Thermodynamics of adaptive molecular resolution

Delgado‐Buscalioni, Rafael

doi:10.1098/rsta.2016.0152

Cited by 11 publications

(8 citation statements)

References 28 publications

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“…Many recent AdResS advances are addressing the computation of statistical mechanical quantities, e.g., entropy, free energy, chemical potential, which are needed for studying phase transitions 56–60 . The Hamiltonian formulation of AdResS 61 permits also the adaptive resolution Monte Carlo simulations 62 .…”

Section: Methodsmentioning

confidence: 99%

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Zavadlav

Podgornik

Praprotnik

2017

Sci Rep

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While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.

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Section: Methodsmentioning

confidence: 99%

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Zavadlav

Podgornik

Praprotnik

2017

Sci Rep

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“…The most efficient way to tackle such situations is using multiscale modeling approaches, in particular, concurrent multiscale methods, which couple fine‐ and CG resolutions at the same time in the simulation box, for example, refs. [6, 7, 98–117].…”

Section: Molecular Dynamics (Md) and (Particle‐based) Multiscale Simumentioning

confidence: 99%

Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications

Site

Praprotnik

Bell

et al. 2020

Advcd Theory and Sims

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This work is motivated by the goal of designing simulation software for technical devices that, at their functional core, rely on atomistic-scale processes embedded in a larger-scale fluid environment. The core of the problem is the conceptual and technical approach for coupling particle and continuum representations of a fluid. The state of the art for key aspects including physical modeling, mathematical formalization, computational implementation, and applications, is discussed and organized in a consistent picture across the relevant physical regimes.Key building blocks of the related developments that we will summarize and appraise in some detail below are i) finite volume FHD solvers following Bell, Donev, Garcia, Nonaka and colleagues [4] (see Section 2), ii) the "adaptive resolution simulation" (AdResS) approach that enables molecular dynamics simulations on limited size domains [5][6][7] (see Section 3), and iii) the recent mathematical formalization of open molecular systems by two of the authors [8] (see Section 4). In Section 5, we discuss scaling regimes and the rationale behind possible MD-FHD coupling strategies, finally, Section 6 is dedicated to the description of some representative examples, while Section 7 outlines future perspectives and summarizes our conclusions.

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“…Many attempts have been deployed so far in order to tackle this problem, and a number of concurrent hybrid approaches have been proposed to investigate a vast spectrum of physics problems, including soft matter and molecular fluids, fluctuating hydrodynamics, as well as both dilute and dense hydrodynamics. [1][2][3][4][5][6] In concurrent approaches, most of the physical domain is solved by employing a macroscopic (continuum) description, while only small selected portions are investigated through particle-based methods.…”

Section: Doi: 101002/adts201900250mentioning

confidence: 99%

A Multiresolution Mesoscale Approach for Microscale Hydrodynamics

Montessori

Tiribocchi

Lauricella

et al. 2020

Advcd Theory and Sims

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A new class of multiscale scheme is presented for micro‐hydrodynamic problems based on a dual representation of the fluid observables. The hybrid model is first tested against the classical flow between two parallel plates and then applied to a plug flow within a micrometer‐sized striction and a shear flow within a microcavity. Both cases demonstrate the capability of the multiscale approach to reproduce the correct macroscopic hydrodynamics also in the presence of refined grids (one and two levels), while retaining the correct thermal fluctuations, embedded in the multiparticle collision method. This provides the first step toward a novel class of fully mesoscale hybrid approaches able to capture the physics of fluids at the micro‐ and nanoscales whenever a continuum representation of the fluid falls short of providing the complete physical information, due to a lack of resolution and thermal fluctuations.

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Thermodynamics of adaptive molecular resolution

Cited by 11 publications

References 28 publications

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications

A Multiresolution Mesoscale Approach for Microscale Hydrodynamics

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