Related papers: Dynamic coarse-graining of polymer systems using m…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
This study focuses on comparing the individual polymer chain dynamics in an entangled polymeric liquid under different shear and extension rates. Polymer chains under various shear rates and extension rates were simulated using a…
We poorly understand the macroscopic properties of complex fluids and of amorphous bodies in general. This is mainly due to the interplay between phenomena at different levels and length-scales. In particular, it is not necessarily true…
Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the…
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…
Fine-grained visual classification can be addressed by deep representation learning under supervision of manually pre-defined targets (e.g., one-hot or the Hadamard codes). Such target coding schemes are less flexible to model inter-class…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-Polybutadiene melts where each…
Gaussian splatting has become a popular representation for novel-view synthesis, exhibiting clear strengths in efficiency, photometric quality, and compositional edibility. Following its success, many works have extended Gaussians to 4D,…
Coarse-graining (CG) reduces molecular details to extend the time and length scales of molecular dynamics simulations to microseconds and micrometers. However, the CG approaches have long been limited by the difficulty of constructing both…
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…
In molecular dynamics and sampling of high dimensional Gibbs measures coarse-graining is an important technique to reduce the dimensionality of the problem. We will study and quantify the coarse-graining error between the coarse-grained…
The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…
Some basic questions about the hydrodynamical approach to relativistic heavy ion collisions are discussed aiming to clarify how far we can go with such an approach to extract useful information on the properties and dynamics of the QCD…
We introduce the spatial disorder-generalized Langevin equation (SD-GLE), a data-driven method for constructing coarse-grained (CG) dynamics in heterogeneous systems. Unlike conventional CG approaches that rely on a mean-field potential,…
This paper introduces a four-dimensional (4D) geometry-based stochastic model (GBSM) for polarized multiple-input multiple-output (MIMO) systems with moving scatterers. We propose a novel motion path model with high degrees of freedom based…
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving…