Related papers: Analysis of Two-State Folding Using Parabolic Appr…
We describe a model of electron transfer reactions affected by local binding to the donor or acceptor sites of a particle in equilibrium with the solution. The statistics of fluctuations of the donor-acceptor energy gap caused by…
An approach is presented which allows a self-consistent description of the fragmentation of single-particle strength for nucleons in finite nuclei employing the Greens function formalism. The self-energy to be considered in the Dyson…
Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. Many proteins have amino acidic compositions compatible both…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
The paper is devoted to the thermodynamics of normal surface electromagnetic fields within a nonuniform dispersive and absorptive system. This system is formed by vacuum and lossy medium separated by a plane interface. As a medium, we used…
In the context of finite elasticity, we propose plate models describing the spontaneous bending of nematic elastomer thin films due to variations along the thickness of the nematic order parameters. Reduced energy functionals are deduced…
We consider quantum quenches in the so-called $q$-boson lattice model. We argue that the Generalized Eigenstate Thermalization Hypothesis holds in this model, therefore the Generalized Gibbs Ensemble (GGE) gives a valid description of the…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
The theory of self-consistent effective interactions in nuclei is extended for a system with a velocity dependent mean potential. By means of the field coupling method, we present a general prescription to derive effective interactions…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
From Hamilton's principle of stationary action, we derive governing equations of two-fluid mixtures and extend the model to the dissipative case without chemical reactions. For both conservative and dissipative cases, an algebraic identity…
Stress-based ensembles incorporating temperature-like variables have been proposed as a route to an equation of state for granular materials. To test the efficacy of this approach, we perform experiments on a two-dimensional photoelastic…
We present two new developments for computing excited state energies within the $GW$ approximation. First, calculations of the Green's function and the screened Coulomb interaction are decomposed into two parts: one is deterministic while…
The long-time relaxation of ideal two dimensional magnetohydrodynamic turbulence subject to the conservation of two infinite families of constants of motion---the magnetic and the "cross" topology invariants--is examined. The analysis of…
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…
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…
This paper extends the distributed rolling contact FrBD framework to linear viscoelasticity by considering classic derivative Generalised Maxwell and Kelvin-Voigt rheological representations of the bristle element. With this modelling…
I investigate a disordered version of a simplified model of protein folding, with binary degrees of freedom, applied to an ideal beta-hairpin structure. Disorder is introduced by assuming that the contact energies are independent and…
Level crossing models for two-state quantum systems are applicable to a wide variety of physical problems. We address the special case of level glancing, i.e., when energy levels reach a degeneracy at a specific point of time, but never…
Two microscopic models, UrQMD and QGSM, are used to extract the effective equation of state (EOS) of locally equilibrated nuclear matter produced in heavy-ion collisions at energies from 11.6 AGeV to 160 AGeV. Analysis is performed for the…