Related papers: Chromosome Compaction and Chromatin Stiffness Enha…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
Sacrificial bonds and hidden length (SBHL) in structural molecules provide a mechanism for energy dissipation at the nanoscale. It is hypothesized that their presence leads to greater fracture toughness than what is observed in materials…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
The 2-step staggered (also called leap-frog) time discretisation of linear 2nd-order Hamiltonian systems (typically linear elastodynamics in a stress-velocity form) is extended for a 3-step staggered discretisation applicable for systems…
Bistability and snap-through instabilities are central to various mechanisms in nature and engineering, enabling rapid movement and large shape changes with minimal energy input. These phenomena are easily demonstrated by bending a piece of…
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$…
Excess pore pressure in granular--fluid mixtures can transiently suppress frictional contacts and dramatically enhance flow mobility, yet its evolution is commonly modeled using constant effective diffusivities. Here we show that the…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are…
We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential, and a sideways constant…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to…
We have studied the mobility of the folding catalyst, protein disulphide-isomerase (PDI), by molecular dynamics and by a rapid approach based on flexibility. We analysed our simulations using measures of backbone movement, relative…
Sliding along frictional interfaces separating dissimilar elastic materials is qualitatively different from sliding along interfaces separating identical materials due to the existence of an elastodynamic coupling between interfacial slip…
Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to…
In this work, we analyse the stick-slip motion of a soft elastomeric block on a smooth, hard surface under the application of shear, which is induced by a puller moving at a steady velocity. The frictional stress is generated by make-break…
The simulation of industrial processes involving cold compaction of powders allows for the optimization of the production of both traditional and advanced ceramics. The capabilities of a constitutive model previously proposed by the authors…
Using numerical simulations, we study the dynamical evolution of particles interacting via competing long-range repulsion and short-range attraction in two dimensions. The particles are compressed using a time-dependent quasi-one…
Elastic confinements are an important component of many biological systems and dictate the transport properties of suspended particles under flow. In this chapter, we review the Brownian motion of a particle moving in the vicinity of a…
Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is…