Related papers: Analysis of Two-State Folding Using Parabolic Appr…
To study temperature dependent elastic constants, a new computational method is proposed by combining continuum elasticity theory and first principles calculations. A Gibbs free energy function with one variable with respect to strain at…
The thermodynamic theory of dislocation-enabled plasticity is based on two unconventional hypotheses. The first of these is that a system of dislocations, driven by external forces and irreversibly exchanging heat with its environment, must…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
The model under consideration is a two-dimensional two-component plasma, stable against collapse for the dimensionless coupling constant $\beta<2$. The combination of a technique of renormalized Mayer expansion with the mapping onto the…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
We study the relationship between the entanglement, mixedness and energy of two-qubit and two-mode Gaussian quantum states. We parametrize the set of allowed states of these two fundamentally different physical systems using measures of…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
We study nonequilibrium thermodynamics in a fermionic resonant level model with arbitrary coupling strength to a fermionic bath, taking the wide-band limit. In contrast to previous theories, we consider a system where both the level energy…
We present the detailed study of the thermodynamics of vibrational modes in disordered elastic systems such as the Bragg glass phase of lattices pinned by quenched impurities. Our study and our results are valid within the (mean field)…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
A joint experimental / theoretical investigation of the elastin-like octapeptide GVG(VPGVG) was carried out. In this paper a comprehensive molecular dynamics study of the temperature dependent folding and unfolding of the octapeptide is…
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…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
We discuss the possibility of preparing highly entangled states by simply cooling atoms into the ground state of an applied interaction Hamiltonian. As in laser sideband cooling, we take advantage of a relatively large detuning of the…
A new two-pole approximation, which allows to describe the transition from an insulating state to a metallic one at increase of bandwidth, and also the observable in some compounds transition from a metalic state to an insulating one with…
The properties of some complex many body systems can be modeled by introducing in the dissipative dynamics of each single component a set of kinetic constraints that depend on the state of the neighbor systems. Here, we characterize this…
We investigate the thermodynamic behavior of open quantum systems through the Hamiltonian of Mean Force, focusing on two models: a two-qubit system interacting with a thermal bath and a Jaynes-Cummings Model without the rotating wave…
Starting from the Helmholtz free energy we calculate analytically first- and second-order derivatives, as internal energy and specific heats, for the ideal system and the exchange and correlation interactions covering a broad range of…
The features of the fundamental thermodynamical relation (expressing entropy as function of state variables) that arise from the self-gravitating character of a system are analyzed. The models studied include not only a spherically…
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, describing the stretch-induced unfolding of macromolecules (proteins, silks, nanopolymers, DNA/RNA). The model is…