Related papers: Adaptive Resolution Force Probe Simulations: Coars…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
In a recent paper, J. Chem. Phys. 162, 214101 (2025), a novel approach for the rigidification of a molecular cluster was proposed, in which starting with an all-atom (AA) potential, a coarse-grained (CG) potential for the associated cluster…
Given that the physical properties of polymeric liquids extend on a wide range of lengthscales, it is computationally convenient to represent them by coarse-grained (CG) descriptions at various granularities to investigate local and global…
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics…
This paper presents a heterogeneous adaptive mesh refinement (AMR) framework for efficient simulation of moderately stiff reactive problems. This framework features an elaborate subcycling-in-time algorithm along with a specialized…
We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…
We present a high-fidelity three dimensional computational framework for simulating the bulk mechanical behavior of granular aggregates composed of deformable brittle grains. Departing from classical discrete element methods (DEM), our…
Coarse graining (CG) is an important task for efficient modeling and simulation of complex multi-scale systems, such as the conformational dynamics of biomolecules. This work presents a projection-based coarse-graining formalism for general…
We propose to couple a state-resolved rovibrational coarse-grain model to a stochastic particle method for simulating internal energy excitation and dissociation of a molecular gas. An existing coarse-grain model based on the NASA Ames ab…
This paper presents novel refinement sensors for the application to adaptive mesh and algorithm refinement (AMAR) with kinetic models, such as discrete velocity and lattice Boltzmann methods. While refinement criteria for AMAR based on…
Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…
The accuracy and efficiency of a coarse-grained (CG) force field are pivotal for high-precision molecular simulations of large systems with complex molecules. We present an automated mapping and optimization framework for molecular…
Implicit solvers present strong limitations when used on supercomputing facilities and in particular for adaptive mesh-refinement codes. We present a new method for implicit adaptive time-stepping on adaptive mesh refinement-grids. We…
An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…
Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
Pyrene-functional PMMAs were prepared via ATRP-controlled polymerization and click reaction, as efficient dispersing agents for the exfoliation of few-layered graphene sheets (GS) in easily processable low boiling point chloroform. In…
We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonical-like version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018 (2013)], to calculate the excess chemical potential, $\mu^{ex}$, of various liquids and…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…