Related papers: Unfolding Rates for the Diffusion-Collision Model
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
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 present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
Consider a particle diffusing in a confined volume which is divided into two equal regions. In one region the diffusion coefficient is twice the value of the diffusion coefficient in the other region. Will the particle spend equal…
A model investigating the role of geometry on the alpha dose rate of spent nuclear fuel has been developed. This novel approach utilises a new piecewise function to describe the probability of alpha escape as a function of particulate…
The barrier distribution, originated from channel coupling effects in heavy-ion fusion reactions, has been extracted experimentally for many systems using either a fusion excitation function or an excitation function of large-angle…
A significant deviation from the Debye model of rotational diffusion in the dynamics of orientational degrees of freedom in an equimolar mixture of ellipsoids of revolution and spheres is found to begin precisely at a temperature at which…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
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 $alpha$…
We study the kinetics of helix-coil transition in water solutions of gelatin (collagen protein) by optical rotation techniques combined with thermal characterization. By examining the rates of secondary helix folding, and covering a very…
We introduce and study interval partition diffusions with Poisson--Dirichlet$(\alpha,\theta)$ stationary distribution for parameters $\alpha\in(0,1)$ and $\theta\ge 0$. This extends previous work on the cases $(\alpha,0)$ and…
Fusion can be described by the time evolution of a dinuclear system with two degrees of freedom, the relative motion and transfer of nucleons. In the presence of the coupling between two collective modes, we solve the Fokker-Planck equation…
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…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
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.…