1
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Kim J, Rotenberg B. Donnan equilibrium in charged slit-pores from a hybrid nonequilibrium molecular dynamics/Monte Carlo method with ions and solvent exchange. J Chem Phys 2024; 161:054107. [PMID: 39087531 DOI: 10.1063/5.0220913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/14/2024] [Indexed: 08/02/2024] Open
Abstract
Ion partitioning between different compartments (e.g., a porous material and a bulk solution reservoir), known as Donnan equilibrium, plays a fundamental role in various contexts such as energy, environment, or water treatment. The linearized Poisson-Boltzmann (PB) equation, capturing the thermal motion of the ions with mean-field electrostatic interactions, is practically useful to understand and predict ion partitioning, despite its limited applicability to conditions of low salt concentrations and surface charge densities. Here, we investigate the Donnan equilibrium of coarse-grained dilute electrolytes confined in charged slit-pores in equilibrium with a reservoir of ions and solvent. We introduce and use an extension to confined systems of a recently developed hybrid nonequilibrium molecular dynamics/grand canonical Monte Carlo simulation method ("H4D"), which enhances the efficiency of solvent and ion-pair exchange via a fourth spatial dimension. We show that the validity range of linearized PB theory to predict the Donnan equilibrium of dilute electrolytes can be extended to highly charged pores by simply considering renormalized surface charge densities. We compare with simulations of implicit solvent models of electrolytes and show that in the low salt concentrations and thin electric double layer limit considered here, an explicit solvent has a limited effect on the Donnan equilibrium and that the main limitations of the analytical predictions are not due to the breakdown of the mean-field description but rather to the charge renormalization approximation, because it only focuses on the behavior far from the surfaces.
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Affiliation(s)
- Jeongmin Kim
- Department of Energy Engineering, Korea Institute of Energy Technology (KENTECH), Naju 58330, Republic of Korea
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, 80039 Amiens Cedex, France
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2
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Chaimovich M, Chaimovich A. Relative Resolution: An Analysis with the Kullback-Leibler Entropy. J Chem Theory Comput 2024; 20:2074-2087. [PMID: 38416535 DOI: 10.1021/acs.jctc.3c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
A novel type of a multiscale approach, called Relative Resolution (RelRes), can correctly retrieve the behavior of various nonpolar liquids while speeding up molecular simulations by almost an order of magnitude. In this approach in a single system, molecules switch their resolution in terms of their relative separation, with near neighbors interacting via fine-grained potentials, yet far neighbors interacting via coarse-grained potentials; notably, these two potentials are analytically parametrized by a multipole approximation. Our current work focuses on analyzing RelRes by relating it with the Kullback-Leibler (KL) entropy, which is a useful metric for multiscale errors. In particular, we thoroughly examine the exact and approximate versions of this informatic measure for several alkane systems. By analyzing its dependency on the system size, we devise a formula for predicting the exact KL entropy of an "infinite" system via the computation of the approximate KL entropy of an "infinitesimal" system. Demonstrating that the KL entropy can holistically capture many multiscale errors, we settle bounds for the KL entropy that ensure a sufficient representation of the structural and thermal behavior by the RelRes algorithm. This, in turn, allows the scientific community to readily determine the ideal switching distance for an arbitrary RelRes system.
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Affiliation(s)
- Mark Chaimovich
- Russian School of Mathematics, North Bethesda, Maryland 20852, United States
| | - Aviel Chaimovich
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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3
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Smith ER, Theodorakis PE. Multiscale simulation of fluids: coupling molecular and continuum. Phys Chem Chem Phys 2024; 26:724-744. [PMID: 38113114 DOI: 10.1039/d3cp03579d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In molecular dynamics (MD) simulation, the length and time scales that can be captured are limited, while computational fluid dynamics (CFD) methods are built on a range of assumptions, from the continuum hypothesis itself, to a variety of closure assumptions. To address these issues, the coupling of different methodologies provides a way to retain the best of both methods. Here, we provide a perspective on multiscale simulation based on the coupling of MD and CFD with each a distinct part of the same simulation domain. This style of coupling allows molecular detail to be present only where it is needed, so CFD can model larger scales than possible with MD alone. We present a unified perspective of the literature, showing the links between the two main types of coupling, state and flux, and discuss the varying assumptions in their use. A unique challenge in such coupled simulation is obtaining averages and constraining local parts of a molecular simulation. We highlight that incorrect localisation has resulted in an error in the literature. We then finish with some applications, focused on the simulation of fluids. Thus, we hope to motivate further research in this exciting area with applications across the spectrum of scientific disciplines.
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Affiliation(s)
- Edward R Smith
- Department of Mechanical and Aerospace Engineering, Brunel University London, Uxbridge, Middlesex UB8 3PH, UK.
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4
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Tran AL, Guidez EB, Lin H. Adaptive-Partitioning Multilayer Dynamics Simulations: 2. Implementations of the Permuted and Interpolated Adaptive-Partitioning Gradients. J Phys Chem A 2023; 127:10320-10333. [PMID: 38058156 PMCID: PMC10712430 DOI: 10.1021/acs.jpca.3c05600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 12/08/2023]
Abstract
Recently, an adaptive-partitioning multilayer Q1/Q2/MM method was proposed, where Q1 and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the molecular-mechanical force fields. Such a multilayer model resembles the ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) model by Morokuma and co-workers, but it is distinguished by on-the-fly reclassifying atoms to be Q1, Q2, or MM in dynamics simulations. To smoothly blend the levels of descriptions of the atoms, buffer zones are introduced between adjacent layers, and the energy is smoothly interpolated. In particular, the Q1/Q2 interaction energy was expressed in two different formalisms: permuted and interpolated adaptive-partitioning (PAP and IAP), respectively. While the PAP energy is based on a weighted many-body expansion, the IAP energy is derived via alchemical quantum calculations with interpolated Fock and overlap matrices. In this article, we examine in-depth the irregularities in the IAP energy near the boundary between the buffer and Q2 zones, which were found prominent in some calculations. These irregularities are due to basis-set linear dependencies, which can be effectively suppressed using a cutoff for the weighted atomic orbital coefficients. Furthermore, we derived and implemented the gradients for both PAP and IAP. Test calculations on a series of water cluster models show perfectly smooth gradients in PAP, while a minor discontinuity occurs in IAP gradients at the buffer/Q2 boundary. The energy and gradient discontinuities in IAP become smaller when moving the buffer/Q2 boundary further away from the Q1 center and when increasing the size of the basis sets used. Overall, those discontinuities are controllable, and possible ways to further diminish them are discussed.
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Affiliation(s)
- Anh L. Tran
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
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5
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Zha J, Xia F. Developing Hybrid All-Atom and Ultra-Coarse-Grained Models to Investigate Taxol-Binding and Dynein Interactions on Microtubules. J Chem Theory Comput 2023; 19:5621-5632. [PMID: 37489636 DOI: 10.1021/acs.jctc.3c00275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Simulating the conformations and functions of biological macromolecules by using all-atom (AA) models is a challenging task due to expensive computational costs. One possible strategy to solve this problem is to develop hybrid all-atom and ultra-coarse-grained (AA/UCG) models of the biological macromolecules. In the AA/UCG scheme, the interest regions are described by AA models, while the other regions are described in the UCG representation. In this study, we develop the hybrid AA/UCG models and apply them to investigate the conformational changes of microtubule-bound tubulins. The simulation results of the hybrid models elucidated the mechanism of why the taxol molecules selectively bound microtubules but not tubulin dimers. In addition, we also explore the interactions of the microtubules and dyneins. Our study shows that the hybrid AA/UCG model has great application potential in studying the function of complex biological systems.
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Affiliation(s)
- Jinyin Zha
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai 200062, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai 200062, China
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6
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Renner J, Schmidt M, de Las Heras D. Reduced-variance orientational distribution functions from torque sampling. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:235901. [PMID: 36974000 DOI: 10.1088/1361-648x/acc522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
We introduce a method to sample the orientational distribution function in computer simulations. The method is based on the exact torque balance equation for classical many-body systems of interacting anisotropic particles in equilibrium. Instead of the traditional counting of events, we reconstruct the orientational distribution function via an orientational integral of the torque acting on the particles. We test the torque sampling method in two- and three-dimensions, using both Langevin dynamics and overdamped Brownian dynamics, and with two interparticle interaction potentials. In all cases the torque sampling method produces profiles of the orientational distribution function with better accuracy than those obtained with the traditional counting method. The accuracy of the torque sampling method is independent of the bin size, and hence it is possible to resolve the orientational distribution function with arbitrarily small angular resolutions.
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Affiliation(s)
- Johannes Renner
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Daniel de Las Heras
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
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7
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Potisk T, Sablić J, Svenšek D, Diego ES, Teran FJ, Praprotnik M. Analyte‐Driven Clustering of Bio‐Conjugated Magnetic Nanoparticles. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Tilen Potisk
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Faculty of Mathematics and Physics University of Ljubljana SI‐1001 Ljubljana Slovenia
| | - Jurij Sablić
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Department of Condensed Matter Physics University of Barcelona E‐08028 Barcelona Spain
- Centre Européen de Calcul Atomique et Moléculaire École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Daniel Svenšek
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Faculty of Mathematics and Physics University of Ljubljana SI‐1001 Ljubljana Slovenia
| | | | - Francisco J. Teran
- IMDEA Nanociencia Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
- Nanobiotecnología (iMdea‐Nanociencia) Unidad Asociada al Centro Nacional de Biotecnología (CSIC) 28049 Madrid Spain
| | - Matej Praprotnik
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Faculty of Mathematics and Physics University of Ljubljana SI‐1001 Ljubljana Slovenia
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8
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Panahian Jand S, Nourbakhsh Z, Delle Site L. Nuclear quantum effects in fullerene-fullerene aggregation in water. Front Chem 2022; 10:1072665. [PMID: 36590278 PMCID: PMC9799252 DOI: 10.3389/fchem.2022.1072665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/23/2022] [Indexed: 12/16/2022] Open
Abstract
We studied the effects of the quantum delocalization in space of the hydrogen atoms of water in the aggregation process of two fullerene molecules. We considered a case using a purely repulsive water-fullerene interaction, as such a situation has shown that water-mediated effects play a key role in the aggregation process. This study becomes feasible, at a reduced computational price, by combining the path integral (PI) molecular dynamics (MD) method with a recently developed open-system MD technique. Specifically, only the mandatory solvation shell of the two fullerene molecules was considered at full quantum resolution, while the rest of the system was represented as a mean-field macroscopic reservoir of particles and energy. Our results showed that the quantum nature of the hydrogen atoms leads to a sizable difference in the curve of the free energy of aggregation; that is, that nuclear quantum effects play a relevant role.
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9
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Shmilovich K, Stieffenhofer M, Charron NE, Hoffmann M. Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution. J Phys Chem A 2022; 126:9124-9139. [PMID: 36417670 PMCID: PMC9743211 DOI: 10.1021/acs.jpca.2c07716] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done efficiently using coarse-grained simulations, from which meaningful physicochemical information can be inferred if the corresponding all-atom configurations are reconstructed. However, this procedure of backmapping to reintroduce the lost atomistic detail into coarse-grain structures has proven a challenging task due to the many feasible atomistic configurations that can be associated with one coarse-grain structure. Existing backmapping methods are strictly frame-based, relying on either heuristics to replace coarse-grain particles with atomic fragments and subsequent relaxation or parametrized models to propose atomic coordinates separately and independently for each coarse-grain structure. These approaches neglect information from previous trajectory frames that is critical to ensuring temporal coherence of the backmapped trajectory, while also offering information potentially helpful to producing higher-fidelity atomic reconstructions. In this work, we present a deep learning-enabled data-driven approach for temporally coherent backmapping that explicitly incorporates information from preceding trajectory structures. Our method trains a conditional variational autoencoder to nondeterministically reconstruct atomistic detail conditioned on both the target coarse-grain configuration and the previously reconstructed atomistic configuration. We demonstrate our backmapping approach on two exemplar biomolecular systems: alanine dipeptide and the miniprotein chignolin. We show that our backmapped trajectories accurately recover the structural, thermodynamic, and kinetic properties of the atomistic trajectory data.
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Affiliation(s)
- Kirill Shmilovich
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois60637, United States,E-mail:
| | | | - Nicholas E. Charron
- Weiss
School of Natural Sciences, Department of Physics and Astronomy, Rice University, Houston, Texas77005, United States,Department
of Physics, Freie Universität Berlin, Berlin14195, Germany
| | - Moritz Hoffmann
- Fachbereich
Mathematik und Informatik, Freie Universität
Berlin, Berlin14195, Germany
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10
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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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11
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Schmid F. Understanding and Modeling Polymers: The Challenge of Multiple Scales. ACS POLYMERS AU 2022. [DOI: 10.1021/acspolymersau.2c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128Mainz, Germany
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12
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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: 80] [Impact Index Per Article: 40.0] [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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13
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Rohrbach PB, Kobayashi H, Scheichl R, Wilding NB, Jack RL. Multilevel simulation of hard-sphere mixtures. J Chem Phys 2022; 157:124109. [DOI: 10.1063/5.0102875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a multilevel Monte Carlo simulation method for analysing multi-scale physical systems via a hierarchy of coarse-grained representations, to obtain numerically-exact results, at the most detailed level. We apply the method to a mixture of size-asymmetric hard spheres, in the grand canonical ensemble. A three-level version of the method is compared with a previously-studied two-level version. The extra level interpolates between the full mixture and a coarse-grained description where only the large particles are present -- this is achieved by restricting the small particles to regions close to the large ones. The three-level method improves the performance of the estimator, at fixed computational cost. We analyse the asymptotic variance of the estimator, and discuss the mechanisms for the improved performance.
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Affiliation(s)
- Paul B Rohrbach
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge Department of Applied Mathematics and Theoretical Physics, United Kingdom
| | | | | | - Nigel B. Wilding
- School of Physics, University of Bristol School of Physics, United Kingdom
| | - Robert L. Jack
- DAMTP, University of Cambridge Department of Applied Mathematics and Theoretical Physics, United Kingdom
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14
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López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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15
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Floyd JE, Lukes JR. A neural network-assisted open boundary molecular dynamics simulation method. J Chem Phys 2022; 156:184114. [PMID: 35568556 DOI: 10.1063/5.0083198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A neural network-assisted molecular dynamics method is developed to reduce the computational cost of open boundary simulations. Particle influxes and neural network-derived forces are applied at the boundaries of an open domain consisting of explicitly modeled Lennard-Jones atoms in order to represent the effects of the unmodeled surrounding fluid. Canonical ensemble simulations with periodic boundaries are used to train the neural network and to sample boundary fluxes. The method, as implemented in the LAMMPS, yields temperature, kinetic energy, potential energy, and pressure values within 2.5% of those calculated using periodic molecular dynamics and runs two orders of magnitude faster than a comparable grand canonical molecular dynamics system.
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Affiliation(s)
- J E Floyd
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - J R Lukes
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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16
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Evangelakis A, Panahian Jand S, Delle Site L. Path Integral Molecular Dynamics of Liquid Water in a Mean-Field Particle Reservoir. ChemistryOpen 2022; 11:e202100286. [PMID: 35218165 PMCID: PMC8973269 DOI: 10.1002/open.202100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
We present a simulation scheme for path integral simulation of molecular liquids where a small open region is embedded in a large reservoir of non interacting point-particles. The scheme is based on the latest development of the adaptive resolution technique AdResS and allows for the space-dependent change of molecular resolution from a path integral representation with 120 degrees of freedom to a point particle that does not interact with other molecules and vice versa. The method is applied to liquid water and implies a sizable gain regarding the request of computational resources compared to full path integral simulations. Given the role of water as universal solvent with a specific hydrogen bonding network, the path integral treatment of water molecules is important to describe the quantum effects of hydrogen atoms' delocalization in space on the hydrogen bonding network. The method presented here implies feasible computational efforts compared to full path integral simulations of liquid water which, on large scales, are often prohibitive.
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Affiliation(s)
| | - Sara Panahian Jand
- Freie Universität BerlinInstitute of MathematicsArnimallee 614195BerlinGermany
| | - Luigi Delle Site
- Freie Universität BerlinInstitute of MathematicsArnimallee 614195BerlinGermany
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17
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Banerjee A, Sevilla M, Rudzinski JF, Cortes-Huerto R. Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions. SOFT MATTER 2022; 18:2373-2382. [PMID: 35258066 DOI: 10.1039/d2sm00089j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We compute partial structure factors, Kirkwood-Buff integrals (KBIs) and chemical potentials of model supercooled liquids with and without attractive interactions. We aim at investigating whether relatively small differences in the tail of the radial distribution functions result in contrasting thermodynamic properties. Our results suggest that the attractive potential favours the nucleation of long-range structures. Indeed, upon decreasing temperature, Bathia-Thornton structure factors display anomalous behaviour in the k→0 limit. KBIs extrapolated to the thermodynamic limit confirm this picture, and excess coordination numbers identify the anomaly with long-range concentration fluctuations. By contrast, the purely repulsive system remains perfectly miscible for the same temperature interval and only reveals qualitatively similar concentration fluctuations in the crystalline state. Furthermore, differences in both isothermal compressibilities and chemical potentials show that thermodynamics is not entirely governed by the short-range repulsive part of the interaction potential, emphasising the nonperturbative role of attractive interactions. Finally, at higher density, where both systems display nearly identical dynamical properties and repulsive interactions become dominant, the anomaly disappears, and both systems also exhibit similar thermodynamic properties.
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Affiliation(s)
- Atreyee Banerjee
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Mauricio Sevilla
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Joseph F Rudzinski
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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18
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Schmid F. Editorial: Multiscale simulation methods for soft matter systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:160401. [PMID: 35179129 DOI: 10.1088/1361-648x/ac5071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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19
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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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20
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Wang H, Zheng X. Theoretical Study of Macrocyclic Host Molecules: From Supramolecular Recognition to Self-Assembly. Phys Chem Chem Phys 2022; 24:19011-19028. [DOI: 10.1039/d2cp02152h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Supramolecular chemistry focuses on molecular recognition and self-assembly of various building blocks through weak non-covalent interactions, including anion-π, hydrogen bond (HB), hydrophobic interactions, van der Waals (vdW) interactions, etc, which...
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21
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Delle Site L. Investigation of water-mediated intermolecular interactions with the adaptive resolution simulation technique. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:115101. [PMID: 34560676 DOI: 10.1088/1361-648x/ac29e2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
We use the adaptive resolution simulation (AdResS) technique to estimate the region in space where water-mediated effects in molecule-molecule interactions are relevant. AdResS is employed to identify the region around the solute (solvation shell) where the atomistic details of the hydrogen bonding network are relevant while outside water plays the role of a thermodynamic bath that can be described at simplified macroscopic level. The consequence is that for the interaction of two solutes the intermolecular distance at which water mediated effects start to be relevant is represented by the sum of the radii of the two respective solvation shells identified via AdResS. The hypothesis formulated above will be proven by calculating the solute-solute potential of mean force for different solutes. As test molecules we use amino acids derived from fragments of the FCHo2-F-BAR domain protein; this choice stems from the fact that the current results, beside proving the technical capability of AdResS in this context, may provide data for future actual coarse-grained models.
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Affiliation(s)
- Luigi Delle Site
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
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22
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Banerjee A, Lu CY, Dutt M. A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides. Phys Chem Chem Phys 2021; 24:1553-1568. [PMID: 34940778 DOI: 10.1039/d1cp04205j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reconstituted photosynthetic proteins which are activated upon exposure to solar energy hold enormous potential for powering future solid state devices and solar cells. The functionality and integration of these proteins into such devices has been successfully enabled by lipid-like peptides. Yet, a fundamental understanding of the organization of these peptides with respect to the photosynthetic proteins and themselves remains unknown and is critical for guiding the design of such light-activated devices. This study investigates the relative organization of one such peptide sequence V6K2 (V: valine and K: lysine) within assemblies. Given the expansive spatiotemporal scales associated with this study, a hybrid coarse-grained (CG) model which captures the structure, conformation and aggregation of the peptide is adopted. The CG model uses a combination of iterative Boltzmann inversion and force matching to provide insight into the relative organization of V6K2 in assemblies. The CG model reproduces the structure of a V6K2 peptide sequence along with its all atom (AA) solvation structure. The relative organization of multiple peptides in an assembly, as captured by CG simulations, is in agreement with corresponding results from AA simulations. Also, a backmapping procedure reintroduces the AA details of the peptides within the aggregates captured by the CG model to demonstrate the relative organization of the peptides. Furthermore, a large number of peptides self-assemble into an elongated micelle in the CG simulation, which is consistent with experimental findings. The coarse-graining procedure is tested for transferability to longer peptide sequences, and hence can be extended to other amphiphilic peptide sequences.
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Affiliation(s)
- Akash Banerjee
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
| | - Chien Yu Lu
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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23
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Liu X, Korotkin I, Rao Z, Karabasov S. A Thermostat‐Consistent Fully Coupled Molecular Dynamics–Generalized Fluctuating Hydrodynamics Model for Non‐Equilibrium Flows. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xinjian Liu
- School of Electrical and Power Engineering China University of Mining and Technology Xuzhou 221116 China
- The School of Engineering and Materials Science Queen Mary University of London Mile End Road London E1 4NS UK
| | - Ivan Korotkin
- Mathematical Sciences University of Southampton University Rd. Southampton SO17 1BJ UK
| | - Zhonghao Rao
- School of Electrical and Power Engineering China University of Mining and Technology Xuzhou 221116 China
| | - Sergey Karabasov
- The School of Engineering and Materials Science Queen Mary University of London Mile End Road London E1 4NS UK
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24
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Gholami A, Klein R, Delle Site L. On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Abbas Gholami
- Institute of Mathematics Freie Universität Berlin Arnimallee 6 Berlin 14195 Germany
| | - Rupert Klein
- Institute of Mathematics Freie Universität Berlin Arnimallee 6 Berlin 14195 Germany
| | - Luigi Delle Site
- Institute of Mathematics Freie Universität Berlin Arnimallee 6 Berlin 14195 Germany
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25
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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26
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Liu Y, de Vries AH, Pezeshkian W, Marrink SJ. Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:5876-5884. [PMID: 34165988 PMCID: PMC8444333 DOI: 10.1021/acs.jctc.1c00151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Understanding the
lateral organization in plasma membranes remains
an open problem and is of great interest to many researchers. Model
membranes consisting of coexisting domains are commonly used as simplified
models of plasma membranes. The coarse-grained (CG) Martini force
field has successfully captured spontaneous separation of ternary
membranes into a liquid-disordered and a liquid-ordered domain. With
all-atom (AA) models, however, phase separation is much harder to
achieve due to the slow underlying dynamics. To remedy this problem,
here, we apply the virtual site (VS) hybrid method on a ternary membrane
composed of saturated lipids, unsaturated lipids, and cholesterol
to investigate the phase separation. The VS scheme couples the two
membrane leaflets at CG and AA resolution. We found that the rapid
phase separation reached by the CG leaflet can accelerate and guide
this process in the AA leaflet.
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Affiliation(s)
- Yang Liu
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747AG, The Netherlands
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27
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Kubincová A, Riniker S, Hünenberger PH. Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme. J Chem Phys 2021; 155:094107. [PMID: 34496576 DOI: 10.1063/5.0057384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new approach termed Adaptive Solvent-Scaling (AdSoS) is introduced for performing simulations of a solute embedded in a fine-grained (FG) solvent region itself surrounded by a coarse-grained (CG) solvent region, with a continuous FG ↔ CG switching of the solvent resolution across a buffer layer. Instead of relying on a distinct CG solvent model, the AdSoS scheme is based on CG models defined by a dimensional scaling of the FG solvent by a factor s, accompanied by an s-dependent modulation of the atomic masses and interaction parameters. The latter changes are designed to achieve an isomorphism between the dynamics of the FG and CG models, and to preserve the dispersive and dielectric solvation properties of the solvent with respect to a solute at FG resolution. This scaling approach offers a number of advantages compared to traditional coarse-graining: (i) the CG parameters are immediately related to those of the FG model (no need to parameterize a distinct CG model); (ii) nearly ideal mixing is expected for CG variants with similar s-values (ideal mixing holding in the limit of identical s-values); (iii) the solvent relaxation timescales should be preserved (no dynamical acceleration typical for coarse-graining); (iv) the graining level NG (number of FG molecules represented by one CG molecule) can be chosen arbitrarily (in particular, NG = s3 is not necessarily an integer); and (v) in an adaptive-resolution scheme, this level can be varied continuously as a function of the position (without requiring a bundling mechanism), and this variation occurs at a constant number of particles per molecule (no occurrence of fractional degrees of freedom in the buffer layer). By construction, the AdSoS scheme minimizes the thermodynamic mismatch between the different regions of the adaptive-resolution system, leading to a nearly homogeneous scaled solvent density s3ρ. Residual density artifacts in and at the surface of the boundary layer can easily be corrected by means of a grid-based biasing potential constructed in a preliminary pure-solvent simulation. This article introduces the AdSoS scheme and provides an initial application to pure atomic liquids (no solute) with Lennard-Jones plus Coulomb interactions in a slab geometry.
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Affiliation(s)
- Alžbeta Kubincová
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
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28
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Li F, Korotkin I, Farafonov V, Karabasov SA. Lateral migration of peptides in transversely sheared flows in water: An atomistic-scale-resolving simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Zhang Z, Krajniak J, Ganesan V. A Multiscale Simulation Study of Influence of Morphology on Ion Transport in Block Copolymeric Ionic Liquids. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zidan Zhang
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jakub Krajniak
- Independent researcher, os. Kosmonautow 13/56, 61-631 Poznan, Poland
| | - Venkat Ganesan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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30
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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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31
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Klein R, Ebrahimi Viand R, Höfling F, Delle Site L. Nonequilibrium Induced by Reservoirs: Physico‐Mathematical Models and Numerical Tests. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Rupert Klein
- Institute of Mathematics Freie Universität Berlin Arnimallee 6 14195 Berlin Germany
| | - Roya Ebrahimi Viand
- Institute of Mathematics Freie Universität Berlin Arnimallee 6 14195 Berlin Germany
| | - Felix Höfling
- Institute of Mathematics Freie Universität Berlin Arnimallee 6 14195 Berlin Germany
- Division of Parallel and Distributed Computing Zuse Institute Berlin Takustr. 7 14195 Berlin Germany
| | - Luigi Delle Site
- Institute of Mathematics Freie Universität Berlin Arnimallee 6 14195 Berlin Germany
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32
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Baptista LA, Dutta RC, Sevilla M, Heidari M, Potestio R, Kremer K, Cortes-Huerto R. Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:184003. [PMID: 33690194 DOI: 10.1088/1361-648x/abed1d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
In the Hamiltonian adaptive resolution simulation method (H-AdResS) it is possible to simulate coexisting atomistic (AT) and ideal gas representations of a physical system that belong to different subdomains within the simulation box. The Hamiltonian includes a field that bridges both models by smoothly switching on (off) the intermolecular potential as particles enter (leave) the AT region. In practice, external one-body forces are calculated and applied to enforce a reference density throughout the simulation box, and the resulting external potential adds up to the Hamiltonian. This procedure suggests an apparent dependence of the final Hamiltonian on the system's thermodynamic state that challenges the method's statistical mechanics consistency. In this paper, we explicitly include an external potential that depends on the switching function. Hence, we build a grand canonical potential for this inhomogeneous system to find the equivalence between H-AdResS and density functional theory (DFT). We thus verify that the external potential inducing a constant density profile is equal to the system's excess chemical potential. Given DFT's one-to-one correspondence between external potential and equilibrium density, we find that a Hamiltonian description of the system is compatible with the numerical implementation based on enforcing the reference density across the simulation box. In the second part of the manuscript, we focus on assessing our approach's convergence and computing efficiency concerning various model parameters, including sample size and solute concentrations. To this aim, we compute the excess chemical potential of water, aqueous urea solutions and Lennard-Jones (LJ) mixtures. The results' convergence and accuracy are convincing in all cases, thus emphasising the method's robustness and capabilities.
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Affiliation(s)
- L A Baptista
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - R C Dutta
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - M Sevilla
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - M Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - R Potestio
- Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
| | - K Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - R Cortes-Huerto
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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33
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Zhu W, Zhang J, Wang J, Li W, Wang W. Enhanced sampling method with coarse graining of conformational space. Phys Rev E 2021; 103:032404. [PMID: 33862709 DOI: 10.1103/physreve.103.032404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 02/17/2021] [Indexed: 11/07/2022]
Abstract
The sampling of conformations in the molecular simulations for systems with complicated free energy landscapes is always difficult. Here, we report a method for enhanced sampling based on the coarse-graining of conformational space. In this method, the locally converged region of the conformational space is coarse-grained with its population characterized by the related average residence time and visiting number, and at the same time, the direct simulations inside it are eliminated. The detailed balance is satisfied by updating the visiting number and generating outgoing trajectories of this region. This kind of coarse-graining operation can be further carried out by merging all the neighboring regions which are already converged together. The global equilibrium is achieved when the local equilibrated regions cover all the interested areas of the landscape. We tested the method by applying it to two model potentials and one protein system with multiple-basin energy landscapes. The sampling efficiency is found to be enhanced by more than three orders of magnitude compared to conventional molecular simulations, and are comparable with other widely used enhanced sampling methods. In addition, the kinetic information can also be well captured. All these results demonstrate that our method can help to solve the sampling problems efficiently and precisely without applying high temperatures or biasing potentials.
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Affiliation(s)
- Wentao Zhu
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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34
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Sweere AJM, Patham B, Sugur V, Handgraaf J, Rodgers P. A Multiscale Approach for Estimating Permeability and Migration of Large Permeants through Poly(Phenylene Ether). MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202000070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Bhaskar Patham
- SABIC Research and Technology Private Limited SABIC Technology Center Bangalore 562125 India
| | - Vijayakumar Sugur
- SABIC Research and Technology Private Limited SABIC Technology Center Bangalore 562125 India
| | | | - Patrick Rodgers
- SABIC Global Product Stewardship SABIC Technology Center Houston TX 77042 USA
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35
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Gholami A, Höfling F, Klein R, Delle Site L. Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000303] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Abbas Gholami
- Freie Universität Berlin Institute of Mathematics Arnimallee 6 Berlin 14195 Germany
| | - Felix Höfling
- Freie Universität Berlin Institute of Mathematics Arnimallee 6 Berlin 14195 Germany
- Zuse Institute Berlin Takustr. 7 Berlin 14195 Germany
| | - Rupert Klein
- Freie Universität Berlin Institute of Mathematics Arnimallee 6 Berlin 14195 Germany
| | - Luigi Delle Site
- Freie Universität Berlin Institute of Mathematics Arnimallee 6 Berlin 14195 Germany
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36
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Chaimovich M, Chaimovich A. Relative Resolution: A Computationally Efficient Implementation in LAMMPS. J Chem Theory Comput 2021; 17:1045-1059. [PMID: 33512166 DOI: 10.1021/acs.jctc.0c01003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recently, a novel type of multiscale simulation, called Relative Resolution (RelRes), was introduced. In a single system, molecules switch their resolution in terms of their relative separation, with near neighbors interacting via fine-grained potentials yet far neighbors interacting via coarse-grained potentials; notably, these two potentials are analytically parametrized by a multipole approximation. This multiscale approach is consequently able to correctly retrieve across state space the structural and thermal, as well as static and dynamic, behavior of various nonpolar mixtures. Our current work focuses on the practical implementation of RelRes in LAMMPS, specifically for the commonly used Lennard-Jones potential. By examining various correlations and properties of several alkane liquids, including complex solutions of alternate cooligomers and block copolymers, we confirm the validity of this automated LAMMPS algorithm. Most importantly, we demonstrate that this RelRes implementation gains almost an order of magnitude in computational efficiency, as compared with conventional simulations. We thus recommend this novel LAMMPS algorithm for anyone studying systems governed by Lennard-Jones interactions.
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Affiliation(s)
- Mark Chaimovich
- Russian School of Mathematics, North Bethesda, Maryland 20852, United States
| | - Aviel Chaimovich
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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37
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Korshunova K, Carloni P. Ligand Affinities within the Open-Boundary Molecular Mechanics/Coarse-Grained Framework (I): Alchemical Transformations within the Hamiltonian Adaptive Resolution Scheme. J Phys Chem B 2021; 125:789-797. [PMID: 33443434 DOI: 10.1021/acs.jpcb.0c09805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Our recently developed Open-Boundary Molecular Mechanics/Coarse Grained (OB-MM/CG) framework predicts ligand poses in important pharmaceutical targets, such as G-protein Coupled Receptors, even when experimental structural information is lacking. The approach, which is based on GROMOS and AMBER force fields, allows for grand-canonical simulations of protein-ligand complexes by using the Hamiltonian Adaptive Resolution Scheme (H-AdResS) for the solvent. Here, we present a key step toward the estimation of ligand binding affinities for their targets within this approach. This is the implementation of the H-AdResS in the GROMACS code. The accuracy of our implementation is established by calculating hydration free energies of several molecules in water by means of alchemical transformations. The deviations of the GROMOS- and AMBER-based H-AdResS results from the reference fully atomistic simulations are smaller than the accuracy of the force field and/or they are in the range of the published results. Importantly, our predictions are in good agreement with experimental data. The current implementation paves the way to the use of the OB-MM/CG framework for the study of large biological systems.
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Affiliation(s)
- Ksenia Korshunova
- Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Paolo Carloni
- Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
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38
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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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39
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Liu X, Korotkin I, Rao Z, Karabasov S. A Thermostat‐Consistent Fully Coupled Molecular Dynamics—Generalized Fluctuating Hydrodynamics Model. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xinjian Liu
- School of Electrical and Power Engineering China University of Mining and Technology Xuzhou 221116 China
- The School of Engineering and Materials Science Queen Mary University of London Mile End Road London E1 4NS UK
| | - Ivan Korotkin
- Mathematical Sciences University of Southampton University Rd. Southampton SO17 1BJ UK
| | - Zhonghao Rao
- School of Electrical and Power Engineering China University of Mining and Technology Xuzhou 221116 China
| | - Sergey Karabasov
- The School of Engineering and Materials Science Queen Mary University of London Mile End Road London E1 4NS UK
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40
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Wu K, Xu S, Wan B, Xiu P, Zhou X. A novel multiscale scheme to accelerate atomistic simulations of bio-macromolecules by adaptively driving coarse-grained coordinates. J Chem Phys 2020; 152:114115. [PMID: 32199430 DOI: 10.1063/1.5135309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
All-atom molecular dynamics (MD) simulations of bio-macromolecules can yield relatively accurate results while suffering from the limitation of insufficient conformational sampling. On the other hand, the coarse-grained (CG) MD simulations efficiently accelerate conformational changes in biomolecules but lose atomistic details and accuracy. Here, we propose a novel multiscale simulation method called the adaptively driving multiscale simulation (ADMS)-it efficiently accelerates biomolecular dynamics by adaptively driving virtual CG atoms on the fly while maintaining the atomistic details and focusing on important conformations of the original system with irrelevant conformations rarely sampled. Herein, the "adaptive driving" is based on the short-time-averaging response of the system (i.e., an approximate free energy surface of the original system), without requiring the construction of the CG force field. We apply the ADMS to two peptides (deca-alanine and Ace-GGPGGG-Nme) and one small protein (HP35) as illustrations. The simulations show that the ADMS not only efficiently captures important conformational states of biomolecules and drives fast interstate transitions but also yields, although it might be in part, reliable protein folding pathways. Remarkably, a ∼100-ns explicit-solvent ADMS trajectory of HP35 with three CG atoms realizes folding and unfolding repeatedly and captures the important states comparable to those from a 398-µs standard all-atom MD simulation.
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Affiliation(s)
- Kai Wu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
| | - Shun Xu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Biao Wan
- Beijing Computational Science Research Center, Beijing 1100193, China
| | - Peng Xiu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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41
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Ebrahimi Viand R, Höfling F, Klein R, Delle Site L. Theory and simulation of open systems out of equilibrium. J Chem Phys 2020; 153:101102. [PMID: 32933284 DOI: 10.1063/5.0014065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations.
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Affiliation(s)
- R Ebrahimi Viand
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - F Höfling
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - R Klein
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - L Delle Site
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
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42
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Liu Y, Pezeshkian W, Barnoud J, de Vries AH, Marrink SJ. Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange. J Chem Theory Comput 2020; 16:5313-5322. [PMID: 32569465 PMCID: PMC7426904 DOI: 10.1021/acs.jctc.0c00429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The energy landscape of biomolecular
systems contains many local
minima that are separated by high energy barriers. Sampling this landscape
in molecular dynamics simulations is a challenging task and often
requires the use of enhanced sampling techniques. Here, we increase
the sampling efficiency by coupling the fine-grained (FG) GROMOS force
field to the coarse-grained (CG) Martini force field via the Hamiltonian
replica exchange method (HREM). We tested the efficiency of this procedure
using a lutein/octane system. In traditional simulations, cis–trans
transitions of lutein are barely observed due to the high energy barrier
separating these states. However, many of these transitions are sampled
with our HREM scheme. The proposed method offers new possibilities
for enhanced sampling of biomolecular conformations, making use of
CG models without compromising the accuracy of the FG model.
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Affiliation(s)
- Yang Liu
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen 9747 AG, The Netherlands
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43
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Fiorentini R, Kremer K, Potestio R. Ligand-protein interactions in lysozyme investigated through a dual-resolution model. Proteins 2020; 88:1351-1360. [PMID: 32525263 PMCID: PMC7497117 DOI: 10.1002/prot.25954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/04/2020] [Accepted: 05/16/2020] [Indexed: 12/12/2022]
Abstract
A fully atomistic (AT) modeling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and a posteriori analysis. This difficulty can be overcome with the use of multiresolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes, computationally expensive AT detail is crucial in the modeling of the active site in order to capture, for example, the chemically subtle process of ligand binding. In contrast, important yet more collective properties of the remainder of the protein can be reproduced with a coarser description. In the present work, we demonstrate the effectiveness of this approach through the calculation of the binding free energy of hen egg white lysozyme with the inhibitor di-N-acetylchitotriose. Particular attention is payed to the impact of the mapping, that is, the selection of AT and coarse-grained residues, on the binding free energy. It is shown that, in spite of small variations of the binding free energy with respect to the active site resolution, the separate contributions coming from different energetic terms (such as electrostatic and van der Waals interactions) manifest a stronger dependence on the mapping, thus pointing to the existence of an optimal level of intermediate resolution.
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Affiliation(s)
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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44
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Sweere AJM, Patham B, Sugur V, Handgraaf J. A Multiscale Approach for Estimating Permeability Properties of Polymers with Complex Aromatic Backbones: A Case Study on Diffusivity of Small Gas Molecules in Polyphenylene Ether. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Bhaskar Patham
- SABIC Research and Technology Private LimitedSABIC Technology Center Bangalore 562125 India
| | - Vijayakumar Sugur
- SABIC Research and Technology Private LimitedSABIC Technology Center Bangalore 562125 India
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45
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Hu H, Chen B, Zheng D, Huang G. Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods. PeerJ 2020; 8:e9241. [PMID: 32509471 PMCID: PMC7255342 DOI: 10.7717/peerj.9241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/03/2022] Open
Abstract
Background Research has shown that Poly-ADP-ribose polymerases 1 (PARP-1) is a potential therapeutic target in the clinical treatment of breast cancer. An increasing number of studies have focused on the development of highly selective inhibitors that target PARP-1 over PARP-2, its closest isoform, to mitigate potential side effects. However, due to the highly conserved and similar binding sites of PARP-1 and PARP-2, there is a huge challenge for the discovery and design of PARP-1 inhibitors. Recently, it was reported that a potent PARP-1 inhibitor named NMS-P118 exhibited greater selectivity to PARP-1 over PARP-2 compared with a previously reported drug (Niraparib). However, the mechanisms underlying the effect of this inhibitor remains unclear. Methods In the present study, classical molecular dynamics (MD) simulations and accelerated molecular dynamics (aMD) simulations combined with structural and energetic analysis were used to investigate the structural dynamics and selective mechanisms of PARP-1 and PARP-2 that are bound to NMS-P118 and Niraparib with distinct selectivity. Results The results from classical MD simulations indicated that the selectivity of inhibitors may be controlled by electrostatic interactions, which were mainly due to the residues of Gln-322, Ser-328, Glu-335, and Tyr-455 in helix αF. The energetic differences were corroborated by the results from aMD simulations. Conclusion This study provides new insights about how inhibitors specifically bind to PARP-1 over PARP-2, which may help facilitate the design of highly selective PARP-1 inhibitors in the future.
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Affiliation(s)
- Hongye Hu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Buran Chen
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Danni Zheng
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, China
| | - Guanli Huang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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46
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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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47
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Heidari M, Kremer K, Golestanian R, Potestio R, Cortes-Huerto R. Open-boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations. J Chem Phys 2020; 152:194104. [DOI: 10.1063/1.5143268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Maziar Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Raffaello Potestio
- Physics Department, University of Trento, Via Sommarive, 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
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48
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Gujt J, Zimmer P, Zysk F, Süß V, Felser C, Bauer M, Kühne TD. Water structure near the surface of Weyl semimetals as catalysts in photocatalytic proton reduction. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:034101. [PMID: 32478126 PMCID: PMC7228780 DOI: 10.1063/4.0000008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
In this work, second-generation Car-Parrinello-based mixed quantum-classical mechanics molecular dynamics simulations of small nanoparticles of NbP, NbAs, TaAs, and 1T-TaS2 in water are presented. The first three materials are topological Weyl semimetals, which were recently discovered to be active catalysts in photocatalytic water splitting. The aim of this research was to correlate potential differences in the water structure in the vicinity of the nanoparticle surface with the photocatalytic activity of these materials in light induced proton reduction. The results presented herein allow explaining the catalytic activity of these Weyl semimetals: the most active material, NbP, exhibits a particularly low water coordination near the surface of the nanoparticle, whereas for 1T-TaS2, with the lowest catalytic activity, the water structure at the surface is most ordered. In addition, the photocatalytic activity of several organic and metalorganic photosensitizers in the hydrogen evolution reaction was experimentally investigated with NbP as the proton reduction catalyst. Unexpectedly, the charge of the photosensitizer plays a decisive role for the photocatalytic performance.
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Affiliation(s)
- Jure Gujt
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Peter Zimmer
- Department of Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Frederik Zysk
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Vicky Süß
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Str. 40, D-01187 Dresden, Germany
| | - Claudia Felser
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Str. 40, D-01187 Dresden, Germany
| | - Matthias Bauer
- Department of Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
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49
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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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50
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Karmakar T, Piaggi PM, Parrinello M. Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential. J Chem Theory Comput 2019; 15:6923-6930. [DOI: 10.1021/acs.jctc.9b00795] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tarak Karmakar
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - Pablo M. Piaggi
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
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