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Many researchers have been encouraged to describe the dynamics of chromosomal loci in chromatin using the classical Rouse model of polymer dynamics by the agreement between the measured mean square displacement (MSD) versus time of…
Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains"…
Correlation of interacting particles is studied in their dynamics and localization in ideal and disordered lattice systems with the help of numerical tools. Both 1D and 2D systems are considered. In 1D lattices with long-range hopping,…
Dynamic fragmentation simulations are essential for predicting material response at high strain rates, yet explicit dynamic simulations that combine an extrinsic cohesive-zone model (CZM) with penalty-based contact often exhibit severe…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
The paper studies the relationship between diffraction and dynamics for uniformly discrete ergodic point processes in real spaces. This relationship takes the form of an isometric embedding of two L^2 spaces. Diffraction (or equivalently…
Gels in soft-matter systems are an important nonergodic state of matter. We study a colloid-polymer mixture which is quenched by increasing the polymer concentration, from a fluid to a gel. Using confocal microscopy, we study both the…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
We study spatial correlations and structure factors in a three-state stochastic lattice gas, consisting of holes and two oppositely ``charged'' species of particles, subject to an ``electric'' field at zero total charge. The dynamics…
Disclinations lines play a key role in many physical processes, from the fracture of materials to the formation of the early universe. Achieving versatile control over disclinations is key to developing novel electro-optical devices,…
By analytically solving some simple models of phase-ordering kinetics, we suggest a mechanism for the onset of non-equilibrium behaviour in colloid-polymer mixtures. These mixtures can function as models of atomic systems; their physics…
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…
The processes of Coulomb gas ordering in 3D layered system are studied by means of Brownian dynamics approach. It is found that at different densities of the carriers the 3D lattice of charges as well as new specific structures are possible…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
We extend a previous analysis [PRL {\bf 80}, 4693 (1998)] of breakdown of dynamical scale invariance in the coarsening of two-dimensional DLAs (diffusion-limited aggregates) as described by the Cahn-Hilliard equation. Existence of a second…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long distance regulatory interactions. The mechanistic basis…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Liquid crystal elastomers are cross-linked polymer networks covalently bonded with liquid crystal mesogens. In the nematic phase, due to strong coupling between mechanical strain and orientational order, these materials display…