相关论文: Unfolding Rates for the Diffusion-Collision Model

In the diffusion-collision model, the unfolding or backward rates are given by the likelihood of secondary structural cluster dissociation. In this work, we introduce a backward rate calculation modeled from a Kramers-type thermal tunneling…

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 use the periodic unfolding technique to derive corrector estimates for a reaction-diffusion system describing concrete corrosion penetration in the sewer pipes. The system, defined in a periodically-perforated domain, is semi-linear,…

$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

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…

We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…

Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…

Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…

Diffusion rates are calculated on the basis of van Hove's formula for the dynamical structure factor (DSF) related to particle scattering at mobile adsorbates. The formula is evaluated quantum mechanically using eigenfunctions obtained from…

The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…

The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion,…

We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…

We present an investigation into diffusion models for molecular generation, with the aim of better understanding how their predictions compare to the results of physics-based calculations. The investigation into these models is driven by…

We consider any pseudo holomorphic integral 2-cycle in an arbitrary almost complex manifold and perform a blow up analysis at an arbitrary point. Building upon a pseudo algebraic blow up (previously introduced by the author) we prove a…

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…

Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…