Related papers: Protein Unfolding and the Diffusion Collision Mode…
Griffith's energetic criterion, or `energy balance', has for a century formed the basis for fracture mechanics; the energy flowing into a crack front is precisely balanced by the dissipation (fracture energy) at the front. If the crack…
The tunneling probability for a system modelling macroscopic quantum tunneling is computed. We consider an open quantum system with one degree of freedom consisting of a particle trapped in a cubic potential interacting with an environment…
The understanding of the fusion probability is of particular importance to reveal the mechanism of producing superheavy elements. We present a microscopic study of the compound nucleus formation by combining time-dependent density…
A fiber bundle model in $(1+1)$-dimensions for the breaking of fibrous composite matrix is introduced. The model consists of $N$ parallel fibers fixed in two plates. When one of the plates is pulled in the direction parallel to the fibers,…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
The fusion probability for the production of superheavy nuclei in cold fusion reactions was investigated and compared with recent experimental results for $^{48}$Ca, $^{50}$Ti, and $^{54}$Cr incident on a $^{208}$Pb target. Calculations…
The two-dimensional cage model for polymer motion is discussed with an emphasis on the effect of sideways motions, which cross the barriers imposed by the lattice. Using the Density Matrix Method as a solver of the Master Equation, the…
According to the 'old view', proteins fold along well-defined sequential pathways, whereas the 'new view' sees protein folding as a highly parallel stochastic process on funnel-shaped energy landscapes. We have analyzed parallel and…
Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been…
Motivated by the phenomenon of transport barriers in fusion plasma devices, we write a mathematical model of heat dispersion in a turbulent fluid with a transport barrier, properly idealized; in a scaling limit of the turbulence model with…
Employing a forward diffusion chain to gradually map the data to a noise distribution, diffusion-based generative models learn how to generate the data by inferring a reverse diffusion chain. However, this approach is slow and costly…
The photoluminescence in amorphous semiconductors decays according to power law $t^{-delta}$ at long times. The photoluminescence is controlled by dispersive transport of electrons. The latter is usually characterized by the power $alpha$…
Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop Proteina, a new large-scale flow-based protein backbone generator that utilizes…
When water is present in a medium with pore sizes in a range around 10nm the corresponding freezing point depression will cause long range broadening of a melting front. Describing the freezing-point depression by the Gibbs-Thomson equation…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
The diffusive motion of colloidal particles dispersed in a premelting solid is analyzed within the framework of irreversible thermodynamics. We determine the mass diffusion coefficient, thermal diffusion coefficient and Soret coefficient of…
Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function.…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…