51
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Dennison M, Kapral R, Stark H. Diffusion in systems crowded by active force-dipole molecules. SOFT MATTER 2017; 13:3741-3749. [PMID: 28463368 DOI: 10.1039/c7sm00400a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Experimental studies of systems containing active proteins that undergo conformational changes driven by catalytic chemical reactions have shown that the diffusion coefficients of passive tracer particles and active molecules are larger than the corresponding values when chemical activity is absent. Various mechanisms have been proposed for such behavior, including, among others, force dipole interactions of molecular motors moving on filaments and collective hydrodynamic effects arising from active proteins. Simulations of a multi-component system containing active dumbbell molecules that cycle between open and closed states, a passive tracer particle and solvent molecules are carried out. Consistent with experiments, it is shown that the diffusion coefficients of both passive particles and the dumbbells themselves are enhanced when the dumbbells are active. The dependence of the diffusion enhancement on the volume fraction of dumbbells is determined, and the effects of crowding by active dumbbell molecules are shown to differ from those due to inactive molecules.
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Affiliation(s)
- Matthew Dennison
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany.
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52
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Ghavami A, Kobayashi H, Winkler RG. Internal dynamics of microgels: A mesoscale hydrodynamic simulation study. J Chem Phys 2017; 145:244902. [PMID: 28049314 DOI: 10.1063/1.4972893] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyze the dynamics of polymers in a microgel system under different swelling conditions. A microgel particle consists of coarse-grained linear polymers which are tetra-functionally crosslinked and undergoes conformational changes in response to the external stimuli. Here, a broad range of microgel sizes, extending from tightly collapsed to strongly swollen particles, is considered. In order to account for hydrodynamic interactions, the microgel is embedded in a multiparticle collision dynamics fluid while hydrophobic attraction is modelled by an attractive Lennard-Jones potential and swelling of ionic microgels is described through the Debye-Hückel potential. The polymer dynamics is analyzed in terms of the monomer mean square displacement and the intermediate scattering function S(q, t). The scattering function decays in a stretched-exponential manner, with a decay rate exhibiting a crossover from a collective diffusive dynamics at low magnitudes of the wavevector q to a hydrodynamic-dominated dynamics at larger q. There is little difference between the intermediate scattering functions of microgels under good solvent conditions and strongly swollen gels, but strongly collapsed gels exhibit a faster decay at short times and hydrodynamic interactions become screened. In addition, we present results for the dynamics of the crosslinks, which exhibit an unexpected, semiflexible polymer-like dynamics.
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Affiliation(s)
- Ali Ghavami
- Institute for Advanced Simulation, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Hideki Kobayashi
- Institute for Advanced Simulation, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Roland G Winkler
- Institute for Advanced Simulation, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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53
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Chen W, Zhang K, Liu L, Chen J, Li Y, An L. Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02636] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Kexin Zhang
- School
of Environmental Science, Northeast Normal University, 5268 Renmin
Street, Changchun, P. R. China 130024
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54
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Katyal D, Kant R. Dynamics of comb-of-comb-network polymers in random layered flows. Phys Rev E 2017; 94:062503. [PMID: 28085413 DOI: 10.1103/physreve.94.062503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 11/07/2022]
Abstract
We analyze the dynamics of comb-of-comb-network polymers in the presence of external random flows. The dynamics of such structures is evaluated through relevant physical quantities, viz., average square displacement (ASD) and the velocity autocorrelation function (VACF). We focus on comparing the dynamics of the comb-of-comb network with the linear polymer. The present work displays an anomalous diffusive behavior of this flexible network in the random layered flows. The effect of the polymer topology on the dynamics is analyzed by varying the number of generations and branch lengths in these networks. In addition, we investigate the influence of external flow on the dynamics by varying flow parameters, like the flow exponent α and flow strength W_{α}. Our analysis highlights two anomalous power-law regimes, viz., subdiffusive (intermediate-time polymer stretching and flow-induced diffusion) and superdiffusive (long-time flow-induced diffusion). The anomalous long-time dynamics is governed by the temporal exponent ν of ASD, viz., ν=2-α/2. Compared to a linear polymer, the comb-of-comb network shows a shorter crossover time (from the subdiffusive to superdiffusive regime) but a reduced magnitude of ASD. Our theory displays an anomalous VACF in the random layered flows that scales as t^{-α/2}. We show that the network with greater total mass moves faster.
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Affiliation(s)
- Divya Katyal
- Complex Systems Group, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Rama Kant
- Complex Systems Group, Department of Chemistry, University of Delhi, Delhi 110007, India
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55
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Xu X, Chen J. Effect of functionality on unentangled star polymers at equilibrium and under shear flow. J Chem Phys 2016; 144:244905. [DOI: 10.1063/1.4955098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xiaolei Xu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, People’s Republic of China
| | - Jizhong Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, People’s Republic of China
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56
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Sablić J, Praprotnik M, Delgado-Buscalioni R. Open boundary molecular dynamics of sheared star-polymer melts. SOFT MATTER 2016; 12:2416-39. [PMID: 26820315 DOI: 10.1039/c5sm02604k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution.
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Affiliation(s)
- Jurij Sablić
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia. and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000 Ljubljana, Slovenia
| | - Rafael Delgado-Buscalioni
- Departamento Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Campus de Cantoblanco, E-28049 Madrid, Spain. and Condensed Matter Physics Center, IFIMAC. Campus de Cantoblanco, E-28049 Madrid, Spain
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57
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Dennison M, Stark H. Viscoelastic properties of marginal networks in a solvent. Phys Rev E 2016; 93:022605. [PMID: 26986375 DOI: 10.1103/physreve.93.022605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Indexed: 06/05/2023]
Abstract
Polymer networks at the margins of mechanical stability are known to be highly sensitive to applied forces and fields and to exhibit an anomalously large resistance to deformation. In this paper, we study the effects of hydrodynamic interactions on the behavior of marginal networks using a hybrid molecular dynamics and multiparticle collision dynamics simulation technique. We examine how the filament and solvent properties affect the response of marginal networks to shear. We find that the stiffening of the network shows a stronger dependence on the shear frequency when hydrodynamic interactions are present than when they are not. The network shear modulus scales as G'∼ω(α(c)), with a critical stiffening exponent α(c) that can be controlled by varying the relative concentrations of the network and the solvent. Our results show that this arises due to the solvent aiding the relaxation of the network and suppressing the network nonaffinity, with the system deforming more affinely when hydrodynamic interactions are maximized.
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Affiliation(s)
- M Dennison
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - H Stark
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
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58
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Ceratti DR, Obliger A, Jardat M, Rotenberg B, Dahirel V. Stochastic rotation dynamics simulation of electro-osmosis. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1037370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Davide R. Ceratti
- Sorbonne Universités, UPMC Univ Paris 06, UMR PHENIX , Paris, France
- CNRS, UMR PHENIX , Paris, France
- Collège de France, UMR 7574, Chimie de la Matière Condensée de Paris
| | - Amaël Obliger
- Concrete Sustainability Hub, Department of Civil and Environmental Engineering, and MIT-CNRS Joint Laboratory, Massachusetts Institute of Technology , Cambridge, MA, United States
| | - Marie Jardat
- Sorbonne Universités, UPMC Univ Paris 06, UMR PHENIX , Paris, France
- CNRS, UMR PHENIX , Paris, France
| | - Benjamin Rotenberg
- Sorbonne Universités, UPMC Univ Paris 06, UMR PHENIX , Paris, France
- CNRS, UMR PHENIX , Paris, France
| | - Vincent Dahirel
- Sorbonne Universités, UPMC Univ Paris 06, UMR PHENIX , Paris, France
- CNRS, UMR PHENIX , Paris, France
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59
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Sarkar A, Eckmann DM, Ayyaswamy PS, Radhakrishnan R. Hydrodynamic interactions of deformable polymeric nanocarriers and the effect of crosslinking. SOFT MATTER 2015; 11:5955-69. [PMID: 26126781 PMCID: PMC4518868 DOI: 10.1039/c5sm00669d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report theoretical as well as numerical investigations of deformable nanocarriers (NCs) under physiologically relevant flow conditions. Specifically, to model the deformable lysozyme-core/dextran-shell crosslinked polymer based NC with internal nanostructure and subject it to external hydrodynamic shear, we have introduced a coarse-grained model for the NC and have adopted a Brownian dynamics framework, which incorporates hydrodynamic interactions, in order to describe the static and dynamic properties of the NC. In order to represent the fluidity of the polymer network in the dextran brush-like corona, we coarse-grain the structure of the NC based on the hypothesis that Brownian motion, polymer melt reptations, and crosslinking density dominate their structure and dynamics. In our model, we specify a crosslinking density and employ the simulated annealing protocol to mimic the experimental synthesis steps in order to obtain the appropriate internal structure of the core-shell polymer. We then compute the equilibrium as well as steady shear rheological properties as functions of the Péclet number and the crosslinking density, in the presence of hydrodynamic interactions. We find that with increasing crosslinking, the stiffness of the nanocarrier increases, the radius of gyration decreases, and as a consequence the self-diffusivity increases. The nanocarrier under shear deforms and orients along the direction of the applied shear and we find that the orientation and deformation under shear are dependent on the shear rate and the crosslinking density. We compare various dynamic properties of the NC as a function of the shear force, such as orientation, deformation, intrinsic stresses etc., with previously reported computational and experimental results of other model systems. The computational approach described here serves as a powerful tool for the rational design of NCs by taking both the physiological as well as the hydrodynamic environments into consideration. Development of such models is essential in order to gain useful insights that may be translated into the optimal design of NCs for diagnostic as well as targeted drug delivery applications.
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Affiliation(s)
- Arijit Sarkar
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, USA
| | - David M. Eckmann
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Portonovo S. Ayyaswamy
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA
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60
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Rai DK, Beaucage G, Ratkanthwar K, Beaucage P, Ramachandran R, Hadjichristidis N. Determination of the interaction parameter and topological scaling features of symmetric star polymers in dilute solution. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012602. [PMID: 26274195 DOI: 10.1103/physreve.92.012602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Indexed: 06/04/2023]
Abstract
Star polymers provide model architectures to understand the dynamic and rheological effects of chain confinement for a range of complex topological structures like branched polymers, colloids, and micelles. It is important to describe the structure of such macromolecular topologies using small-angle neutron and x-ray scattering to facilitate understanding of their structure-property relationships. Modeling of scattering from linear, Gaussian polymers, such as in the melt, has applied the random phase approximation using the Debye polymer scattering function. The Flory-Huggins interaction parameter can be obtained using neutron scattering by this method. Gaussian scaling no longer applies for more complicated chain topologies or when chains are in good solvents. For symmetric star polymers, chain scaling can differ from ν=0.5(d(f)=2) due to excluded volume, steric interaction between arms, and enhanced density due to branching. Further, correlation between arms in a symmetric star leads to an interference term in the scattering function first described by Benoit for Gaussian chains. In this work, a scattering function is derived which accounts for interarm correlations in symmetric star polymers as well as the polymer-solvent interaction parameter for chains of arbitrary scaling dimension using a hybrid Unified scattering function. The approach is demonstrated for linear, four-arm and eight-arm polyisoprene stars in deuterated p-xylene.
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Affiliation(s)
- Durgesh K Rai
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN-37831, USA
| | - Gregory Beaucage
- Materials Science and Engineering, University of Cincinnati, Cincinnati, OH-45221, USA
| | - Kedar Ratkanthwar
- Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peter Beaucage
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY 14853, USA
| | | | - Nikos Hadjichristidis
- Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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61
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62
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Singh SP, Huang CC, Westphal E, Gompper G, Winkler RG. Hydrodynamic correlations and diffusion coefficient of star polymers in solution. J Chem Phys 2015; 141:084901. [PMID: 25173039 DOI: 10.1063/1.4893766] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The center-of-mass dynamics of star polymers in dilute solution is analyzed by hybrid mesoscale simulations. The fluid is modeled by the multiparticle collision dynamics approach, a particle-based hydrodynamic simulation technique, which is combined with molecular dynamics simulations for the polymers. Star polymers of various functionalities are considered. We determine the center-of-mass velocity correlation functions, the corresponding mean square displacements, and diffusion coefficients. The velocity correlation functions exhibit a functionality-dependent and structure-specific intermediate time regime, with a slow decay. It is followed by the long-time tail t(-3/2), which is solely determined by the fluid. Infinite-system-size diffusion coefficients are determined from the velocity correlation function by a combination of simulation and analytical results, as well as from the center-of-mass mean square displacement for various systems sizes and extrapolation. In terms of the hydrodynamic radius, the star polymer hydrodynamic diffusion coefficient exhibits the same universal system-size dependence as a spherical colloid. The functionality dependence of the ratio of hydrodynamic radii and the radii of gyration agrees well with experimental predictions.
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Affiliation(s)
- Sunil P Singh
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Chien-Cheng Huang
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Elmar Westphal
- Peter Grünberg Institute and Jülich Centre for Neutron Science, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G Winkler
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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63
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Xu X, Chen J, An L. Shear thinning behavior of linear polymer melts under shear flow via nonequilibrium molecular dynamics. J Chem Phys 2015; 140:174902. [PMID: 24811663 DOI: 10.1063/1.4873709] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The properties of both untangled and entangled linear polymer melts under shear flow are studied by nonequilibrium molecular dynamics simulations. The results reveal that the dependence of shear viscosity η on shear rate γ, expressed by n ~ γ(-n), exhibits three distinct regimes. The first is the well-known Newtonian regime, namely, η independent of shear rate at small shear rates γ < τ0(-1) (where τ0 is the longest polymer relaxation time at equilibrium). In the non-Newtonian regime (γ > τ0(-1)) the shear dependence of viscosity exhibits a crossover at a critical shear rate γc dividing this regime into two different regimes, shear thinning regime I (ST-I) and II (ST-II), respectively. In the ST-I regime (τ0(-1) < γ < γc), the exponent n increases with increasing chain length N, while in the ST-II regime (γ > γc) a universal power law n ~ γ(-0.37) is found for considered chain lengths. Furthermore, the longer the polymer chain is, the smaller the shear viscosity for a given shear rate in the ST-II regime. The simulation also shows that a characteristic chain length, below which γc will be equal to τ0(-1), lies in the interval 30 < N < 50. For all considered chain lengths in the ST-II regime, we also find that the first and second normal stress differences N1 and N2 follow power laws of N1 ~ γ(2/3) and N2 ~ γ(0.82), respectively; the orientation resistance parameter mG follows the relation mG ~ γ(0.75) and the tumbling frequency ftb follows ftb ~ γ(0.75). These results imply that the effects of entanglement on the shear dependences of these properties may be negligible in the ST-II regime. These findings may shed some light on the nature of shear thinning in flexible linear polymer melts.
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Affiliation(s)
- Xiaolei Xu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jizhong Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
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64
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Katyal D, Kant R. Dynamics of generalized Gaussian polymeric structures in random layered flows. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:042602. [PMID: 25974520 DOI: 10.1103/physreve.91.042602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Indexed: 06/04/2023]
Abstract
We develop a formalism for the dynamics of a flexible branched polymer with arbitrary topology in the presence of random flows. This is achieved by employing the generalized Gaussian structure (GGS) approach and the Matheron-de Marsily model for the random layered flow. The expression for the average square displacement (ASD) of the center of mass of the GGS is obtained in such flow. The averaging is done over both the thermal noise and the external random flow. Although the formalism is valid for branched polymers with various complex topologies, we mainly focus here on the dynamics of the flexible star and dendrimer. We analyze the effect of the topology (the number and length of branches for stars and the number of generations for dendrimers) on the dynamics under the influence of external flow, which is characterized by their root-mean-square velocity, persistence flow length, and flow exponent α. Our analysis shows two anomalous power-law regimes, viz., subdiffusive (intermediate-time polymer stretching and flow-induced diffusion) and superdiffusive (long-time flow-induced diffusion). The influence of the topology of the GGS is unraveled in the intermediate-time regime, while the long-time regime is only weakly dependent on the topology of the polymer. With the decrease in the value of α, the magnitude of the ASD decreases, while the temporal exponent of the ASD increases in both the time regimes. Also there is an increase in both the magnitude of the ASD and the crossover time (from the subdiffusive to the superdiffusive regime) with an increase in the total mass of the polymeric structure.
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Affiliation(s)
- Divya Katyal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Rama Kant
- Department of Chemistry, University of Delhi, Delhi 110007, India
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65
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Theers M, Winkler RG. Bulk viscosity of multiparticle collision dynamics fluids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:033309. [PMID: 25871248 DOI: 10.1103/physreve.91.033309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 06/04/2023]
Abstract
We determine the viscosity parameters of the multiparticle collision dynamics (MPC) approach, a particle-based mesoscale hydrodynamic simulation method for fluids. We perform analytical calculations and verify our results by simulations. The stochastic rotation dynamics and the Andersen thermostat variant of MPC are considered, both with and without angular momentum conservation. As an important result, we find a nonzero bulk viscosity for every MPC version. The explicit calculation shows that the bulk viscosity is determined solely by the collisional interactions of MPC.
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Affiliation(s)
- Mario Theers
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation and Institute of Complex Systems, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation and Institute of Complex Systems, Forschungszentrum Jülich, D-52425 Jülich, Germany
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66
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Xu X, Chen J, An L. Simulation studies on architecture dependence of unentangled polymer melts. J Chem Phys 2015; 142:074903. [DOI: 10.1063/1.4908262] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Xiaolei Xu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Jizhong Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
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67
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Huang CC, Varghese A, Gompper G, Winkler RG. Thermostat for nonequilibrium multiparticle-collision-dynamics simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:013310. [PMID: 25679742 DOI: 10.1103/physreve.91.013310] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 05/15/2023]
Abstract
Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for complex fluid, is widely employed in nonequilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization of the fluid is often required for certain MPC variants. We investigate the influence of three thermostats on the nonequilibrium properties of a MPC fluid under shear or in Poiseuille flow. In all cases, the local velocities are scaled by a factor, which is either determined via a local simple scaling approach (LSS), a Monte Carlo-like procedure (MCS), or by the Maxwell-Boltzmann distribution of kinetic energy (MBS). We find that the various scaling schemes leave the flow profile unchanged and maintain the local temperature well. The fluid viscosities extracted from the various simulations are in close agreement. Moreover, the numerically determined viscosities are in remarkably good agreement with the respective theoretically predicted values. At equilibrium, the calculation of the dynamic structure factor reveals that the MBS method closely resembles an isothermal ensemble, whereas the MCS procedure exhibits signatures of an adiabatic system at larger collision-time steps. Since the velocity distribution of the LSS approach is non-Gaussian, we recommend to apply the MBS thermostat, which has been shown to produce the correct velocity distribution even under nonequilibrium conditions.
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Affiliation(s)
- Chien-Cheng Huang
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anoop Varghese
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G Winkler
- Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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68
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69
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Nikoubashman A, Mahynski NA, Howard MP, Panagiotopoulos AZ. Erratum: Flow-induced demixing of polymer-colloid mixtures in microfluidic channels [J. Chem. Phys. 140, 094903 (2014)]. J Chem Phys 2014. [DOI: 10.1063/1.4897157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Arash Nikoubashman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Nathan A. Mahynski
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Michael P. Howard
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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70
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Poblete S, Wysocki A, Gompper G, Winkler RG. Hydrodynamics of discrete-particle models of spherical colloids: a multiparticle collision dynamics simulation study. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:033314. [PMID: 25314571 DOI: 10.1103/physreve.90.033314] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Indexed: 06/04/2023]
Abstract
We investigate the hydrodynamic properties of a spherical colloid model, which is composed of a shell of point particles by hybrid mesoscale simulations, which combine molecular dynamics simulations for the sphere with the multiparticle collision dynamics approach for the fluid. Results are presented for the center-of-mass and angular velocity correlation functions. The simulation results are compared with theoretical results for a rigid colloid obtained as a solution of the Stokes equation with no-slip boundary conditions. Similarly, analytical results of a point-particle model are presented, which account for the finite size of the simulated system. The simulation results agree well with both approaches on appropriative time scales; specifically, the long-time correlations are quantitatively reproduced. Moreover, a procedure is proposed to obtain the infinite-system-size diffusion coefficient based on a combination of simulation results and analytical predictions. In addition, we present the velocity field in the vicinity of the colloid and demonstrate its close agreement with the theoretical prediction. Our studies show that a point-particle model of a sphere is very well suited to describe the hydrodynamic properties of spherical colloids, with a significantly reduced numerical effort.
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Affiliation(s)
- Simón Poblete
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Adam Wysocki
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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71
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Liu Z, Liu J, Xiao M, Wang R, Chen YL. Conformation-dependent translocation of a star polymer through a nanochannel. BIOMICROFLUIDICS 2014; 8:054107. [PMID: 25332744 PMCID: PMC4189700 DOI: 10.1063/1.4893637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/11/2014] [Indexed: 06/04/2023]
Abstract
The translocation process of star polymers through a nanochannel is investigated by dissipative particle dynamics simulations. The translocation process is strongly influenced by the star arm arrangement as the polymer enters the channel, and a scaling relation between the translocation time [Formula: see text] and the total number of beads N tot is obtained. Qualitative agreements are found with predictions of the nucleation and growth model for linear block co-polymer translocation. In the intermediate stage where the center of the star polymer is at the channel entrance, the translocation time is found to have power law-dependence on the number of arms outside the channel and very weakly dependent on the number of arms in the channel. Increasing the total number of star arms also increases the star translocation time.
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Affiliation(s)
- Zhu Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Jiannan Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Mengying Xiao
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Rong Wang
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Yeng-Long Chen
- Institute of Physics , Academia Sinica, Taipei 11529, Taiwan
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72
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Nikoubashman A, Mahynski NA, Pirayandeh AH, Panagiotopoulos AZ. Flow-induced demixing of polymer-colloid mixtures in microfluidic channels. J Chem Phys 2014; 140:094903. [DOI: 10.1063/1.4866762] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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73
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Zhang H, Lin Y, Xu Y, Weng W. Mechanochemistry of Topological Complex Polymer Systems. Top Curr Chem (Cham) 2014; 369:135-207. [PMID: 25791486 DOI: 10.1007/128_2014_617] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Although existing since the concept of macromolecules, polymer mechanochemistry is a burgeoning field which attracts great scientific interest in its ability to bias conventional reaction pathways and its potential to fabricate mechanoresponsive materials. We review here the effect of topology on the mechanical degradation of polymer chains and the activation of mechanophores in polymer backbones. The chapter focuses on both experimental and theoretical work carried out in the past 70 years. After a general introduction (Sect. 1), where the concept, the history, and the application of polymer mechanochemistry are briefly described, flow fields to study polymer mechanochemistry are discussed (Sect. 2), results of mechanochemistry study are presented for linear polymers (Sect. 3), cyclic polymers (Sect. 4), graft polymers (Sect. 5), star-shaped polymers (Sect. 6), hyperbranched polymers and dendrimers (Sect. 7), and systems with dynamic topology (Sect. 8). Here we focus on (1) experimental results involving the topological effect on the coil-to-stretch transition and the fracture of the polymer chains, (2) the underlying mechanisms and the key factor that determines the mechanical stability of the macromolecules, (3) theoretical models that relate to the experimental observations, and (4) rational design of mechanophores in complex topology to achieve multiple activations according to the existing results observed in chain degradation.
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Affiliation(s)
- Huan Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| | - Yangju Lin
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| | - Yuanze Xu
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China
| | - Wengui Weng
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, P. R. China.
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74
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Ghatage D, Chatterji A. Modeling steady-state dynamics of macromolecules in exponential-stretching flow using multiscale molecular-dynamics-multiparticle-collision simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:043303. [PMID: 24229300 DOI: 10.1103/physreve.88.043303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Indexed: 06/02/2023]
Abstract
We introduce a method to obtain steady-state uniaxial exponential-stretching flow of a fluid (akin to extensional flow) in the incompressible limit, which enables us to study the response of suspended macromolecules to the flow by computer simulations. The flow field in this flow is defined by v(x) = εx, where v(x) is the velocity of the fluid and ε is the stretch flow gradient. To eliminate the effect of confining boundaries, we produce the flow in a channel of uniform square cross section with periodic boundary conditions in directions perpendicular to the flow, but simultaneously maintain uniform density of fluid along the length of the tube. In experiments a perfect elongational flow is obtained only along the axis of symmetry in a four-roll geometry or a filament-stretching rheometer. We can reproduce flow conditions very similar to extensional flow near the axis of symmetry by exponential-stretching flow; we do this by adding the right amounts of fluid along the length of the flow in our simulations. The fluid particles added along the length of the tube are the same fluid particles which exit the channel due to the flow; thus mass conservation is maintained in our model by default. We also suggest a scheme for possible realization of exponential-stretching flow in experiments. To establish our method as a useful tool to study various soft matter systems in extensional flow, we embed (i) spherical colloids with excluded volume interactions (modeled by the Weeks-Chandler potential) as well as (ii) a bead-spring model of star polymers in the fluid to study their responses to the exponential-stretched flow and show that the responses of macromolecules in the two flows are very similar. We demonstrate that the variation of number density of the suspended colloids along the direction of flow is in tune with our expectations. We also conclude from our study of the deformation of star polymers with different numbers of arms f that the critical flow gradient ε(c) at which the star undergoes the coil-to-stretch transition is independent of f for f = 2,5,10, and 20.
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Affiliation(s)
- Dhairyasheel Ghatage
- Mechanical Engineering Department, College of Engineering, Shivajinagar, Pune-411005, India
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75
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Singh SP, Chatterji A, Gompper G, Winkler RG. Dynamical and Rheological Properties of Ultrasoft Colloids under Shear Flow. Macromolecules 2013. [DOI: 10.1021/ma401571k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sunil P. Singh
- Theoretical
Soft Matter and Biophysics, Institute for Advanced Simulation and
Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Apratim Chatterji
- Physics
Department, Indian Institute of Science Education and Research (IISER) , Pune 411021, India
| | - Gerhard Gompper
- Theoretical
Soft Matter and Biophysics, Institute for Advanced Simulation and
Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Roland G. Winkler
- Theoretical
Soft Matter and Biophysics, Institute for Advanced Simulation and
Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany
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76
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Chen W, Chen J, Liu L, Xu X, An L. Effects of Chain Stiffness on Conformational and Dynamical Properties of Individual Ring Polymers in Shear Flow. Macromolecules 2013. [DOI: 10.1021/ma401137c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenduo Chen
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Jizhong Chen
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Lijun Liu
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Xiaolei Xu
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Lijia An
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
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77
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Zhao T, Wang X, Jiang L, Larson RG. Assessment of mesoscopic particle-based methods in microfluidic geometries. J Chem Phys 2013; 139:084109. [DOI: 10.1063/1.4819124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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78
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Lamura A, Winkler RG. Semiflexible polymers under external fields confined to two dimensions. J Chem Phys 2012; 137:244909. [DOI: 10.1063/1.4772748] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Lamura
- Istituto Applicazioni Calcolo, CNR, Via Amendola 122/D, 70126 Bari, Italy
| | - R. G. Winkler
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany
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79
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Huang CC, Gompper G, Winkler RG. Non-Equilibrium Properties of Semidilute Polymer Solutions under Shear Flow. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/392/1/012003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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80
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81
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Gupta S, Kundu SK, Stellbrink J, Willner L, Allgaier J, Richter D. Advanced rheological characterization of soft colloidal model systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:464102. [PMID: 23114080 DOI: 10.1088/0953-8984/24/46/464102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The complex flow behavior of polymer-based soft colloidal model systems was investigated using steady and oscillatory shear to prove new concepts for advanced rheological characterization. In the very dilute regime we investigated high molecular weight polybutadiene star polymers to quantify the internal relaxation time arising from the polymeric nature of these ultra-soft colloids. The observed shear-induced brush deformation is interpreted in terms of the internal Zimm time τ(z). The observed dependence of τ(z) on matrix viscosity can be explained by shrinkage of the star polymer due to an increasing incompatibility with increasing matrix molecular weight. The influence of the polymeric nature on the characteristic structural relaxation time in the concentrated regime was investigated using non-linear rheology following Wyss et al (SRFS) (2007 Phys. Rev. Lett. 98 238303). Here we used star-like block copolymer micelles to systematically tune the 'softness' of the colloids by variation of the block ratio. A master curve with proper scaling parameters could be generated independent of the degree of colloidal 'softness'. However, the obtained strain-rate independent structural relaxation time τ(0) was not observed in the linear regime. In addition, a high frequency discrepancy was clearly found in all our experimental data. Both reflect the shortcomings of the SRFS approach.
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Affiliation(s)
- S Gupta
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich, D-52425 Jülich, Germany
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82
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Singh SP, Fedosov DA, Chatterji A, Winkler RG, Gompper G. Conformational and dynamical properties of ultra-soft colloids in semi-dilute solutions under shear flow. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:464103. [PMID: 23114112 DOI: 10.1088/0953-8984/24/46/464103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We investigate structural and dynamical properties of ultra-soft colloids in dilute and semi-dilute solutions by hybrid mesoscale simulations under linear shear flow. In particular, the influence of functionality on these properties is addressed. Our study combines molecular dynamics simulations for the solute with the multiparticle collision dynamics approach for the coarse-grained solvent. The star polymers exhibit large conformational and orientational changes in shear flow, which we characterize by the radius of gyration tensor and the alignment angle. These quantities show a universal dependence on a concentration- and functionality-dependent Weissenberg number with slight deviations at high shear rates. Moreover, the star polymers display a rotational dynamics with a shear-rate- and concentration-dependent rotation frequency. We attribute the concentration dependence to the screening of hydrodynamic interactions in semi-dilute star-polymer solutions.
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Affiliation(s)
- Sunil P Singh
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany.
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83
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84
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Huang CC, Gompper G, Winkler RG. Hydrodynamic correlations in multiparticle collision dynamics fluids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:056711. [PMID: 23214910 DOI: 10.1103/physreve.86.056711] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Indexed: 05/15/2023]
Abstract
The emergent fluctuating hydrodynamics of the multiparticle collision dynamics (MPC) approach, a particle-based mesoscale simulation technique for fluid dynamics, is analyzed theoretically and numerically. We focus on the stochastic rotation dynamics implementation of the MPC method. The fluid is characterized by its longitudinal and transverse velocity correlation functions in Fourier space and velocity autocorrelation functions in real space. Particular attention is paid to the role of sound, which leads to piecewise negative correlation functions. Moreover, finite system-size effects are addressed with an emphasis on the role of sound. Analytical expressions are provided for the transverse and longitudinal velocity correlations, which are derived from the linearized Landau-Lifshitz Navier-Stokes equation adopted for an isothermal MPC fluid. The comparison of the analytical results with simulations shows excellent agreement above a minimal length scale. The simulations indicate a breakdown in hydrodynamics on length scales smaller than this minimal length. This demonstrates that we have an excellent analytical description and understanding of the MPC method and its limitations in terms of time and length scales.
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Affiliation(s)
- Chien-Cheng Huang
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems, Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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85
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Lüsebrink D, Yang M, Ripoll M. Thermophoresis of colloids by mesoscale simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:284132. [PMID: 22739145 DOI: 10.1088/0953-8984/24/28/284132] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The motion of a colloid induced by a temperature gradient is simulated by means of multiparticle collision dynamics, a mesoscale simulation technique. Two algorithms to quantify the thermophoretic behavior are employed and contrasted. The validity of the methods is verified as a function of the temperature gradient, system size, and algorithm parameters. The variation of the solvent-colloid interaction from attractive to purely repulsive interestingly results in the change of the colloid behavior from thermophobic to thermophilic.
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Affiliation(s)
- Daniel Lüsebrink
- Theoretical Soft-Matter and Biophysics, Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany
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86
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Huang CC, Gompper G, Winkler RG. Non-equilibrium relaxation and tumbling times of polymers in semidilute solution. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:284131. [PMID: 22739124 DOI: 10.1088/0953-8984/24/28/284131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The end-over-end tumbling dynamics of individual polymers in dilute and semidilute solutions is studied under shear flow by large-scale mesoscale hydrodynamic simulations. End-to-end vector relaxation times are determined along the flow, gradient, and vorticity directions. Along the flow and gradient directions, the correlation functions decay exponentially with sinusoidal modulations at short times. In dilute solution, the decay times of the various directions are very similar. However, in semidilute solutions, the relaxation behaviors are rather different along the various directions, with the longest relaxation time in the vorticity direction and the shortest time in the flow direction. The various relaxation times exhibit a power-law shear-rate dependence with the exponent - 2/3 at high shear rates. Quantitatively, the relaxation times are equal to the tumbling times extracted from cross-correlation functions of fluctuations of radius-of-gyration components along the flow and gradient direction.
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Affiliation(s)
- Chien-Cheng Huang
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation and Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany.
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87
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Reid DAP, Hildenbrandt H, Padding JT, Hemelrijk CK. Fluid dynamics of moving fish in a two-dimensional multiparticle collision dynamics model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:021901. [PMID: 22463238 DOI: 10.1103/physreve.85.021901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 01/20/2011] [Indexed: 05/31/2023]
Abstract
The fluid dynamics of animal locomotion, such as that of an undulating fish, are of great interest to both biologists and engineers. However, experimentally studying these fluid dynamics is difficult and time consuming. Model studies can be of great help because of their simpler and more detailed analysis. Their insights may guide empirical work. Particularly the recently introduced multiparticle collision dynamics method may be suitable for the study of moving organisms because it is computationally fast, simple to implement, and has a continuous representation of space. As regards the study of hydrodynamics of moving organisms, the method has only been applied at low Reynolds numbers (below 120) for soft, permeable bodies, and static fishlike shapes. In the present paper we use it to study the hydrodynamics of an undulating fish at Reynolds numbers 1100-1500, after confirming its performance for a moving insect wing at Reynolds number 75. We measure (1) drag, thrust, and lift forces, (2) swimming efficiency and spatial structure of the wake, and (3) distribution of forces along the fish body. We confirm the resemblance between the simulated undulating fish and empirical data. In contrast to theoretical predictions, our model shows that for steadily undulating fish, thrust is produced by the rear 2/3 of the body and that the slip ratio U/V (with U the forward swimming speed and V the rearward speed of the body wave) correlates negatively (instead of positively) with the actual Froude efficiency of swimming. Besides, we show that the common practice of modeling individuals while constraining their sideways acceleration causes them to resemble unconstrained fish with a higher tailbeat frequency.
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Affiliation(s)
- Daniel A P Reid
- Behavioural Ecology & Self-organization & Theoretical Biology, Rijksuniversiteit Groningen, Nijenborgh 7, Groningen, The Netherlands
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88
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Jia XX, Li ZW, Sun ZY, Lu ZY. Hierarchical Self-Assembly of Soft Disklike Particles under Shear Flow. J Phys Chem B 2011; 115:13441-8. [DOI: 10.1021/jp205683x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiao-Xi Jia
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, China
| | - Zhan-Wei Li
- State Key Laboratory of Polymer Chemistry and Physics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhao-Yan Sun
- State Key Laboratory of Polymer Chemistry and Physics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhong-Yuan Lu
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, China
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89
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Singh SP, Winkler RG, Gompper G. Nonequilibrium forces between dragged ultrasoft colloids. PHYSICAL REVIEW LETTERS 2011; 107:158301. [PMID: 22107322 DOI: 10.1103/physrevlett.107.158301] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Indexed: 05/31/2023]
Abstract
The dynamical deformation of ultrasoft colloids as well as their dynamic frictional forces are numerically investigated, when one colloid is dragged past another at constant velocity. Hydrodynamic interactions are captured by a particle-based mesoscopic simulation method. At vanishing relative velocity, the equilibrium repulsive force-distance curve is obtained. At large drag velocities, in contrast, we find an apparent attractive force for departing colloids along the dragging direction. The deformation, in the close encounter of colloids, and the energy dissipation are examined as a function of the drag velocity and their separation.
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Affiliation(s)
- Sunil P Singh
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation and Institute of Complex Systems, Forschungszentrum Jülich, D-52425 Jülich, Germany
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90
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Götze IO, Gompper G. Dynamic self-assembly and directed flow of rotating colloids in microchannels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031404. [PMID: 22060368 DOI: 10.1103/physreve.84.031404] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Indexed: 05/23/2023]
Abstract
Nonequilibrium structure formation and dynamics in suspensions of superparamagnetic colloids driven by an external rotating magnetic field are studied by particle-based mesoscale hydrodynamics simulations in confined geometry. We address the fundamental question how the rotation of the colloids about their own axes can be converted into a translational motion by breaking the symmetry of the confining geometry. We study a two-dimensional system of colloids with short-range repulsive interactions, which mimics flow in shallow microchannels. In straight channels, we observe a two-way traffic but--for symmetry reasons--no net transport. However, by keeping some colloids fixed near one of the two walls, net transport can be achieved. This approach allows the control and switchability of the flow in complex microchannel networks. A minimal geometry that fulfills the requirement of broken symmetry are ring channels. We determine the translational velocity of the spinning colloids and study its dependence on the channel width for various median radii. We conclude that spinning colloids present a promising alternative for flow generation and control in microfluidic devices.
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Affiliation(s)
- Ingo O Götze
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich D-52425, Germany.
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91
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Huang CC, Winkler RG, Sutmann G, Gompper G. Semidilute Polymer Solutions at Equilibrium and under Shear Flow. Macromolecules 2010. [DOI: 10.1021/ma101836x] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chien-Cheng Huang
- Theoretical Soft Matter and Biophysics, Institut für Festkörperforschung and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Roland G. Winkler
- Theoretical Soft Matter and Biophysics, Institut für Festkörperforschung and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Godehard Sutmann
- Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institut für Festkörperforschung and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
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92
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Winkler RG. Conformational and rheological properties of semiflexible polymers in shear flow. J Chem Phys 2010; 133:164905. [DOI: 10.1063/1.3497642] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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93
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Nikoubashman A, Likos CN. Flow-induced polymer translocation through narrow and patterned channels. J Chem Phys 2010; 133:074901. [DOI: 10.1063/1.3466918] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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94
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Tüzel E, Pan G, Kroll DM. Dynamics of thermally driven capillary waves for two-dimensional droplets. J Chem Phys 2010; 132:174701. [DOI: 10.1063/1.3374437] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Affiliation(s)
- Arash Nikoubashman
- Institute of Theoretical Physics, Heinrich Heine University of Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Christos N. Likos
- Institute of Theoretical Physics, Heinrich Heine University of Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
- Faculty of Physics, University of Vienna, Sensengasse 8/12, A-1090 Vienna, Austria
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Nardai MM, Zifferer G. Simulation of dilute solutions of linear and star-branched polymers by dissipative particle dynamics. J Chem Phys 2009; 131:124903. [PMID: 19791917 DOI: 10.1063/1.3231854] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A most promising off-lattice technique in order to simulate not only static but in addition dynamic behavior of linear and star-branched chains is the dissipative particle dynamics (DPD) method. In this model the atomistic representation of polymer molecules is replaced by a (coarse-grained) equivalent chain consisting of beads which are repulsive for each other in order to mimic the excluded volume effect (successive beads in addition are linked by springs). Likewise solvent molecules are combined to beads which in turn are repulsive for each other as well as for the polymer segments. The system is relaxed by molecular dynamics solving Newton's laws under the influence of short ranged conservative forces (i.e., repulsion between nonbonded beads and a proper balance of repulsion and attraction between bonded segments) and dissipative forces due to friction between particles, the latter representing the thermostat in conjunction with proper random forces. A variation of the strength of the repulsion between different types of beads allows the simulation of any desired thermodynamic situation. Static and dynamic properties of isolated linear and star-branched chains embedded in athermal, exothermal, and endothermal solvent are presented and theta conditions are examined. The generally accepted scaling concept for athermal systems is fairly well reproduced by linear and star-branched DPD chains and theta conditions appear for a unique parameter independent of functionality as in the case of Monte Carlo simulations. Furthermore, the correspondence between DPD and Monte Carlo data referring to the shape of chains and stars is fairly well, too. For dilute solutions the Zimm behavior is expected for dynamic properties which is indeed realized in DPD systems.
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Affiliation(s)
- M M Nardai
- Department of Physical Chemistry, University of Vienna, Wahringer Str. 42, A-1090 Wien, Austria
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Slater GW, Holm C, Chubynsky MV, de Haan HW, Dubé A, Grass K, Hickey OA, Kingsburry C, Sean D, Shendruk TN, Zhan L. Modeling the separation of macromolecules: A review of current computer simulation methods. Electrophoresis 2009; 30:792-818. [DOI: 10.1002/elps.200800673] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Winkler RG, Huang CC. Stress tensors of multiparticle collision dynamics fluids. J Chem Phys 2009; 130:074907. [DOI: 10.1063/1.3077860] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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100
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Ihle T. Chapman–Enskog expansion for multi-particle collision models. Phys Chem Chem Phys 2009; 11:9667-76. [DOI: 10.1039/b910356b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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