Related papers: Predicting Non-Equilibrium Folding Behavior of Pol…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3,…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
In this work we study thermal leptogenesis using non-equilibrium quantum field theory. Starting from fundamental equations for correlators of the quantum fields we describe the steps necessary to obtain quantum kinetic equations for…
Most natural systems operate far from equilibrium, displaying time-asymmetric, irreversible dynamics characterized by a positive entropy production while exchanging energy and matter with the environment. Although stochastic thermodynamics…
When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
Despite substantial progress in non-equilibrium physics, steady-state (s.s.) probabilities remain intractable to analysis. For a Markov process, s.s. probabilities can be expressed in terms of transition rates using the Matrix-Tree theorem…
We investigate the particle and heat transport in quantum junctions with the geometry of star graphs. The system is in a nonequilibrium steady state, characterized by the different temperatures and chemical potentials of the heat reservoirs…
Dynamical response functions are fundamental quantities to describe the excited-state properties in quantum many-body systems. Quantum algorithms have been proposed to evaluate these quantities by means of quantum phase estimation (QPE),…
The thermodynamic model of ultrathin lubricant film melting, confined between two atomically-flat solid surfaces, is built using the Landau phase transition approach. Non-equilibrium entropy is introduced describing the part of thermal…
In this work, we report our results on the phase transition of a flexible homopolymer from a stretched chain to a compact globule. The Wang-landau method is used to study the thermodynamic properties of a the chain up to 512 monomers. We…
Alternative approach for description of the non-equilibrium phenomena arising in solids at a severe external loading is analyzed. The approach is based on the new form of kinetic equations in terms of the internal and modified free energy.…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
How do we search for the entire family tree without unwanted random guesses, starting from a high-index and high-energy stationary state on the energy landscape? Here we introduce a general numerical method that constructs the pathway map…
A method for reconstructing the energy landscape of simple polypeptidic chains is described. We show that we can construct an equivalent representation of the energy landscape by a suitable directed graph. Its topological and dynamical…
A quasi-particle model is employed to derive from available lattice QCD calculations an equation of state useable in hydrodynamical simulations of the expansion stage of strongly interacting matter created in ultra-relativistic heavy-ion…
We present an efficient sampling method for computing a partition function and accelerating configuration sampling. The method performs a random walk in the $\lambda$ space, with $\lambda$ being any thermodynamic variable that characterizes…
The recently developed Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) is investigated for a wide range of model parameters including the parameter m representing the chain length and the thermodynamic temperature T and…
Poly-N-isopropylacrylamide (PNIPAM) is a thermoresponsive polymer, an essential building block of a large family of soft smart materials. In neat water it undergoes upon heating at $\approx$305K a phase transition from swollen to collapsed…