Related papers: Protein Unfolding and the Diffusion Collision Mode…

A new model is proposed for fusion mechanisms of massive nuclear systems where so-called fusion hindrance exists. The model describes two-body collision processes in an approaching phase and shape evolutions of an amalgamated system into…

We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…

Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…

Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

A diffusion model of the time evolution of loss rates caused by a step in collimator position is presented. It builds upon the model of Seidel (1994) and its assumptions: (1) constant diffusion rate within the range of the step and (2)…

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…

The important, and often dominant, role of tunneling in low temperature kinetics has resulted in numerous theoretical explorations into the methodology for predicting it. Nevertheless, there are still key aspects of the derivations that are…

Continuum mathematical models for collective cell motion normally involve reaction-diffusion equations, such as the Fisher-KPP equation, with a linear diffusion term to describe cell motility and a logistic term to describe cell…

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…

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…

Information on dissipation in the entrance channel of heavy-ion collisions is extracted by macroscopic reduction procedure of Time-Dependent Hartree-Fock theory. The method gives access to a fully microscopic description of the friction…

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…

Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying…

Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery.…

To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…

The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…

Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…

A feed-forward neural network is demonstrated to efficiently unfold the energy distribution of protons and alpha particles passing through passive material. This model-independent approach works with unbinned data and does not require…

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…