Related papers: Analysis of Two-State Folding Using Parabolic Appr…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
We show that when an isolated doublet of unbound states of a physical system becomes degenerate for some values of the control parameters of the system, the energy hypersurfaces representing the complex resonance energy eigenvalues as…
The dynamical convergence of a system to the thermal distribution, or Gibbs state, is a standard assumption across all of the physical sciences. The Gibbs state is determined just by temperature and the system's energies alone. But at…
The construction of meta generalized gradient approximations based on the density matrix expansion (DME) is considered as one of the most accurate technique to design semilocal exchange energy functionals in two-dimensional density…
We demonstrate the approach towards a Gibbs-like equilibrium state, with a common temperature and a chemical potential, of two finite metallic grains, prepared with a different number of noninteracting electrons, connected by a weak link…
We experimentally study the infinite-size limit of the Dicke model of quantum optics with a parity-breaking deformation strength that couples the system to an external bosonic reservoir. We focus on the dynamical consequences of such…
Using the Gaussian Ansatz for the monomer-monomer correlation functions we derive a set of the self-consistent equations for determination of the conformational state in the bead-and-spring copolymer model. The latter is based on the…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
A Hubbard-like model with SU(4) symmetry for electrons with two-fold orbital degeneracy is studied extensively. Exact solution in one dimension is derived by means of Bethe ansatz, where the sites are supposed to be occupied by at most two…
Analytical formulas for the excitation energies as well as for the electric quadrupole reduced transition probabilities in the ground, beta and gamma bands were derived within the coherent state model for the near vibrational and well…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
The generalized Gibbs ensemble (GGE) was introduced ten years ago to describe observables in isolated integrable quantum systems after equilibration. Since then, the GGE has been demonstrated to be a powerful tool to predict the outcome of…
Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single…
Based on previous works, analytical calculational procedures for dealing with the strongly interacting fermions ground state are further developed through a medium dependent potential in terms of the Bethe-Peierls contact interaction model.…
Chemical theories involving thermodynamical equilibrium states invariably utilize statistical mechanical equilibrium density distributions. Here, a definition of heat-work transformation termed thermo mechanical coherence is first made, and…
Dependent generalized extreme value (dGEV) models have attracted much attention due to the dependency structure that often appears in real datasets. To construct a dGEV model, a natural approach is to assume that some parameters in the…