Related papers: Receptor-ligand rebinding kinetics in confinement
We study the relaxation of an elastic string in a two dimensional pinning landscape using Langevin dynamics simulations. The relaxation of a line, initially flat, is characterized by a growing length, $L(t)$, separating the equilibrated…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We devise a method for predicting certain receptor-ligand binding behaviors, based on stochastic dynamical modelling. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform…
One great challenge of modeling granular systems lies in capturing the rheologic dependencies on scale. For example, there are marked differences between quasi-static, intermediate, and rapid flow regimes. In this study, we demonstrate that…
We present a single, unified, multi-scale model to study the attachment\detachment dynamics of two deforming, near spherical cells, coated with binding ligands and subject to a slow, homogeneous shear flow in a viscous fluid medium. The…
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…
The lateral diffusion and trapping of protein receptors within the postsynaptic membrane of a neuron plays a key role in determining the strength of synaptic connections and their regulation during learning and memory. In this paper we…
Diffusion with an incorporated resetting mechanism provides a reference framework for modeling a wide range of natural phenomena. Within this framework, the optimal resetting rate is a key quantity that arises from the optimization of the…
Detailed comparisons are reported between laboratory observations of electron-scale dissipation layers near a reconnecting X-line and direct two-dimensional full-particle simulations. Many experimental features of the electron layers, such…
Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using $\beta$-lactoglobulin fibrils as a model, that semiflexible…
The escape of the randomly accelerated undamped particle from the finite interval under action of stochastic resetting is studied. The motion of such a particle is described by the full Langevin equation and the particle is characterized by…
We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…
We investigate the mechanics of two asymmetric ribbons bound at one end and pulled apart at the other ends. We characterize the elastic junction near the bonding and conceptualize it as a bending boundary layer. While the size of this…
The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion (SALR) potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk.…
One of the promising frontiers of bioengineering is the controlled release of a therapeuticdrug from a vehicle across the skin (transdermal drug delivery). In order to study the complete process, a two-phase mathematical model describing…
We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound…
Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters. During the review period, a wide range of enhanced sampling…
Encounter-based models of diffusion provide a probabilistic framework for analyzing the effects of a partially absorbing reactive surface, in which the probability of absorption depends upon the amount of surface-particle contact time.…
Many biological tissues feature a heterogeneous network of fibers whose tensile and bending rigidity contribute substantially to these tissues' elastic properties. Rigidity percolation has emerged as a important paradigm for relating these…
Riboswitches, RNA elements found in the untranslated region, regulate gene expression by binding to target metaboloites with exquisite specificity. Binding of metabolites to the conserved aptamer domain allosterically alters the…