Related papers: A consistency study of coarse-grained dynamical ch…
Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics governing an entire family of free-energy landscapes,…
A computational tool for coarse-graining nonlinear systems of ordinary differential equations in time is discussed. Three illustrative model examples are worked out that demonstrate the range of capability of the method. This includes the…
We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a quasi-equilibrium approximation of the particle distribution function, the model closely captures important analytical properties of the…
It is known that a finite-size homogeneous granular fluid develops an hydrodynamic-like instability when dissipation crosses a threshold value. This instability is analyzed in terms of modified hydrodynamic equations: first, a source term…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Coarse-graining is central to reducing dimensionality in molecular dynamics, and is typically characterized by a mapping which projects the full state of the system to a smaller class of variables. While extensive literature has been…
Smoothed Dissipative Particle Dynamics (SDPD) is a mesoscopic method which allows to select the level of resolution at which a fluid is simulated. In this work, we study the consistency of the resulting thermodynamic properties as a…
The study of granular crystals, metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics,…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Granular materials are involved in most industrial and environmental processes, as well as many civil engineering applications. Although significant advances have been made in understanding the statics and dynamics of cohesionless grains…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…
A Chain of Springs and Masses (CSM) model is used in the interpretation of molecular dynamics (MD) simulations of movement of atoms in orientated FCC crystals. A force of dynamic origin is found that is perpendicular to the direction of the…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Mesoscale phenomena -- involving a level of description between the finest atomistic scale and the macroscopic continuum -- can be studied by a variation on the usual atomistic-level molecular dynamics (MD) simulation technique. In…
We study an atomistic model that describes the microscopic formation of material voids inside elastically stressed solids under an additional curvature regularization at the discrete level. Using a discrete-to-continuum analysis, by means…
In many far-from-equilibrium biological systems, energy injected by irreversible processes at microscopic scales propagates to larger scales to fulfill important biological functions. But given dissipative dynamics at the microscale, how…
Many approaches of coarse-graining have been developed under the names of Cosserat theory or polar-fluid theory, for those materials in which some component elements undergo non-affine deformations, such as elastic materials with inclusions…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
A kinetic model for granular mixtures is considered to study three different non-equilibrium situations. The model is based on the equivalence between a gas of elastic hard spheres subjected to a drag force proportional to the particle…