Related papers: Multiple barriers in forced rupture of protein com…
Colliding heavy nuclear systems in the deep-inelastic regime may undergo partitioning into multiple fragments when fusion can not be achieved. While multiple breakups are common at Fermi energy, they are rather exotic in the deep-inelastic…
Using the molecular dynamics method, we examine a discrete deterministic model for the motion of spherical particles in three-dimensional space. The model takes into account multiparticle collisions in arbitrary forms. Using fractional…
We consider the ground states of binary atomic boson-boson and fermion-fermion mixtures confined in one-dimensional box potentials by simulating the systems using few-body models with delta-function interactions and many-body models with…
A potential model to describe the total cross section of nuclear fusion reactions at low energies is proposed. It is shown that within an approach with a simple, single barrier potential a satisfactory description of data is hindered, while…
The multinucleon transfer reactions near barrier energies has been investigated with a multistep model based on the dinuclear system (DNS) concept, in which the capture of two colliding nuclei, the transfer dynamics and the de-excitation…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
The strength of a simple soft bond under constant loading rate is studied theoretically. We find a scaling regime where rebinding is negligible and the rupture force of the bond scales as $const. + (\ln (kv))^{2/3}$, where $kv$ is the…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
We study the failure properties of fiber bundles when continuous rupture goes on due to the application of external load on the bundles. We take the two extreme models: equal load sharing model (democratic fiber bundles) and local load…
The dependence of fission barriers on the excitation energy of the compound nucleus impacts the survival probability of superheavy nuclei synthesized in heavy-ion fusion reactions. In this work, we investigate the isentropic fission…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Fluids confined to quasi-one-dimensional channels exhibit a dynamic crossover from single file diffusion to normal diffusion as the channel becomes wide enough for particles to hop past each other. In the crossover regime, where hopping…
Assessing the structural properties of large proteins is important to gain an understanding of their function in, e.g., biological systems or biomedical applications. We propose a method to examine the mechanical properties of proteins…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
We comprehensively study external forcing-driven dynamical structure formation in a binary dusty plasma mixture. Using two-dimensional driven-dissipative molecular dynamics simulations, we demonstrate phase segregation into bands and lanes…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
Dynamic rupture propagation along an interface between two different elastic solids under shear dominated loading is studied numerically by a 2-D lattice particle model (LPM). The configuration of the lattice particle model consists of two…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
The thermal activation process by which a system passes from one local energy minimum to another is a recurring motif in physics, chemistry, and biology. For instance, biopolymer chains are typically modeled in terms of energy landscapes,…