Related papers: Unfolding Rates for the Diffusion-Collision Model
Molecular simulations have provided valuable insight into the microscopic mechanisms underlying homogeneous ice nucleation. While empirical models have been used extensively to study this phenomenon, simulations based on first-principles…
We compute profile likelihoods for a stochastic model of diffusive transport motivated by experimental observations of heat conduction in layered skin tissues. This process is modelled as a random walk in a layered one-dimensional material,…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
We concider, the blow-up solutions for a coupled reaction diffusion system with gradient terms. The main purpose is to understand whether the gradient terms effect the blow-up properties. We derive the upper and lower blow-up rate estimates…
Finite mixture models are fitted to spherical data. Kent distributions are used for the components of the mixture because they allow considerable flexibility. Previous work on such mixtures has used an approximate maximum likelihood…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…
In this study, the additional heat capacity which appear during the water dissociation of the proteins that are one of the soft materials, have been considered by the statistical mechanical methods. For this purpose, taking the electric…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is…
The microscopic approach of fission rates and neutron emission rates in compound nuclei have been applied to $^{258}$No and $^{286}$Cn. The microscopic framework is based on the finite-temperature Skyrme-Hartree-Fock+BCS calculations, in…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Demixing of binary fluids subjected to slow temperature ramps shows repeated waves of nucleation which arise as a consequence of the competition between generation of supersaturation by the temperature ramp and relaxation of supersaturation…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
The temperature-dependent diffusion coefficients of interstitial helium atom in $\alpha$-Ti are predicted using the transition state theory. The microscopic parameters in the pre-factor and activation energy of the impurity diffusion…
We study the identified particle ratios produced at mid-rapidity in heavy ion collisions, along with their correlations with the collision energy. We employ our earlier proposed Unified Statistical Thermal Freeze-out Model (USTFM), which…
The formation of clusters in supercooled liquids close to the glass transition temperature is described by rate equations in which the coefficients are determined on physical grounds rather than in terms of thermodynamic quantities such as…