Related papers: Size limits sensitivity in all kinetic schemes
We introduce a new measure of the structure of a liquid which is the softness of the mean-field potential developed by us earlier. We find that this softness is sensitive to small changes in the structure. We then study its correlation with…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Just like the weakly interacting QED can support non-perturbative phenomena, like atoms, so can the weak and Higgs interactions. Especially, there are strong field-theoretical arguments that only bound states can be the (quasi-)asymptotic…
Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of…
We simulate a model of repulsively interacting colloids on a commensurate two-dimensional triangular pinning substrate where the amount of heterogeneous motion that appears at melting can be controlled systematically by turning off a…
Sensitivity analysis is an effective tool for systematically identifying specific perturbations in parameters that have significant effects on the behavior of a given biosystem, at the scale investigated. In this work, using a…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
We revisit a classical continuum model for the diffusion of multiple species with size-exclusion constraint, which leads to a degenerate nonlinear cross-diffusion system. The purpose of this article is twofold: first, it aims at a…
The mean-field approximations of many-boson dynamics are known to be effective in many physical relevant situations. The mathematical justifications of such approximations rely generally on specific considerations which depend too much on…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
Facilitated spin models on random graphs provide an ideal microscopic realization of the mode-coupling theory of supercooled liquids: they undergo a purely dynamic glass transition with no thermodynamic singularity. In this paper we study…
We consider the dynamics of $N$ interacting bosons in three dimensions which are strongly confined in one or two directions. We analyze the two cases where the interaction potential $w$ is rescaled by either $N^{-1}w(\cdot)$ or…
We propose a model of mass-conserving heterogeneous nucleation to describe the dynamics of ligand-receptor binding in closed cellular compartments. When the ligand dissociation rate is small, competition among receptors for free ligands…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…
The membrane model is a Gaussian interface model with a Hamiltonian involving second derivatives of the interface height. We consider the model in dimension $\mathsf{d}\ge4$ under the influence of $\delta$-pinning of strength $\varepsilon$.…
Molecular dynamics is a powerful method for studying the behaviour of materials at high temperature. In practice, however, its effectiveness in representing real systems is limited by the accuracy of the forces, finite size effects,…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed…
Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior…