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Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Patterns forming spontaneously in extended, three-dimensional, dissipative systems are likely to excite several homogeneous soft modes ($\approx$ hydrodynamic modes) of the underlying physical system, much more than quasi one- and…
Nominal two-dimensional (2D) shear layers have been studied extensively, and their principal dynamics are well understood. In practical configurations, however, the behavior of such shear layers is affected by proximal surfaces. In this…
When liquid-crystal elastomers are prepared without any alignment, disordered polydomain structures emerge as the materials are cooled into the nematic phase. These polydomain structures have been attributed to quenched disorder in the…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
By means of the isoconfigurational method we calculate the change in the propensity for motion that the structure of a glass-forming system experiences during its relaxation dynamics. The relaxation of such a system has been demonstrated to…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
We extend the notions of multipole and subsystem symmetries to more general {\it spatially modulated} symmetries. We uncover two instances with exponential and (quasi)-periodic modulations, and provide simple microscopic models in one, two…
A multi-time extension of a density correlation function is introduced to reveal temporal information about dynamical heterogeneity in glass-forming liquids. We utilize a multi-time correlation function that is analogous to the higher-order…
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer…
We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above…
We construct the equations for the growth kinetics of an aging structural glass within mode-coupling theory through a non-stationary variant of the 3-density correlator defined in Phys. Rev. Lett. {\bf 97}, 195701 (2006). We solve a…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
Understanding thermal fluctuations yields insights into a wide range of behaviors in many-body systems. In this work, we analyze the dynamical adaptation of two-dimensional crystalline lattice system under harmonic interaction in response…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
We focus on mesoscopic dislocation patterning via a continuum dislocation dynamics theory (CDD) in three dimensions (3D). We study three distinct physically motivated dynamics which consistently lead to fractal formation in 3D with rather…
Recent research has provided a wealth of evidence highlighting the pivotal role of high-order interdependencies in supporting the information-processing capabilities of distributed complex systems. These findings may suggest that high-order…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…