Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions
Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …
membraneless compartmentalization of the nucleus. Because chromatin compaction and …
Molecular simulation of liquid crystals
MP Allen - Molecular Physics, 2019 - Taylor & Francis
This article reviews recent progress in the computer simulation of liquid crystals at the
molecular level. It covers the use of simple rigid-body models of the constituent molecules …
molecular level. It covers the use of simple rigid-body models of the constituent molecules …
How to simulate patchy particles
L Rovigatti, J Russo, F Romano - The European Physical Journal E, 2018 - Springer
Patchy particles is the name given to a large class of systems of mesoscopic particles
characterized by a repulsive core and a discrete number of short-range and highly …
characterized by a repulsive core and a discrete number of short-range and highly …
Diffusion and spatial correlations in suspensions of swimming particles
PT Underhill, JP Hernandez-Ortiz, MD Graham - Physical review letters, 2008 - APS
Populations of swimming micro-organisms produce fluid motions that lead to dramatically
enhanced diffusion of tracer particles. Using simulations of suspensions of swimming …
enhanced diffusion of tracer particles. Using simulations of suspensions of swimming …
Dynamics of confined suspensions of swimming particles
JP Hernandez-Ortiz, PT Underhill… - Journal of Physics …, 2009 - iopscience.iop.org
Low Reynolds number direct simulations of large populations of hydrodynamically
interacting swimming particles confined between planar walls are performed. The results of …
interacting swimming particles confined between planar walls are performed. The results of …
Coarse-grained simulation of DNA using LAMMPS: An implementation of the oxDNA model and its applications
During the last decade coarse-grained nucleotide models have emerged that allow us to
study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a …
study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a …
Mechanisms of chromosome biorientation and bipolar spindle assembly analyzed by computational modeling
C Edelmaier, AR Lamson, ZR Gergely, S Ansari… - Elife, 2020 - elifesciences.org
The essential functions required for mitotic spindle assembly and chromosome biorientation
and segregation are not fully understood, despite extensive study. To illuminate the …
and segregation are not fully understood, despite extensive study. To illuminate the …
Field response and switching times in biaxial nematics
We study by means of virtual molecular dynamics computer experiments the response of a
bulk biaxial nematic to an applied external field and, in particular, the relative speed of …
bulk biaxial nematic to an applied external field and, in particular, the relative speed of …
Systematic bottom-up molecular coarse-graining via force and torque matching using anisotropic particles
HTL Nguyen, DM Huang - The Journal of Chemical Physics, 2022 - pubs.aip.org
We derive a systematic and general method for parameterizing coarse-grained molecular
models consisting of anisotropic particles from fine-grained (eg, all-atom) models for …
models consisting of anisotropic particles from fine-grained (eg, all-atom) models for …
Liquid crystal nanodroplets in solution
The aggregation of liquid crystal nanodroplets from a homogeneous solution is studied by
molecular dynamics simulations. The liquid crystal particles are modeled as elongated …
molecular dynamics simulations. The liquid crystal particles are modeled as elongated …