Related papers: Force-induced Unbinding Dynamics in a Multidimensi…
When two or more atoms bind to a solid surface, the substrate can mediate an interaction between them. In this paper, we use density-functional theory to quantify the substrate-mediated pair interaction between two adatoms on a…
The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
This paper presents a modeling framework to describe the driving mechanisms of cyclic failure in brittle and ductile materials, including cyclic plasticity and fatigue crack growth. A variational model is devised using the energetic…
The proteins involved in cells' mechanobiological processes have evolved specialized and surprising responses to applied forces. Biochemical transformations that show catch-to-slip switching and force-induced pathway switching serve…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Chemical reactions subjected to time-varying external forces cannot generally be described through a fixed bottleneck near the transition state barrier or dividing surface. A naive dividing surface attached to the instantaneous, but moving,…
The microscopic studies on nuclear fission require the evaluation of the potential energy surface as a function of the collective coordinates. A reasonable choice of constraints on multipole moments should be made to describe the topography…
Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…
We demonstrate that absorbing phase transitions in one dimension may be induced by the dynamics of a single site. As an example we consider a one-dimensional model of diffusing particles, where a single site at the boundary evolves…
Surface-active agents (surfactants) release potential energy as they migrate from one of two adjacent fluids onto their fluid-fluid interface, a process that profoundly impacts the system's energy and entropy householding. The continuum…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
In various cellular processes, biofilaments like F-actin and F-tubulin are able to exploit chemical energy associated to polymerization to perform mechanical work against an external load. The force-velocity relationship quantitatively…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
We present a simple time dependent model for the excitation of a nucleon from a bound state to a continuum resonant state in a neutron-core complex potential which acts as a final state interaction. The final state is described by an…