1
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Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J Chem Theory Comput 2022; 18:5759-5791. [PMID: 36070494 PMCID: PMC9558379 DOI: 10.1021/acs.jctc.2c00643] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/14/2023]
Abstract
Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander J. Pak
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksander E. P. Durumeric
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy D. Loose
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
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2
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Papež P, Praprotnik M. Dissipative Particle Dynamics Simulation of Ultrasound Propagation through Liquid Water. J Chem Theory Comput 2022; 18:1227-1240. [PMID: 35001631 PMCID: PMC8830050 DOI: 10.1021/acs.jctc.1c01020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Ultrasound is widely
used as a noninvasive method in therapeutic
and diagnostic applications. These can be further optimized by computational
approaches, as they allow for controlled testing and rational optimization
of the ultrasound parameters, such as frequency and amplitude. Usually,
continuum numerical methods are used to simulate ultrasound propagating
through different tissue types. In contrast, ultrasound simulations
using particle description are less common, as the implementation
is challenging. In this work, a dissipative particle dynamics model
is used to perform ultrasound simulations in liquid water. The effects
of frequency and thermostat parameters are studied and discussed.
We show that frequency and thermostat parameters affect not only the
attenuation but also the computed speed of sound. The present study
paves the way for development and optimization of a virtual ultrasound
machine for large-scale biomolecular simulations.
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Affiliation(s)
- Petra Papež
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI-1001, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana, SI-1000, Slovenia
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI-1001, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana, SI-1000, Slovenia
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3
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Han Y, Jin J, Voth GA. Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining. J Chem Phys 2021; 154:084122. [PMID: 33639745 DOI: 10.1063/5.0035184] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Since their emergence in the 1990s, mesoscopic models of fluids have been widely used to study complex organization and transport phenomena beyond the molecular scale. Even though these models are designed based on results from physics at the meso- and macroscale, such as fluid mechanics and statistical field theory, the underlying microscopic foundation of these models is not as well defined. This paper aims to build such a systematic connection using bottom-up coarse-graining methods. From the recently developed dynamic coarse-graining scheme, we introduce a statistical inference framework of explicit many-body conservative interaction that quantitatively recapitulates the mesoscopic structure of the underlying fluid. To further consider the dissipative and fluctuation forces, we design a novel algorithm that parameterizes these forces. By utilizing this algorithm, we derive pairwise decomposable friction kernels under both non-Markovian and Markovian limits where both short- and long-time features of the coarse-grained dynamics are reproduced. Finally, through these new developments, the many-body dissipative particle dynamics type of equations of motion are successfully derived. The methodologies developed in this work thus open a new avenue for the construction of direct bottom-up mesoscopic models that naturally bridge the meso- and macroscopic physics.
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Affiliation(s)
- Yining Han
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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4
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Cortes-Huerto R, Praprotnik M, Kremer K, Delle Site L. From adaptive resolution to molecular dynamics of open systems. THE EUROPEAN PHYSICAL JOURNAL. B 2021; 94:189. [PMID: 34720711 PMCID: PMC8547219 DOI: 10.1140/epjb/s10051-021-00193-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/31/2021] [Indexed: 05/14/2023]
Abstract
ABSTRACT We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.
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Affiliation(s)
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Luigi Delle Site
- Department of Mathematics and Computer Science, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
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5
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Taylor PA, Jayaraman A. Molecular Modeling and Simulations of Peptide–Polymer Conjugates. Annu Rev Chem Biomol Eng 2020; 11:257-276. [DOI: 10.1146/annurev-chembioeng-092319-083243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide–polymer conjugates are a class of soft materials composed of covalently linked blocks of protein/polypeptides and synthetic/natural polymers. These materials are practically useful in biological applications, such as drug delivery, DNA/gene delivery, and antimicrobial coatings, as well as nonbiological applications, such as electronics, separations, optics, and sensing. Given their broad applicability, there is motivation to understand the molecular and macroscale structure, dynamics, and thermodynamic behavior exhibited by such materials. We focus on the past and ongoing molecular simulation studies aimed at obtaining such fundamental understanding and predicting molecular design rules for the target function. We describe briefly the experimental work in this field that validates or motivates these computational studies. We also describe the various models (e.g., atomistic, coarse-grained, or hybrid) and simulation methods (e.g., stochastic versus deterministic, enhanced sampling) that have been used and the types of questions that have been answered using these computational approaches.
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Affiliation(s)
- Phillip A. Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
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6
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Delle Site L, Praprotnik M, Bell JB, Klein R. Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.201900232] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Luigi Delle Site
- Freie Universität Berlin Institute of Mathematics Arnimallee 6, 14195 Berlin Germany
| | - Matej Praprotnik
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana, Slovenia & Department of Physics Faculty of Mathematics and Physics University of Ljubljana SI‐1000 Ljubljana Slovenia
| | - John B. Bell
- Lawrence Berkeley National Lab 1 Cyclotron Rd. Berkeley CA 94720 USA
| | - Rupert Klein
- Freie Universität Berlin Institute of Mathematics Arnimallee 6, 14195 Berlin Germany
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7
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Zavadlav J, Marrink SJ, Praprotnik M. SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 2019; 9:20180075. [PMID: 31065343 PMCID: PMC6501350 DOI: 10.1098/rsfs.2018.0075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
In this contribution, we review recent developments and applications of a dynamic clustering algorithm SWINGER tailored for the multiscale molecular simulations of biomolecular systems. The algorithm on-the-fly redistributes solvent molecules among supramolecular clusters. In particular, we focus on its applications in combination with the adaptive resolution scheme, which concurrently couples atomistic and coarse-grained molecular representations. We showcase the versatility of our multiscale approach on a few applications to biomolecular systems coupling atomistic and supramolecular water models such as the well-established MARTINI and dissipative particle dynamics models and provide an outlook for future work.
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Affiliation(s)
- Julija Zavadlav
- Computational Science and Engineering Laboratory, ETH-Zurich, Clausiusstrasse 33, 8092 Zurich, Switzerland
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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8
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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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9
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Hu J, Korotkin I, Karabasov S. Hybrid multiscale simulation reveals focusing of a diffusing peptide molecule by parallel shear flow in water. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Wang Y, Li Z, Xu J, Yang C, Karniadakis GE. Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces. SOFT MATTER 2019; 15:1747-1757. [PMID: 30672954 PMCID: PMC6414210 DOI: 10.1039/c8sm02170h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometers to microns and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an all-atom molecular dynamics (MD) description for specific atomistic details in the vicinity of the functional surface with a dissipative particle dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain away from the functional surface. In order to achieve a seamless transition in dynamic properties we endow the MD simulation with a DPD thermostat, which is validated against experimental results by modeling water at different temperatures. We then validate the MD-DPD coupling method for transient Couette and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can resolve accurately the continuum-based analytical solutions. Subsequently, we simulate shear flows over grafted polydimethylsiloxane (PDMS) surfaces (polymer brushes) for various grafting densities, and investigate the slip flow as a function of the shear stress. We verify that a "universal" power law exists for the slip length, in agreement with published results. Having validated the MD-DPD coupling method, we simulate time-dependent flows past an endothelial glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate the dynamics of the EGL changing from an equilibrium state to a compressed state under shear by aligning the molecular structures along the shear direction. MD-DPD simulation results agree well with results of a single MD simulation, but with the former more than two orders of magnitude faster than the latter for system sizes above one micron.
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Affiliation(s)
- Yuying Wang
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Li
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Junbo Xu
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Chao Yang
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Shadrack Jabes B, Krekeler C, Klein R, Delle Site L. Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique. J Chem Phys 2018; 148:193804. [PMID: 30307223 DOI: 10.1063/1.5009066] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.
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Affiliation(s)
- B Shadrack Jabes
- Institute for Mathematics, Freie Universitat Berlin, D-14195 Berlin, Germany
| | - C Krekeler
- Institute for Mathematics, Freie Universitat Berlin, D-14195 Berlin, Germany
| | - R Klein
- Institute for Mathematics, Freie Universitat Berlin, D-14195 Berlin, Germany
| | - L Delle Site
- Institute for Mathematics, Freie Universitat Berlin, D-14195 Berlin, Germany
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12
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Hu J, Korotkin IA, Karabasov SA. A multi-resolution particle/fluctuating hydrodynamics model for hybrid simulations of liquids based on the two-phase flow analogy. J Chem Phys 2018; 149:084108. [PMID: 30193466 DOI: 10.1063/1.5040962] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A triple-scale model of a molecular liquid, where atomistic, coarse-grained, and hydrodynamic descriptions of the same substance are consistently combined, is developed. Following the two-phase analogy method, the continuum and discrete particle representations of the same substance are coupled together in the framework of conservation laws for mass and momentum that are treated as effective phases of a nominally two-phase flow. The effective phase distribution, which governs the model resolution locally, is a user-defined function. In comparison with the previous models of this kind in the literature which used the classical Molecular Dynamics (MD) for the particulate phase, the current approach uses the Adaptive Resolution Scheme (AdResS) and stochastic integration to smoothen the particle transition from non-bonded atom dynamics to hydrodynamics. Accuracy and robustness of the new AdResS-Fluctuating Hydrodynamics (FH) model for water at equilibrium conditions is compared with the previous implementation of the two-phase analogy model based on the MD-FH method. To demonstrate that the AdResS-FH method can accurately support hydrodynamic fluctuations of mass and momentum, a test problem of high-frequency acoustic wave propagation through a small hybrid computational domain region is considered.
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Affiliation(s)
- J Hu
- The School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
| | - I A Korotkin
- The School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
| | - S A Karabasov
- The School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
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13
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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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14
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Zavadlav J, Sablić J, Podgornik R, Praprotnik M. Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution. Biophys J 2018; 114:2352-2362. [PMID: 29650370 PMCID: PMC6129463 DOI: 10.1016/j.bpj.2018.02.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/24/2018] [Accepted: 02/28/2018] [Indexed: 12/24/2022] Open
Abstract
The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.
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Affiliation(s)
- Julija Zavadlav
- Computational Science & Engineering Laboratory, ETH Zurich, Zurich, Switzerland
| | - Jurij Sablić
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Rudolf Podgornik
- Theoretical Physics Department, J. Stefan Institute, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.
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15
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Lafond PG, Izvekov S. Multiscale Coarse-Graining with Effective Polarizabilities: A Fully Bottom-Up Approach. J Chem Theory Comput 2018; 14:1873-1886. [DOI: 10.1021/acs.jctc.7b00917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Patrick G. Lafond
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Sergei Izvekov
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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16
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Zavadlav J, Marrink SJ, Praprotnik M. Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm. J Chem Theory Comput 2018; 14:1754-1761. [PMID: 29439560 DOI: 10.1021/acs.jctc.7b01129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to modified AT water models, such as the bundled-simple point charge (SPC) models, that use semiharmonic springs to restrict the relative movement of water molecules within a cluster. Those models can have a significant impact on the simulated biomolecules and can lead, for example, to a partial unfolding of a protein. In this work, we employ the recently developed alternative approach with a dynamical clustering algorithm, SWINGER, which enables a direct coupling of original unmodified AT and SCG water models. We perform an adaptive resolution molecular dynamics simulation of a Trp-Cage miniprotein in multiscale water, where the standard SPC water model is interfaced with the widely used MARTINI SCG model, and demonstrate that, compared to the corresponding full-blown AT simulations, the structural and dynamic properties of the solvated protein and surrounding solvent are well reproduced by our approach.
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Affiliation(s)
- Julija Zavadlav
- Computational Science & Engineering Laboratory , ETH Zurich , Clausiusstrasse 33 , CH-8092 Zurich , Switzerland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Matej Praprotnik
- Laboratory for Molecular Modeling , National Institute of Chemistry , Hajdrihova 19 , SI-1001 Ljubljana , Slovenia.,Department of Physics, Faculty of Mathematics and Physics , University of Ljubljana , Jadranska 19 , SI-1000 Ljubljana , Slovenia
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17
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Petsev ND, Leal LG, Shell MS. Coupling discrete and continuum concentration particle models for multiscale and hybrid molecular-continuum simulations. J Chem Phys 2017; 147:234112. [DOI: 10.1063/1.5001703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nikolai D. Petsev
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - L. Gary Leal
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
| | - M. Scott Shell
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
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