Related papers: Simulating the Entropic Collapse of Coarse-Grained…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase…
The role of plastic deformation in the high-pressure compaction of granular material is investigated using bonded particle model simulations. Grains are discretized into a set of computational particles connected by pairwise bonds. Bonds…
The dynamics of structural relaxation in a model polymer glass subject to spatially-homogeneous, time-periodic shear deformation is investigated using molecular dynamics simulations. We study a coarse-grained bead-spring model of short…
We present simulations of causal dynamical collapse models of field theories on a 1+1 null lattice. We use our simulations to compare and contrast two possible interpretations of the models, one in which the field values are real and the…
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavour to match any…
Due to the complex interplay between surface adsorption and hydrodynamic interactions, representative microscopic mechanisms of colloidal membrane fouling are still not well understood. Numerical simulations overcome experimental…
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…
We simulate a densely jammed, athermal assembly of repulsive soft particles immersed in a solvent. Starting from an initial condition corresponding to a quench from a high temperature, we find non-trivial slow dynamics driven by a gradual…
The structure and mechanical properties of a simple two-dimensional model of a cohesive powder are investigated by molecular dynamics simulations. Micromechanical ingredients involve elasticity, friction, a short range attraction and,…
Polymer-grafted nanoparticles are versatile building blocks that self-assemble into a rich diversity of mesostructures. Coarse-grained molecular simulations have commonly accompanied experiments by resolving structure formation pathways and…
In submerged sandy slopes, soil is frequently eroded as a combination of two main mechanisms: breaching, which refers to the retrogressive failure of a steep slope forming a turbidity current, and, instantaneous sliding wedges, known as…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
Dissociative electron attachment, that is, the cleavage of chemical bonds induced by low-energy electrons, is difficult to model with standard quantum-chemical methods because the involved anions are not bound but subject to autodetachment.…
Molecular dynamics simulations are used to investigate the effects of deformation on the segmental dynamics in an aging polymer glass. Individual particle trajectories are decomposed into a series of discontinuous hops, from which we obtain…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
We propose that the degree of sweeling of the 30nm chromatin fiber (a "measure" of its transcriptional activity) is mainly determined by the short-ranged electrostatical interaction between different sections of the "folded" DNA chain.…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
We examine the dynamics of two-dimensional colloidal systems using numerical simulations of a system with a drive applied to a thin region in the middle of the sample to produce a local shear. For a monodisperse colloidal assembly, we find…
Homopolymer chain with beads forming pairwise reversible bonds is a well-known model in polymer physics. We studied kinetics of homopolymer chain collapse, which was induced by pairwise reversible bonds formation. We compared kinetic…