Related papers: Simulating the Entropic Collapse of Coarse-Grained…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
We investigate the structure and dynamics of a hard colloid-star polymer mixture in the range of its arrested phase separation, where an incipient demixing transition is interfering with a nearby vitrification line, focusing on the protein…
This paper investigates the effect of initial volume fraction on the runout characteristics of collapse of granular columns on slopes in fluid. Two-dimensional sub-grain scale numerical simulations are performed to understand the flow…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
Compressing a porous, fluid-filled material will drive the interstitial fluid out of the pore space, as when squeezing water out of a kitchen sponge. Inversely, injecting fluid into a porous material can deform the solid structure, as when…
Using exact enumeration methods and Monte Carlo simulations we study the phase diagram relative to the conformational transitions of a two dimensional diblock copolymer. The polymer is made of two homogeneous strands of monomers of…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
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…
We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Simulation results are presented on the collapse of granular columns composed of rod-like particles. Columns can be stable and free-standing if either the friction coefficient is large enough, or the rods long enough. Destabilizing…
Although the behavior of entangled polymers in startup shear flows with constant shear rates has been thoroughly investigated, the response under creep has not been frequently considered. In this study, primitive chain network simulations,…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
We discuss recent models of chemical evolution in the developing and collapsing protostellar envelopes associated with low-mass star formation. In particular, the effects of depletion of gas-phase molecules onto grain surfaces is…
By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed…