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Gholami A, Klein R, Delle Site L. Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir. PHYSICAL REVIEW LETTERS 2022; 129:230603. [PMID: 36563201 DOI: 10.1103/physrevlett.129.230603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/04/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this Letter, we show a novel approach where the latest version of the adaptive resolution scheme (AdResS), with noninteracting tracers as particles' reservoir, is combined with a fluctuating hydrodynamics (FHD) solver. The resulting algorithm, supported by a solid mathematical model, allows for a physically consistent exchange of matter and energy between the particle domain and its fluctuating continuum reservoir. Numerical tests are performed to show the validity of the algorithm. Differently from previous algorithms of the same kind, the current approach allows for simulations where, in addition to density fluctuations, also thermal fluctuations can be accounted for, thus large complex molecular systems, as, for example, hydrated biological membranes in a thermal field, can now be efficiently treated.
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Affiliation(s)
- Abbas Gholami
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Rupert Klein
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Luigi Delle Site
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
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2
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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3
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Bachmann J, Doltsinis NL. Adaptive partitioning molecular dynamics using an extended Hamiltonian approach. J Chem Phys 2021; 155:144104. [PMID: 34654314 DOI: 10.1063/5.0059206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A recently proposed extended Hamiltonian approach to switching interaction potentials is generalized to enable adaptive partitioning molecular dynamics simulations. Switching is performed along a fictitious classical degree of freedom whose value determines the mixing ratio of the two potentials on a time scale determined by its associated mass. We propose to choose this associated fictitious mass adaptively so as to ensure a constant time scale for all switching processes. For different model systems, including a harmonic oscillator and a Lennard-Jones fluid, we investigate the window of switching time scales that guarantees the conservation of the extended Hamiltonian for a large number of switching events. The methodology is first applied in the microcanonical ensemble and then generalized to the canonical ensemble using a Nosé-Hoover chain thermostat. It is shown that the method is stable for thousands of consecutive switching events during a single simulation, with constant temperature and a conserved extended Hamiltonian. A slight modification of the original Hamiltonian is introduced to avoid accumulation of small numerical errors incurred after each switching process.
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Affiliation(s)
- Jim Bachmann
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany
| | - Nikos L Doltsinis
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Str. 10, 48149 Münster, Germany
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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5
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Ovchinnikov V, Conti S, Lau EY, Lightstone FC, Karplus M. Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model. J Chem Theory Comput 2020; 16:1866-1881. [DOI: 10.1021/acs.jctc.9b01072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Simone Conti
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Edmond Y. Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Felice C. Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
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Flood E, Boiteux C, Lev B, Vorobyov I, Allen TW. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chem Rev 2019; 119:7737-7832. [DOI: 10.1021/acs.chemrev.8b00630] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Bogdan Lev
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology/Department of Pharmacology, University of California, Davis, 95616, United States
| | - Toby W. Allen
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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Machado MR, Zeida A, Darré L, Pantano S. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019; 9:20180085. [PMID: 31065347 PMCID: PMC6501346 DOI: 10.1098/rsfs.2018.0085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.
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Affiliation(s)
- Matías R. Machado
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Darré
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Institut Pasteur de Montevideo, Functional Genomics Unit, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
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Ciccotti G, Delle Site L. The physics of open systems for the simulation of complex molecular environments in soft matter. SOFT MATTER 2019; 15:2114-2124. [PMID: 30761396 DOI: 10.1039/c8sm02523a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Molecular dynamics (MD) has become one of the most powerful tools of investigation in soft matter. Despite such success, simulations of large molecular environments are mostly run using the approximation of closed systems without the possibility of exchange of matter. Due to the molecular complexity of soft matter systems, an optimal simulation strategy would require the application of concurrent multiscale resolution approaches such that each part of a large system can be considered as an open subsystem at a high resolution embedded in a large coarser reservoir of energy and particles. This paper discusses the current capability and the future perspectives of multiscale adaptive resolution MD methods to satisfy the conceptual principles of open systems and to perform simulations of complex molecular environments in soft matter.
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Affiliation(s)
- Giovanni Ciccotti
- Instituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerche, and Universita' La Sapienza, Rome, Italy.
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Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations. Curr Opin Struct Biol 2018; 56:1-10. [PMID: 30439585 DOI: 10.1016/j.sbi.2018.10.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 11/22/2022]
Abstract
While many proteins and protein regions utilize a complex repertoire of amino acids to achieve their biological function, a subset of protein sequences are enriched in a reduced set of amino acids. These so-called low complexity (LC) sequences, specifically intrinsically disordered variants of LC sequences, have been the focus of recent investigations owing to their roles in a range of biological functions, specifically phase separation. Computational studies of LC sequences have provided rich insights into their behavior both as individual proteins in dilute solutions and as the drivers and modulators of higher-order assemblies. Here, we review how simulations performed across distinct resolutions have provided different types of insights into the biological role of LC sequences.
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