and Environment Science and Technology, Idaho National Laboratory, Idaho Falls, Idaho 83415, United States
| | - Qi Rao
- Energy and Environment Science and Technology, Idaho National Laboratory, Idaho Falls, Idaho 83415, United States
| | - Ahmed Hamed
- Energy and Environment Science and Technology, Idaho National Laboratory, Idaho Falls, Idaho 83415, United States
| | - Joshua Kane
- Materials and Fuels Complex, Idaho National Laboratory, Idaho Falls, Idaho 83415, United States
| | - Viktoriya Semeykina
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States
| | - Ilya Zharov
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States
| | - Milind Deo
- Department of Chemical Engineering, The University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhen Li
- Department of Mechanical Engineering, Clemson University, Clemson, South Carolina 29634, United States
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4
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Rao Q, Xia Y, Li J, Deo M, Li Z. Flow reduction of hydrocarbon liquid in silica nanochannel: Insight from many-body dissipative particle dynamics simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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Okada K, Brumby PE, Yasuoka K. The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function. PLoS One 2021; 16:e0250593. [PMID: 33905444 PMCID: PMC8078758 DOI: 10.1371/journal.pone.0250593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/11/2021] [Indexed: 12/03/2022] Open
Abstract
The tiny encryption algorithm (TEA) is widely used when performing dissipative particle dynamics (DPD) calculations in parallel, usually on distributed memory systems. In this research, we reduced the computational cost of the TEA hash function and investigated the influence of the quality of the random numbers generated on the results of DPD calculations. It has already been established that the randomness, or quality, of the random numbers depend on the number of processes from internal functions such as SHIFT, XOR and ADD, which are commonly referred to as “rounds”. Surprisingly, if we choose seed numbers from high entropy sources, with a minimum number of rounds, the quality of the random numbers generated is sufficient to successfully perform accurate DPD simulations. Although it is well known that using a minimal number of rounds is insufficient for generating high-quality random numbers, the combination of selecting good seed numbers and the robustness of DPD simulations means that we can reduce the random number generation cost without reducing the accuracy of the simulation results.
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Affiliation(s)
- Kiyoshiro Okada
- Department of Mechanical Engineering, Keio University,Yokohama, Kanagawa, Japan
| | - Paul E. Brumby
- Department of Mechanical Engineering, Keio University,Yokohama, Kanagawa, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University,Yokohama, Kanagawa, Japan
- * E-mail:
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Kotsalos C, Latt J, Beny J, Chopard B. Digital blood in massively parallel CPU/GPU systems for the study of platelet transport. Interface Focus 2021; 11:20190116. [PMID: 33335703 PMCID: PMC7739916 DOI: 10.1098/rsfs.2019.0116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 01/13/2023] Open
Abstract
We propose a highly versatile computational framework for the simulation of cellular blood flow focusing on extreme performance without compromising accuracy or complexity. The tool couples the lattice Boltzmann solver Palabos for the simulation of blood plasma, a novel finite-element method (FEM) solver for the resolution of deformable blood cells, and an immersed boundary method for the coupling of the two phases. The design of the tool supports hybrid CPU-GPU executions (fluid, fluid-solid interaction on CPUs, deformable bodies on GPUs), and is non-intrusive, as each of the three components can be replaced in a modular way. The FEM-based kernel for solid dynamics outperforms other FEM solvers and its performance is comparable to state-of-the-art mass-spring systems. We perform an exhaustive performance analysis on Piz Daint at the Swiss National Supercomputing Centre and provide case studies focused on platelet transport, implicitly validating the accuracy of our tool. The tests show that this versatile framework combines unprecedented accuracy with massive performance, rendering it suitable for upcoming exascale architectures.
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Affiliation(s)
- Christos Kotsalos
- Computer Science Department, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland
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7
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Rao Q, Xia Y, Li J, McConnell J, Sutherland J, Li Z. A modified many-body dissipative particle dynamics model for mesoscopic fluid simulation: methodology, calibration, and application for hydrocarbon and water. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1876233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Qi Rao
- Energy and Environment Science & Technology, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Yidong Xia
- Energy and Environment Science & Technology, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Jiaoyan Li
- Department of Mechanical and Aerospace Engineering, State University of New York at Buffalo, Buffalo, NY, USA
| | - Joshua McConnell
- Department of Chemical Engineering, University of Utah, Salt Lake City, UT, USA
| | - James Sutherland
- Department of Chemical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Zhen Li
- Department of Mechanical Engineering, Clemson University, Clemson, SC, USA
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8
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Jančigová I, Kovalčíková K, Weeber R, Cimrák I. PyOIF: Computational tool for modelling of multi-cell flows in complex geometries. PLoS Comput Biol 2020; 16:e1008249. [PMID: 33075044 PMCID: PMC7595628 DOI: 10.1371/journal.pcbi.1008249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/29/2020] [Accepted: 08/14/2020] [Indexed: 11/28/2022] Open
Abstract
A user ready, well documented software package PyOIF contains an implementation of a robust validated computational model for cell flow modelling. The software is capable of simulating processes involving biological cells immersed in a fluid. The examples of such processes are flows in microfluidic channels with numerous applications such as cell sorting, rare cell isolation or flow fractionation. Besides the typical usage of such computational model in the design process of microfluidic devices, PyOIF has been used in the computer-aided discovery involving mechanical properties of cell membranes. With this software, single cell, many cell, as well as dense cell suspensions can be simulated. Many cell simulations include cell-cell interactions and analyse their effect on the cells. PyOIF can be used to test the influence of mechanical properties of the membrane in flows and in membrane-membrane interactions. Dense suspensions may be used to study the effect of cell volume fraction on macroscopic phenomena such as cell-free layer, apparent suspension viscosity or cell degradation. The PyOIF module is based on the official ESPResSo distribution with few modifications and is available under the terms of the GNU General Public Licence. PyOIF is based on Python objects representing the cells and on the C++ computational core for fluid and interaction dynamics. The source code is freely available at GitHub repository, runs natively under Linux and MacOS and can be used in Windows Subsystem for Linux. The communication among PyOIF users and developers is maintained using active mailing lists. This work provides a basic background to the underlying computational models and to the implementation of interactions within this framework. We provide the prospective PyOIF users with a practical example of simulation script with reference to our publicly available User Guide.
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Affiliation(s)
- Iveta Jančigová
- Cell-in-fluid Biomedical Modelling and Computation Group, University of Žilina, Žilina, Slovakia
| | - Kristína Kovalčíková
- Cell-in-fluid Biomedical Modelling and Computation Group, University of Žilina, Žilina, Slovakia
| | - Rudolf Weeber
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Ivan Cimrák
- Cell-in-fluid Biomedical Modelling and Computation Group, University of Žilina, Žilina, Slovakia
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9
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Yang SC, Li B, Zhu YL, Laaksonen A, Wang YL. The ENUF method-Ewald summation based on nonuniform fast Fourier transform: Implementation, parallelization, and application. J Comput Chem 2020; 41:2316-2335. [PMID: 32808686 DOI: 10.1002/jcc.26395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 11/12/2022]
Abstract
Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between charged particles constitute a prominent factor in determining structures and states of model systems. How to efficiently calculate electrostatic interactions in simulation systems subjected to partial or full periodic boundary conditions has been a grand challenging task. In the past decades, a large variety of computational schemes has been proposed, among which the Ewald summation method is the most reliable route to accurately deal with electrostatic interactions between charged particles in simulation systems. In addition, extensive efforts have been done to improve computational efficiencies of the Ewald summation based methods. Representative examples are approaches based on cutoffs, reaction fields, multi-poles, multi-grids, and particle-mesh schemes. We sketched an ENUF method, an abbreviation for the Ewald summation method based on the nonuniform fast Fourier transform technique, and have implemented this method in particle-based simulation packages to calculate electrostatic energies and forces at micro- and mesoscopic levels. Extensive computational studies of conformational properties of polyelectrolytes, dendrimer-membrane complexes, and ionic fluids demonstrated that the ENUF method and its derivatives conserve both energy and momentum to floating point accuracy, and exhibit a computational complexity of O N log N with optimal physical parameters. These ENUF based methods are attractive alternatives in molecular simulations where high accuracy and efficiency of simulation methods are needed to accelerate calculations of electrostatic interactions at extended spatiotemporal scales.
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Affiliation(s)
- Sheng-Chun Yang
- School of Computer Science, Northeast Electric Power University, Jilin, China
| | - Bin Li
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai, China
| | - You-Liang Zhu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, Iasi, Romania.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
| | - Yong-Lei Wang
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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10
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Moreira-Soares M, Cunha SP, Bordin JR, Travasso RDM. Adhesion modulates cell morphology and migration within dense fibrous networks. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:314001. [PMID: 32378515 DOI: 10.1088/1361-648x/ab7c17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
One of the most fundamental abilities required for the sustainability of complex life forms is active cell migration, since it is essential in diverse processes from morphogenesis to leukocyte chemotaxis in immune response. The movement of a cell is the result of intricate mechanisms, that involve the coordination between mechanical forces, biochemical regulatory pathways and environmental cues. In particular, epithelial cancer cells have to employ mechanical strategies in order to migrate through the tissue's basement membrane and infiltrate the bloodstream during the invasion stage of metastasis. In this work we explore how mechanical interactions such as spatial restriction and adhesion affect migration of a self-propelled droplet in dense fibrous media. We have performed a systematic analysis using a phase-field model and we propose a novel approach to simulate cell migration with dissipative particle dynamics modelling. With this purpose we have measured in our simulation the cell's velocity and quantified its morphology as a function of the fibre density and of its adhesiveness to the matrix fibres. Furthermore, we have compared our results to a previousin vitromigration assay of fibrosarcoma cells in fibrous matrices. The results show good agreement between the two methodologies and experiments in the literature, which indicates that these minimalist descriptions are able to capture the main features of the system. Our results indicate that adhesiveness is critical for cell migration, by modulating cell morphology in crowded environments and by enhancing cell velocity. In addition, our analysis suggests that matrix metalloproteinases (MMPs) play an important role as adhesiveness modulators. We propose that new assays should be carried out to address the role of adhesion and the effect of different MMPs in cell migration under confined conditions.
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Affiliation(s)
| | - Susana P Cunha
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - José Rafael Bordin
- Department of Physics, Institute of Physics and Mathematics, Federal University of Pelotas, Rua dos Ipês, Capão do Leão, RS, 96050-500, Brazil
| | - Rui D M Travasso
- CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
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11
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Wang S, Li X, Gong X, Liang H. Mechanistic modeling of spontaneous penetration of carbon nanocones into membrane vesicles. NANOSCALE 2020; 12:2686-2694. [PMID: 31916567 DOI: 10.1039/c9nr09098c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Carbon nanocones (CNCs) are promising drug delivery systems that can be functionalized with a variety of biomolecules (such as proteins, peptides, or antibodies), which allow for site-specific, targeted payload delivery to particular cells and organs. However, considerable uncertainty exists with respect to the toxicity of CNCs on their conical shape, and the underlying mechanism that leads to the penetration of CNCs (especially the truncated ones) in and through the cell membrane is not yet well understood. Using a coarse-grained dissipative particle dynamics method, we systematically investigate the spontaneous penetration of untruncated and truncated CNCs into membrane vesicles. For untruncated CNCs, the simulation results show that both pristine and oxidized ones can spontaneously penetrate across or be attached to the vesicle surface without membrane rupture, indicating low or insignificant toxicity. However, for truncated CNCs, we find that both the apex angle and aspect ratio can influence the CNC-membrane interactions and CNC-induced toxicity: a higher apex angle (and/or a lower aspect ratio) yields a higher toxicity of truncated CNCs. Further free energy analysis reveals that the lowest free energy path during the penetration is associated with CNC's orientation and rotation. For a truncated CNC with a low aspect ratio and high apex angle, it tends to rotate itself to a preferred standing-up fashion inside the vesicle membrane, posing an enhanced toxicity of CNCs. These findings may provide useful guidelines for designing effective CNC vehicles 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
| | - Xuejin Li
- Department of Engineering Mechanics and Center for X-Mechanics, Zhejiang University, Hangzhou 310027, P. R. China.
| | - Xiaobo Gong
- 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
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei 230026, P. R. China and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, P. R. China
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12
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Wang S, Li Z, Pan W. Implicit-solvent coarse-grained modeling for polymer solutions via Mori-Zwanzig formalism. SOFT MATTER 2019; 15:7567-7582. [PMID: 31436282 DOI: 10.1039/c9sm01211g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a bottom-up coarse-graining (CG) method to establish implicit-solvent CG modeling for polymers in solution, which conserves the dynamic properties of the reference microscopic system. In particular, tens to hundreds of bonded polymer atoms (or Lennard-Jones beads) are coarse-grained as one CG particle, and the solvent degrees of freedom are eliminated. The dynamics of the CG system is governed by the generalized Langevin equation (GLE) derived via the Mori-Zwanzig formalism, by which the CG variables can be directly and rigorously linked to the microscopic dynamics generated by molecular dynamics (MD) simulations. The solvent-mediated dynamics of polymers is modeled by the non-Markovian stochastic dynamics in GLE, where the memory kernel can be computed from the MD trajectories. To circumvent the difficulty in direct evaluation of the memory term and generation of colored noise, we exploit the equivalence between the non-Markovian dynamics and Markovian dynamics in an extended space. To this end, the CG system is supplemented with auxiliary variables that are coupled linearly to the momentum and among themselves, subject to uncorrelated Gaussian white noise. A high-order time-integration scheme is used to solve the extended dynamics to further accelerate the CG simulations. To assess, validate, and demonstrate the established implicit-solvent CG modeling, we have applied it to study four different types of polymers in solution. The dynamic properties of polymers characterized by the velocity autocorrelation function, diffusion coefficient, and mean square displacement as functions of time are evaluated in both CG and MD simulations. Results show that the extended dynamics with auxiliary variables can construct arbitrarily high-order CG models to reproduce dynamic properties of the reference microscopic system and to characterize long-time dynamics of polymers in solution.
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Affiliation(s)
- Shu Wang
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Zhen Li
- Department of Mechanical Engineering, Clemson University, Clemson, SC 29634, USA
| | - Wenxiao Pan
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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13
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Barber J, Zhu L. Two-dimensional Finite Element Model of Breast Cancer Cell Motion Through a Microfluidic Channel. Bull Math Biol 2019; 81:1238-1259. [DOI: 10.1007/s11538-018-00557-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 12/10/2018] [Indexed: 12/19/2022]
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14
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Huang Y, Marson RL, Larson RG. Inertial migration of a rigid sphere in plane Poiseuille flow as a test of dissipative particle dynamics simulations. J Chem Phys 2018; 149:164912. [DOI: 10.1063/1.5047923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuanding Huang
- School of Mechatronics Engineering, Harbin Institute of Technology, Heilongjiang 150001, People’s Republic of China
- Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ryan L. Marson
- Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
- The Dow Chemical Company, Core R & D, Midland, Michigan 48674, USA
| | - Ronald G. Larson
- Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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