Related papers: Analysis of Two-State Folding Using Parabolic Appr…
The thermodynamics of the dissipative two-state system is calculated exactly for all temperatures and level asymmetries for the case of Ohmic dissipation. We exploit the equivalence of the two-state system to the anisotropic Kondo model and…
An exact solution of the problem of two-atom one- and two-mode Jaynes-Cummings model with intensity-dependent coupling is presented. Asymptotic solutions for system state vectors are obtained in the approximation of large initial coherent…
We show how the stability conditions for a system of interacting fermions that conventionally involve variations of thermodynamic potentials can be rewritten in terms of one- and two-particle correlators. We illustrate the applicability of…
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…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
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…
The light scattered by cold atoms induces mutual optical forces between them, which can lead to bound states. In addition to the trapping potential, this light-induced interaction generates a velocity-dependent force which damps or…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
For small thermodynamic systems in contact with a heat bath, we determine the free energy by imposing the following two conditions. First, the quasi-static work in any configuration change is equal to the free energy difference. Second, the…
Two-body dissipation due to chemical reactions occurs in both ultracold fermionic and bosonic molecular gases. Despite recent advances in achieving quantum degeneracy, the loss dynamics are typically described phenomenologically using rate…
We solve the Schr\"odinger equation with a position-dependent mass (PDM) charged particle interacted via the superposition of the Morse and Coulomb potentials and exposed to external magnetic and Aharonov-Bohm (AB) flux fields. The…
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…
Considering the thermodynamics of bosons in a lattice described by the Bose-Hubbard Hamiltonian, we report the occurrence of anomalous double peaks in their specific heat dependence on temperature. This feature, usually associated with a…
We apply the axiomatic approach to thermodynamics presented by Giles to derive a unique measure of entanglement for bi-partite pure states. This implies that local manipulations of entanglement in quantum information theory and adiabatic…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
We study the finite temperature properties of two-component fermionic atoms trapped in a two-dimensional optical lattice. We apply the self-energy functional approach to the two-dimensional Hubbard model with a harmonic trapping potential,…