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Meyer H, Pelagejcev P, Schilling T. Non-Markovian out-of-equilibrium dynamics: A general numerical procedure to construct time-dependent memory kernels for coarse-grained observables. ACTA ACUST UNITED AC 2020. [DOI: 10.1209/0295-5075/128/40001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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52
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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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53
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Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions. J Math Biol 2019; 80:457-479. [PMID: 31541299 PMCID: PMC7012987 DOI: 10.1007/s00285-019-01433-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/28/2019] [Indexed: 12/28/2022]
Abstract
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or multi-resolution methodologies address this difficulty by using molecular dynamics (MD) and coarse-grained models in different parts of the cell. Their applicability depends on the accuracy and properties of the coarse-grained model which approximates the detailed MD description. A family of stochastic coarse-grained (SCG) models, written as relatively low-dimensional systems of nonlinear stochastic differential equations, is presented. The nonlinear SCG model incorporates the non-Gaussian force distribution which is observed in MD simulations and which cannot be described by linear models. It is shown that the nonlinearities can be chosen in such a way that they do not complicate parametrization of the SCG description by detailed MD simulations. The solution of the SCG model is found in terms of gamma functions.
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Kappler J, Hinrichsen VB, Netz RR. Non-Markovian barrier crossing with two-time-scale memory is dominated by the faster memory component. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:119. [PMID: 31494784 DOI: 10.1140/epje/i2019-11886-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
We investigate non-Markovian barrier-crossing kinetics of a massive particle in one dimension in the presence of a memory function that is the sum of two exponentials with different memory times, [Formula: see text] and [Formula: see text] . Our Langevin simulations for the special case where both exponentials contribute equally to the total friction show that the barrier-crossing time becomes independent of the longer memory time if at least one of the two memory times is larger than the intrinsic diffusion time. When we associate memory effects with coupled degrees of freedom that are orthogonal to a one-dimensional reaction coordinate, this counterintuitive result shows that the faster orthogonal degrees of freedom dominate barrier-crossing kinetics in the non-Markovian limit and that the slower orthogonal degrees become negligible, quite contrary to the standard time-scale separation assumption and with important consequences for the proper setup of coarse-graining procedures in the non-Markovian case. By asymptotic matching and symmetry arguments, we construct a crossover formula for the barrier crossing time that is valid for general multi-exponential memory kernels. This formula can be used to estimate barrier-crossing times for general memory functions for high friction, i.e. in the overdamped regime, as well as for low friction, i.e. in the inertial regime. Typical examples where our results are important include protein folding in the high-friction limit and chemical reactions such as proton-transfer reactions in the low-friction limit.
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Affiliation(s)
- Julian Kappler
- Freie Universität Berlin, Fachbereich Physik, Berlin, Germany
| | | | - Roland R Netz
- Freie Universität Berlin, Fachbereich Physik, Berlin, Germany.
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55
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Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties. COMPUTATION 2019. [DOI: 10.3390/computation7030042] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics governing an entire family of free-energy landscapes, bottom-up CG models are systematically constructed from a higher-resolution model to retain a high level of chemical specificity. The removal of degrees of freedom from the system modifies the relationship between the relative time scales of distinct dynamical processes through both a loss of friction and a “smoothing” of the free-energy landscape. While these effects typically result in faster dynamics, decreasing the computational expense of the model, they also obscure the connection to the true dynamics of the system. The lack of consistent dynamics is a serious limitation for CG models, which not only prevents quantitatively accurate predictions of dynamical observables but can also lead to qualitatively incorrect descriptions of the characteristic dynamical processes. With many methods available for optimizing the structural and thermodynamic properties of chemically-specific CG models, recent years have seen a stark increase in investigations addressing the accurate description of dynamical properties generated from CG simulations. In this review, we present an overview of these efforts, ranging from bottom-up parameterizations of generalized Langevin equations to refinements of the CG force field based on a Markov state modeling framework. We aim to make connections between seemingly disparate approaches, while laying out some of the major challenges as well as potential directions for future efforts.
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56
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Gunaratne RS, Wilson DB, Flegg MB, Erban R. Multi-resolution dimer models in heat baths with short-range and long-range interactions. Interface Focus 2019; 9:20180070. [PMID: 31065341 PMCID: PMC6501348 DOI: 10.1098/rsfs.2018.0070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 11/16/2022] Open
Abstract
This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic springs (long-range). Two types of multi-resolution methodologies are considered in detail: (a) describing parts of the solvent far away from the dimer by a coarser approach; (b) describing each monomer of the dimer by using a model with different level of resolution. These methodologies are then used to investigate the effect of a shared heat bath versus two uncoupled heat baths, one for each monomer. Furthermore, the validity of the multi-resolution methods is discussed by comparison to dynamics of macroscopic Langevin equations.
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Affiliation(s)
- Ravinda S. Gunaratne
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Daniel B. Wilson
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Mark B. Flegg
- School of Mathematical Sciences, Monash University, 9 Rainforest walk, Clayton campus, Victoria 3168, Australia
| | - Radek Erban
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
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57
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Mizuta K, Ishii Y, Kim K, Matubayasi N. Bridging the gap between molecular dynamics and hydrodynamics in nanoscale Brownian motions. SOFT MATTER 2019; 15:4380-4390. [PMID: 31086871 DOI: 10.1039/c9sm00246d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Through molecular dynamics simulations, we examined the hydrodynamic behavior of the Brownian motion of fullerene particles based on molecular interactions. The solvation free energy and velocity autocorrelation function (VACF) were calculated by using the Lennard-Jones (LJ) and Weeks-Chandler-Andersen (WCA) potentials for the solute-solvent and solvent-solvent interactions and by changing the size of the fullerene particles. We also measured the diffusion constant of the fullerene particles and the shear viscosity of the host fluid, and then the hydrodynamic radius aHD was quantified from the Stokes-Einstein relation. The aHD value exceeds that of the gyration radius of the fullerene when the solvation free energy exhibits largely negative values using the LJ potential. In contrast, aHD is similar to the size of bare fullerene when the solvation free energy is positive using the WCA potential. Furthermore, the VACF of the fullerene particles is directly comparable with the analytical expressions utilizing the Navier-Stokes equations both in incompressible and compressible forms. A hydrodynamic long-time tail t-3/2 is demonstrated for timescales longer than the kinematic time of the momentum diffusion over the particle size. However, the VACF at shorter timescales deviates from the hydrodynamic description, particularly for smaller fullerene particles and for the LJ potential. This occurs even though the compressible effect is considered when characterizing the decay of the VACF around the sound-propagation timescale over the particle size. These results indicate that the nanoscale Brownian motion is influenced by the solvation structure around the solute particles originating from the molecular interaction.
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Affiliation(s)
- Keisuke Mizuta
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
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58
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Lee HS, Ahn SH, Darve EF. The multi-dimensional generalized Langevin equation for conformational motion of proteins. J Chem Phys 2019; 150:174113. [PMID: 31067888 DOI: 10.1063/1.5055573] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Using the generalized Langevin equation (GLE) is a promising approach to build coarse-grained (CG) models of molecular systems since the GLE model often leads to more accurate thermodynamic and kinetic predictions than Brownian dynamics or Langevin models by including a more sophisticated friction with memory. The GLE approach has been used for CG coordinates such as the center of mass of a group of atoms with pairwise decomposition and for a single CG coordinate. We present a GLE approach when CG coordinates are multiple generalized coordinates, defined, in general, as nonlinear functions of microscopic atomic coordinates. The CG model for multiple generalized coordinates is described by the multidimensional GLE from the Mori-Zwanzig formalism, which includes an exact memory matrix. We first present a method to compute the memory matrix in a multidimensional GLE using trajectories of a full system. Then, in order to reduce the computational cost of computing the multidimensional friction with memory, we introduce a method that maps the GLE to an extended Markovian system. In addition, we study the effect of using a nonconstant mass matrix in the CG model. In particular, we include mass-dependent terms in the mean force. We used the proposed CG model to describe the conformational motion of a solvated alanine dipeptide system, with two dihedral angles as the CG coordinates. We showed that the CG model can accurately reproduce two important kinetic quantities: the velocity autocorrelation function and the distribution of first passage times.
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Affiliation(s)
- Hee Sun Lee
- Mechanical Engineering Department, Stanford University, Stanford, California 94305, USA
| | - Surl-Hee Ahn
- Chemistry Department, Stanford University, Stanford, California 94305, USA
| | - Eric F Darve
- Mechanical Engineering Department, Stanford University, Stanford, California 94305, USA
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59
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Meyer H, Voigtmann T, Schilling T. On the dynamics of reaction coordinates in classical, time-dependent, many-body processes. J Chem Phys 2019; 150:174118. [DOI: 10.1063/1.5090450] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hugues Meyer
- Physikalisches Institut, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
- Research Unit in Engineering Science, Université du Luxembourg, L-4364 Esch-sur-Alzette, Luxembourg
| | - Thomas Voigtmann
- Institut für Materialphysik im Weltraum, Deutsches Zentrum für Luft- und Raumfahrt (DLR), 51170 Köln, Germany
- Department of Physics, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Tanja Schilling
- Physikalisches Institut, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
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60
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Español P, de la Torre JA, Duque-Zumajo D. Solution to the plateau problem in the Green-Kubo formula. Phys Rev E 2019; 99:022126. [PMID: 30934276 DOI: 10.1103/physreve.99.022126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Indexed: 06/09/2023]
Abstract
Transport coefficients appearing in Markovian dynamic equations for coarse-grained variables have microscopic expressions given by Green-Kubo formulas. These formulas may suffer from the well-known plateau problem. The problem arises because the Green-Kubo running integrals decay as the correlation of the coarse-grained variables themselves. The usual solution is to resort to an extreme timescale separation, for which the plateau problem is minor. Within the context of Mori projection operator formulation, we offer an alternative expression for the transport coefficients that is given by a corrected Green-Kubo expression that has no plateau problem by construction. The only assumption is that the Markovian approximation is valid in such a way that transport coefficients can be defined, even in the case that the separation of timescales is not extreme.
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Affiliation(s)
- Pep Español
- Departamento de Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141 E-28080, Madrid, Spain
| | - J A de la Torre
- Departamento de Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141 E-28080, Madrid, Spain
| | - D Duque-Zumajo
- Departamento de Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141 E-28080, Madrid, Spain
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61
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Deichmann G, van der Vegt NFA. Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations. J Chem Phys 2019; 149:244114. [PMID: 30599732 DOI: 10.1063/1.5064369] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Several molecular coarse-graining methods have been proposed in recent years to derive chemical- and state-point transferable force fields. While these force fields describe structural and thermodynamic properties in good agreement with fine-grained models and experiments, dynamic properties are usually overestimated. Herein, we examine if the long-time dynamic properties of molecular coarse-grained (CG) systems can be correctly represented by employing a dissipative particle dynamics (DPD) thermostat, which is "bottom-up informed" by means of a variant of the Markovian Mori-Zwanzig (MZ) DPD coarse-graining method. We report single-site and multiple-site CG models for a monomer, dimer, and 24mer based on 2,2-dimethyl propane as a chemical repeat unit and report data obtained from MZ-DPD simulations of liquids, polymer solutions, and polymer melts. We find that despite incomplete time scale separation of the molecular CG model, MZ-DPD achieves quantitative accuracy in predicting diffusive dynamics in single-component liquids and polymer solutions (24mers in a dimer solvent). We also find that MZ-DPD simulations of molecular penetrant diffusion in polymer networks do not reach quantitative agreement with the fine-grained model. Modeling diffusion governed by the activated barrier crossing of small molecular penetrants in these dense systems requires an accurate description of energy barriers, presumably combined with the treatment of memory effects. The use of a MZ-DPD thermostat extends the scope and applicability of molecular CG models for multicomponent systems where a correct description of the relative diffusion rates of the different components is important.
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Affiliation(s)
- Gregor Deichmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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62
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Di Pasquale N, Hudson T, Icardi M. Systematic derivation of hybrid coarse-grained models. Phys Rev E 2019; 99:013303. [PMID: 30780282 DOI: 10.1103/physreve.99.013303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Indexed: 06/09/2023]
Abstract
Molecular dynamics represents a key enabling technology for applications ranging from biology to the development of new materials. However, many real-world applications remain inaccessible to fully resolved simulations due to their unsustainable computational costs and must therefore rely on semiempirical coarse-grained models. Significant efforts have been devoted in the last decade towards improving the predictivity of these coarse-grained models and providing a rigorous justification of their use, through a combination of theoretical studies and data-driven approaches. One of the most promising research efforts is the (re)discovery of the Mori-Zwanzig projection as a generic, yet systematic, theoretical tool for deriving coarse-grained models. Despite its clean mathematical formulation and generality, there are still many open questions about its applicability and assumptions. In this work, we propose a detailed derivation of a hybrid multiscale system, generalizing and further investigating the approach developed in Español [Europhys. Lett. 88, 40008 (2009)10.1209/0295-5075/88/40008]. Issues such as the general coexistence of atoms (fully resolved degrees of freedom) and beads (larger coarse-grained units), the role of the fine-to-coarse mapping chosen, and the approximation of effective potentials are discussed. The theoretical discussion is supported by numerical simulations of a monodimensional nonlinear periodic benchmark system with an open-source parallel Julia code, easily extensible to arbitrary potential models and fine-to-coarse mapping functions. The results presented highlight the importance of introducing, in the macroscopic model, nonconstant fluctuating and dissipative terms, given by the Mori-Zwanzig approach, to correctly reproduce the reference fine-grained results, without requiring ad hoc calibration of interaction potentials and thermostats.
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Affiliation(s)
- Nicodemo Di Pasquale
- Department of Mathematics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Thomas Hudson
- Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matteo Icardi
- School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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63
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Jung G, Hanke M, Schmid F. Generalized Langevin dynamics: construction and numerical integration of non-Markovian particle-based models. SOFT MATTER 2018; 14:9368-9382. [PMID: 30427043 DOI: 10.1039/c8sm01817k] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We propose a generalized Langevin dynamics (GLD) technique to construct non-Markovian particle-based coarse-grained models from fine-grained reference simulations and to efficiently integrate them. The proposed GLD model has the form of a discretized generalized Langevin equation with distance-dependent two-particle contributions to the self- and pair-memory kernels. The memory kernels are iteratively reconstructed from the dynamical correlation functions of an underlying fine-grained system. We develop a simulation algorithm for this class of non-Markovian models that scales linearly with the number of coarse-grained particles. Our GLD method is suitable for coarse-grained studies of systems with incomplete time scale separation, as is often encountered, e.g., in soft matter systems. We apply the method to a suspension of nanocolloids with frequency-dependent hydrodynamic interactions. We show that the results from GLD simulations perfectly reproduce the dynamics of the underlying fine-grained system. The effective speedup of these simulations amounts to a factor of about 104. Additionally, the transferability of the coarse-grained model with respect to changes of the nanocolloid density is investigated. The results indicate that the model is transferable to systems with nanocolloid densities that differ by up to one order of magnitude from the density of the reference system.
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Affiliation(s)
- Gerhard Jung
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany.
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64
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Abetz V, Kremer K, Müller M, Reiter G. Functional Macromolecular Systems: Kinetic Pathways to Obtain Tailored Structures. MACROMOL CHEM PHYS 2018. [DOI: 10.1002/macp.201800334] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Volker Abetz
- Institute of Polymer Research; Helmholtz-Zentrum Geesthacht Max-Planck-Straße 1 21502 Geesthacht Germany
- Institute of Physical Chemistry; University of Hamburg; Martin-Luther-King-Platz 6 20146 Hamburg Germany
| | - Kurt Kremer
- Polymer Theory; Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Marcus Müller
- Institute for Theoretical Physics; Georg-August University of Göttingen; Friedrich-Hund-Platz 1 37077 Göttingen Germany
| | - Günter Reiter
- Institute of Physics; Albert-Ludwigs-University of Freiburg; Hermann-Herder-Str. 3 79104 Freiburg Germany
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65
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Han Y, Dama JF, Voth GA. Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. J Chem Phys 2018; 149:044104. [DOI: 10.1063/1.5039738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Yining Han
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - James F. Dama
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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66
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Zavadlav J, Praprotnik M. Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics. J Chem Phys 2018; 147:114110. [PMID: 28938807 DOI: 10.1063/1.4986916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.
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Affiliation(s)
- Julija Zavadlav
- Chair of Computational Science, ETH Zürich, Clausiusstrasse 33, CH-8092 Zurich, Switzerland
| | - Matej Praprotnik
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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67
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Affiliation(s)
- Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
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68
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69
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Meyer H, Voigtmann T, Schilling T. On the non-stationary generalized Langevin equation. J Chem Phys 2017; 147:214110. [DOI: 10.1063/1.5006980] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hugues Meyer
- Physikalisches Institut, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
- Research Unit in Engineering Science, Université du Luxembourg, L-4364 Esch-sur-Alzette, Luxembourg
| | - Thomas Voigtmann
- Institut für Materialphysik im Weltraum, Deutsches Zentrum für Luft- und Raumfahrt (DLR), 51170 Köln, Germany
- Department of Physics, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Tanja Schilling
- Physikalisches Institut, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
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