Related papers: Multiple barriers in forced rupture of protein com…
In cosmological first-order phase transitions, the microscopic interaction of the phase transition fronts with non-equilibrium plasma particles manifests itself macroscopically as friction forces. In general, it is a nontrivial problem to…
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
Quantum decay rates for barrier potentials driven by external stochastic and periodic forces in the strong damping regime are studied. Based on the recently derived quantum Smoluchowski equation [Phys. Rev. Lett. {\bf 87}, 086802 (2001)]…
A variety of phenomena connected with the formation of a dinuclear complex is observed in the heavy ion collisions at low energies. The dinuclear system model allows us to analyze the experimental data and to interpret them by comparison of…
Phase field models have emerged as a powerful and flexible framework for simulating complex interface-driven phenomena across a wide range of scientific and engineering applications. In fracture mechanics, the phase field…
Motivated by claims about the nature of the observed timescales in protein systems said to fold downhill, we have studied the finite, linear master equation which is a model of the downhill process. By solving for the system eigenvalues, we…
We investigate the mechanism of chain exchange in diblock copolymer micelles using two distinct yet complementary simulation techniques. First, enhanced sampling method is combined with coarse-grained molecular dynamics to compute a…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
This paper reports the force spectroscopy analysis of a polymer that translocates from one side of a membrane to the other side through an extended pore, pulled by a cantilever that moves with constant velocity against the damping and the…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
The rupture of the interface joining two materials under frictional contact controls their macroscopic sliding. Interface rupture dynamics depend markedly on the mechanical properties of the bulk materials that bound the frictional…
The standard setup for single-file diffusion is diffusing particles in one dimension which cannot overtake each other, where the dynamics of a tracer (tagged) particle is of main interest. In this article we generalise this system and…
Under an applied external load the global load-sharing fiber bundle model, with individual fiber strength thresholds sampled randomly from a probability distribution, will relax to an equilibrium state, or to complete bundle breakdown. The…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
Low-frequency molecular fluctuations in the translational nonequilibrium zone of one-dimensional strong shock waves are characterised for the first time in a kinetic collisional framework in the Mach number range $2\le M\le 10$. Our…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
The nucleus-nucleus potential is calculated in the frame work of the double folding model (DFM) to obtain the Coulomb barrier parameters (barrier position and height), starting from M3Y-Reid nucleon-nucleon interaction and realistic nuclear…