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We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…

Chemical Physics · Physics 2009-11-07 Gerhard Hummer , Ioannis G. Kevrekidis

We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…

Chemical Physics · Physics 2018-08-15 Linfeng Zhang , Jiequn Han , Han Wang , Roberto Car , Weinan E

The combination of high-dimensionality and disparity of time scales encountered in many problems in computational physics has motivated the development of coarse-grained (CG) models. In this paper, we advocate the paradigm of data-driven…

Computational Physics · Physics 2018-03-05 L. Felsberger , P. S. Koutsourelakis

It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…

Computational Physics · Physics 2014-07-28 Hao Zhang , F. Xavier Trias , Assensi Oliva , Dongmin Yang , Yuanqiang Tan , Shi Shu , Yong Sheng

The rheology of cohesive granular materials, under a constant pressure condition, is studied using molecular dynamics simulations. Depending on the shear rate, pressure, and interparticle cohesiveness, the system exhibits four distinctive…

Soft Condensed Matter · Physics 2018-09-26 Yuta Yamaguchi , Satoshi Takada , Takahiro Hatano

Semi-analytical methods, based on Eulerian perturbation theory, are a promising tool to follow the time evolution of cosmological perturbations at small redshifts and at mildly nonlinear scales. All these schemes are based on two…

Cosmology and Nongalactic Astrophysics · Physics 2015-05-30 Massimo Pietroni , Gianpiero Mangano , Ninetta Saviano , Matteo Viel

First, a meshless simulation method is presented for multiphase fluid-particle flows with a two-way coupled Smoothed Particle Hydrodynamics (SPH) for the fluid and the Discrete Element Method (DEM) for the solid phase. The unresolved fluid…

Fluid Dynamics · Physics 2014-02-28 Martin Robinson , Stefan Luding , Marco Ramaioli

The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on…

Statistical Mechanics · Physics 2009-11-13 B. M. Mognetti , P. Virnau , L. Yelash , W. Paul , K. Binder , M. Mueller , L. G. MacDowell

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…

Chemical Physics · Physics 2018-01-17 Anton V. Sinitskiy , Gregory A. Voth

We present an ``equation-free'' multiscale approach to the simulation of unsteady diffusion in a random medium. The diffusivity of the medium is modeled as a random field with short correlation length, and the governing equations are cast…

Numerical Analysis · Mathematics 2007-05-23 Dongbin Xiu , Ioannis Kevrekidis

A generalized boundary integral method is developed to investigate the rheology of multiple emulsions with orderly structures up to n layers and up to mi droplets in the i-th layer in microchannels with various geometries. Recently, as fine…

Soft Condensed Matter · Physics 2013-02-26 Jingtao Wang , Jinxia Liu , Junjie Han , Jing Guan

We introduce a system of shallow water-type equations to model laboratory experiments of particle-laden flows. We explore homogeneous liquid-solid suspensions of fine, non-cohesive, monodisperse glass beads which propagate as an equivalent…

Fluid Dynamics · Physics 2025-02-11 Andrea Bondesan , Laurence Girolami , François James , Loïc Rousseau

Granular column collapse is a simple but important problem to the granular material community, due to its links to dynamics of natural hazards, such as landslides and pyroclastic flows, and many industrial situations, as well as its…

Soft Condensed Matter · Physics 2025-01-10 Teng Man , Herbert E. Huppert , Sergio Andres Galindo-Torres

Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…

Soft Condensed Matter · Physics 2018-12-27 Tristan Bereau , Joseph F. Rudzinski

This work explores the manner in which classical phase space distribution functions converge to the microcanonical distribution. We first prove a theorem about the lack of convergence, then define a generalization of the coarse-graining…

Statistical Mechanics · Physics 2024-08-26 Casey O. Barkan

Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…

Soft Condensed Matter · Physics 2007-05-23 Roland Faller

This work utilizes soft-particle discrete element simulations to examine the rheology of steady two-dimensional granular flows with reference to a unidirectional shear flow, which has been extensively employed for validating the local…

Soft Condensed Matter · Physics 2018-06-13 Ashish Bhateja , Devang V. Khakhar

We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…

Statistical Mechanics · Physics 2023-07-12 Marltan O. Wilson , David M. Huang

Numerical simulations provide key insights into many physical, real-world problems. However, while these simulations are solved on a full 3D domain, most analysis only require a reduced set of metrics (e.g. plane-level concentrations). This…

Computational Physics · Physics 2025-11-27 Tingkai Xue , Chin Chun Ooi , Zhengwei Ge , Fong Yew Leong , Hongying Li , Chang Wei Kang

We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of…

Soft Condensed Matter · Physics 2020-09-16 Thomas Heinemann , YounJoon Jung