Related papers: Chromosome Compaction and Chromatin Stiffness Enha…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
We investigate the unfolding pathway of a cytosine-rich DNA hairpin structure via Molecular Dynamics simulations. Our results indicate a hidden complexity present in the unfolding process. W e show that this complex behavior arises due to…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Experiment, theory, and simulation are employed to understand the dispersion of colloidal particles in a periodic array of oscillating harmonic traps generated by optical tweezers. In the presence of trap oscillation, a non-monotonic and…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
We present a computational study of sliding between gold clusters and a highly oriented pyrolytic graphite substrate, a material system that exhibits ultra-low friction due to structural lubricity. By means of molecular dynamics, it is…
Complex colloidal cluster morphologies are desirable for the fabrication of advanced materials, such as photonic crystals and meta-materials, and can be formed through evaporation-driven packing. By coupling lattice Boltzmann and discrete…
We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…
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…
Dislocation climb mobilities, assuming vacancy bulk diffusion, are derived and implemented in dislocation dynamics simulations to study the coarsening of vacancy prismatic loops in fcc metals. When loops cannot glide, the comparison of the…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
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…
Extreme deformation of soft matter is central to our understanding of the effects of shock, fracture, and phase change in a variety of systems. Yet, despite, the increasing interest in this area, far-from-equilibrium behaviours of soft…
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
We analyse high resolution slip rate data obtained during dynamic shear rupture experiments by Berman et al. (2020). We use an inverse method to extract the details of strength evolution within the cohesive zone. The overall behaviour is…
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different. Here we study the dynamics of polymers in a viscous medium containing…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…