Related papers: Analysis of Two-State Folding Using Parabolic Appr…
Preparing Gibbs states, which describe systems in equilibrium at finite temperature, is of great importance, particularly at low temperatures. In this work, we propose a new method -- TEPID-ADAPT -- that prepares the thermal Gibbs state of…
We consider the canonical ensemble of a system of point particles on the sphere interacting via a logarithmic pair potential. In this setting, we study the associated Gibbs measure and partition function, and we derive explicit formulas…
The study of quantum thermodynamics aims to elucidate the role played by quantum principles in the emergent features of quantum thermodynamic processes. Specifically, it is of fundamental importance to understand how quantum correlation…
A general nonequilibrium thermodynamic theory is developed for time-dependent Langevin dynamics, starting from the common definition of nonequilibrium Gibbs entropy. It is shown that the notations appearing in the First and the Second Law…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
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…
In this paper, we suppose a possible extension of Gibbs ensemble theory so that it can provide a reasonable description to phase transitions and spontaneous symmetry breaking. The extension is founded on three hypotheses, and can be…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
The mechanical properties of thermally excited two-dimensional crystalline membranes can depend dramatically on their geometry and topology. A particularly relevant example is the effect on the crumpling transition of holes in the membrane.…
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective…
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…
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
We develop a general perturbative theory of finite-coupling quantum thermometry up to second order in probe-sample interaction. By assumption, the probe and sample are in thermal equilibrium, so the probe is described by the mean-force…
A major part of the many thermally driven processes in our natural environment as well as in engineering solutions of Carnot-type machinery is based on the second law of thermodynamics (or principle of entropy increase). An interesting link…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Chaotic dependence on temperature refers to the phenomenon of divergence of Gibbs measures as the temperature approaches a certain value. Models with chaotic behaviour near zero temperature have multiple ground states, none of which are…
We introduce an effective thermodynamics for multipartite entangled pure states and derive an upper bound on extractable energy with feedback control from a subsystem under a local Hamiltonian. The inequality that gives the upper bound…
The entanglement of general pure Gaussian two-mode states is examined in terms of the coefficients of the quadrature components of the wavefunction. The entanglement criterion and the entanglement of formation are directly evaluated as a…
The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native…
A powerful theoretical structure has emerged in recent years on the characterization and quantification of entanglement in continuous-variable systems. After reviewing this framework, we will illustrate it with an original set-up based on a…