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Ledum M, Sen S, Li X, Carrer M, Feng Y, Cascella M, Bore SL. HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter. J Chem Theory Comput 2023; 19:2939-2952. [PMID: 37130290 DOI: 10.1021/acs.jctc.3c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics. The methodology is based on a tunable, grid-independent length-scale of coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence of energies and forces by grid refinement, also eliminating nonphysical force aliasing. Separating the time integration of fast modes associated with internal molecular motion from slow modes associated with their density fields, we enable the first time-reversible, energy-conserving hybrid particle-field simulations. HyMD comprises the optional use of explicit electrostatics, which, in this formalism, corresponds to the long-range potential in particle-mesh Ewald. We demonstrate the ability of HyMD to perform simulations in the microcanonical and canonical ensembles with a series of test cases, comprising lipid bilayers and vesicles, surfactant micelles, and polypeptide chains, comparing our results to established literature. An on-the-fly increase of the characteristic coarse-grain length significantly speeds up dynamics, accelerating self-diffusion and leading to expedited aggregation. Exploiting this acceleration, we find that the time scales involved in the self-assembly of polymeric structures can lie in the tens to hundreds of picoseconds instead of the multimicrosecond regime observed with comparable coarse-grained models.
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Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Samiran Sen
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Xinmeng Li
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Manuel Carrer
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Yu Feng
- Berkeley Center for Cosmological Physics and Department of Physics, University of California, Berkeley, California 94720, United States
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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Sen S, Ledum M, Bore SL, Cascella M. Soft Matter under Pressure: Pushing Particle-Field Molecular Dynamics to the Isobaric Ensemble. J Chem Inf Model 2023; 63:2207-2217. [PMID: 36976890 PMCID: PMC10091448 DOI: 10.1021/acs.jcim.3c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 03/29/2023]
Abstract
Hamiltonian hybrid particle-field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by taking into account the intrinsic spread of the particles in space, which naturally leads to a direct anisotropy in the pressure tensor. The anisotropic contribution is crucial for reliably describing the physics of systems under pressure, as demonstrated by a series of tests on analytical and monatomic model systems as well as realistic water/lipid biphasic systems. Using Bayesian optimization, we parametrize the field interactions of phospholipids to reproduce the structural properties of their lamellar phases, including area per lipid, and local density profiles. The resulting model excels in providing pressure profiles in qualitative agreement with all-atom modeling, and surface tension and area compressibility in quantitative agreement with experimental values, indicating the correct description of long-wavelength undulations in large membranes. Finally, we demonstrate that the model is capable of reproducing the formation of lipid droplets inside a lipid bilayer.
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Affiliation(s)
- Samiran Sen
- Hylleraas Centre for Quantum
Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, 0315 Oslo, Norway
| | - Morten Ledum
- Hylleraas Centre for Quantum
Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, 0315 Oslo, Norway
| | - Sigbjørn Løland Bore
- Hylleraas Centre for Quantum
Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, 0315 Oslo, Norway
| | - Michele Cascella
- Hylleraas Centre for Quantum
Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, 0315 Oslo, Norway
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Revelas CJ, Sgouros AP, Lakkas AT, Theodorou DN. Addressing Nanocomposite Systems via 3D-SCFT: Assessment of Smearing Approximation and Irregular Grafting Distributions. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Constantinos J. Revelas
- School of Chemical Engineering, National Technical University of Athens (NTUA), GR-15780 Athens, Greece
| | - Aristotelis P. Sgouros
- School of Chemical Engineering, National Technical University of Athens (NTUA), GR-15780 Athens, Greece
| | - Apostolos T. Lakkas
- School of Chemical Engineering, National Technical University of Athens (NTUA), GR-15780 Athens, Greece
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens (NTUA), GR-15780 Athens, Greece
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Wu Z, Müller-Plathe F. Slip-Spring Hybrid Particle-Field Molecular Dynamics for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example. J Chem Theory Comput 2022; 18:3814-3828. [PMID: 35617016 DOI: 10.1021/acs.jctc.2c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The topology of chains significantly modifies the dynamical properties of polymer melts. Here, we extend a recently developed efficient simulation method, namely the slip-spring hybrid particle-field (SS-hPF) model, to study the structural and dynamical properties of branched polymer melts over large spatial-temporal scales. In the coarse-grained SS-hPF simulation of polymers, the bonded potentials are derived by iterative Boltzmann inversion from the underlying fine-grained model. The nonbonded potentials are computed from a density functional field instead of pairwise interactions used in standard molecular dynamics simulations, which increases the computational efficiency by a factor of 10-20. The entangled dynamics is lost due to the soft-core nature of density functional field interactions. It is recovered by a multichain slip-spring model that is rigorously parametrized from existing experimental or simulation data. To quantitatively predict the relaxation and diffusion of branched polymers, which are dominated by arm retraction rather than chain reptation, the slip-spring algorithm is augmented to improve the polymer dynamics near the branch point. Multiple dynamical observables, e.g., diffusion coefficients, arm relaxations, and tube survival probabilities, are characterized in an example coarse-grained model of symmetric and asymmetric star-shaped polystyrene melts. Consistent dynamical behaviors are identified and compared with theoretical predictions. With a single rescaling factor, the prediction of diffusion coefficients agrees well with the available experimental measurements. In this work, an efficient approach is provided to build chemistry-specific coarse-grained models for predicting the dynamics of branched polymers.
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Affiliation(s)
- Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
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Razavilar N, Hanna G. Molecular‐Level Insights into the Diffusion of a Hydrophobic Drug in a Disordered Block Copolymer Micelle by Molecular Dynamics Simulation. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202100060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Negin Razavilar
- Department of Chemistry University of Alberta 11227 Saskatchewan Drive Edmonton Alberta T6G 2G2 Canada
| | - Gabriel Hanna
- Department of Chemistry University of Alberta 11227 Saskatchewan Drive Edmonton Alberta T6G 2G2 Canada
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RuSseL: A Self-Consistent Field Theory Code for Inhomogeneous Polymer Interphases. COMPUTATION 2021. [DOI: 10.3390/computation9050057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this article, we publish the one-dimensional version of our in-house code, RuSseL, which has been developed to address polymeric interfaces through Self-Consistent Field calculations. RuSseL can be used for a wide variety of systems in planar and spherical geometries, such as free films, cavities, adsorbed polymer films, polymer-grafted surfaces, and nanoparticles in melt and vacuum phases. The code includes a wide variety of functional potentials for the description of solid–polymer interactions, allowing the user to tune the density profiles and the degree of wetting by the polymer melt. Based on the solution of the Edwards diffusion equation, the equilibrium structural properties and thermodynamics of polymer melts in contact with solid or gas surfaces can be described. We have extended the formulation of Schmid to investigate systems comprising polymer chains, which are chemically grafted on the solid surfaces. We present important details concerning the iterative scheme required to equilibrate the self-consistent field and provide a thorough description of the code. This article will serve as a technical reference for our works addressing one-dimensional polymer interphases with Self-Consistent Field theory. It has been prepared as a guide to anyone who wishes to reproduce our calculations. To this end, we discuss the current possibilities of the code, its performance, and some thoughts for future extensions.
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Zong J, Meng D. Field-accelerated Monte Carlo simulations in the canonical and isothermal–isobaric ensembles. J Chem Phys 2020; 153:144104. [DOI: 10.1063/5.0013627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jing Zong
- Dave C. Swalm School of Chemical Engineering, Mississippi State University, Starkville, Mississippi 39762, USA
| | - Dong Meng
- Dave C. Swalm School of Chemical Engineering, Mississippi State University, Starkville, Mississippi 39762, USA
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Bore SL, Cascella M. Hamiltonian and alias-free hybrid particle–field molecular dynamics. J Chem Phys 2020; 153:094106. [DOI: 10.1063/5.0020733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern 0315, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern 0315, Oslo, Norway
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Carrer M, Škrbić T, Bore SL, Milano G, Cascella M, Giacometti A. Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents? J Phys Chem B 2020; 124:6448-6458. [PMID: 32618191 PMCID: PMC8009519 DOI: 10.1021/acs.jpcb.0c04842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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We investigate the
self-assembly process of a surfactant with inverted
polarity in water and cyclohexane using both all-atom and coarse-grained
hybrid particle-field molecular dynamics simulations. Unlike conventional
surfactants, the molecule under study, proposed in a recent experiment,
is formed by a rigid and compact hydrophobic adamantane moiety, and
a long and floppy triethylene glycol tail. In water, we report the
formation of stable inverted micelles with the adamantane heads grouping
together into a hydrophobic core and the tails forming hydrogen bonds
with water. By contrast, microsecond simulations do not provide evidence
of stable micelle formation in cyclohexane. Validating the computational
results by comparison with experimental diffusion constant and small-angle
X-ray scattering intensity, we show that at laboratory thermodynamic
conditions the mixture resides in the supercritical region of the
phase diagram, where aggregated and free surfactant states coexist
in solution. Our simulations also provide indications as to how to
escape this region to produce thermodynamically stable micellar aggregates.
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Affiliation(s)
- Manuel Carrer
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Tatjana Škrbić
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, United States.,Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia,Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, 992-8510 Yamagata-ken, Japan.,Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia,Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.,European Centre for Living Technology (ECLT) Ca' Bottacin, 3911 Dorsoduro, Calle Crosera, 30123 Venice, Italy
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Ledum M, Løland Bore S, Cascella M. Automated determination of hybrid particle-field parameters by machine learning. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1785571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Morten Ledum
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
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