Related papers: Equilibrium and nonequilibrium effects in the coll…
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…
Nonequilibrium phenomena of the phase transitions are studied. It is shown that due to finite relaxation time of the particle distributions, the use of scalar background dependent distribution functions is inconsistent.This observation may…
We study the adsorption-desorption of fluid molecules on a solid substrate by introducing a schematic model in which the adsorption/desorption transition probabilities are given by irreversible kinetic constraints with a tunable violation…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
High molecular weight polymer solutions have a powerful tendency to deposit adsorbed layers when exposed to even mildly attractive surfaces. The equilibrium properties of these dense interfacial layers have been extensively studied…
Simulations show Gly$_{15}$, a polypeptide lacking any side-chains, can collapse in water. We assess the hydration thermodynamics in this collapse by calculating the hydration free energy at each of the end points of the reaction…
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…
Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding of a tube-like representation of a polypeptide chain gives rise to free energy landscapes that exhibit a small number of metastable minima…
The equilibrium phase behaviour of hard spheres with size polydispersity is studied theoretically. We solve numerically the exact phase equilibrium equations that result from accurate free energy expressions for the fluid and solid phases,…
The nonequilibrium phase transition in a system of diffusing, coagulating particles in the presence of a steady input and evaporation of particles is studied. The system undergoes a transition from a phase in which the average number of…
We study equilibrium states of a drop between flexible sheets clamped on both ends. Revisiting first the case of parallel sheets, we find multiple equilibria which we classify in a parameter space. In solution branching diagrams we identify…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
Models of adhesion of extended particles on linear and planar substrates are of interest in interpreting surface deposition in colloid, polymer, and certain biological systems. An introduction is presented to recent theoretical advances in…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…