Related papers: Predicting Non-Equilibrium Folding Behavior of Pol…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where…
A new mesoscopic non-equilibrium thermodynamic approach is developed. The approach is based on the thermodynamic identity associated the first and second law of thermodynamics. In the framework of the approach different internal dissipative…
A simple solid-on-solid model of adsorbate-induced faceting is studied by using a modified Wang-Landau method. The phase diagram for this system is constructed by computing the density of states in a special two-dimensional energy space. A…
Novel sampling algorithms can significantly impact open questions in computational biology, most notably the in silico protein folding problem. By using computational methods, protein folding aims to find the three-dimensional structure of…
Evaporation/condensation transition of the Potts model on square lattice is numerically investigated by the Wang-Landau sampling method. Intrinsically system size dependent discrete transition between supersaturation state and…
Many-body quantum systems in the ground states have zero-point energy due to the uncertainty relation. In many cases, the system in the ground state accompanies spatially-entangled energy density fluctuation via the noncommutativity of the…
We examine how systems in non-equilibrium steady states close to a continuous phase transition can still be described by a Landau potential if one forgoes the assumption of analyticity. In a system simultaneously coupled to several baths at…
We study under which conditions an overdamped regime can be attained in the dynamic evolution of a quantum field configuration. Using a real-time formulation of finite temperature field theory, we compute the effective evolution equation of…
We consider a class of systems where $N$ identical particles with positions ${\bf q}_1,...,{\bf q}_N$ and momenta ${\bf p}_1,...,{\bf p}_N$ are enclosed in a box of size $L$, and exhibit the scaling $\mathcal{U}(L{\bf r}_1,...,L{\bf…
Long chains of the HP lattice protein model are studied by the Multi-Self-Overlap Ensemble(MSOE) Monte Carlo method, which was developed recently by the authors. MSOE successfully finds the lowest energy states reported before for sequences…
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…
During fast diffusion-influenced polymerization, nonequilibrium behavior of the polymer chains and the surrounding reactive monomers has been reported recently. Based on the laws of thermodynamics, the emerging nonequilibrium structures…
It is analyzed whether the potential energy landscape of a glass-forming system can be effectively mapped on a random model which is described in statistical terms. For this purpose we generalize the simple trap model of Bouchaud and…
The first-order phase transitions and related thermodynamics properties are primary concerns of materials sciences and engineering. In traditional atomistic simulations, the phase transitions and the estimation of their thermodynamic…
We propose a new strategy for determining the equation of state of a relativistic thermal quantum field theory by considering it in a moving reference system. In this frame an observer can measure the entropy density of the system directly…
Computing the equilibrium properties of complex systems, such as free energy differences, is often hampered by rare events in the dynamics. Enhanced sampling methods may be used in order to speed up sampling by, for example, using high…
Non-equilibrium quantum transport is crucial to technological advances ranging from nanoelectronics to thermal management. In essence, it deals with the coherent transfer of energy and (quasi-)particles through quantum channels between…
Many physical and chemical processes, such as folding of biopolymers, are best described as dynamics on large combinatorial energy landscapes. A concise approximate description of dynamics is obtained by partitioning the micro-states of the…
The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…