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The heating of ions and electrons due to turbulent dissipation plays a crucial role in the thermodynamics of the solar wind and other plasma environments. Using magnetic field and thermal plasma observations from the first two perihelia of…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…
Wang and Landau proposed recently, a simple and flexible non-Boltzmann Monte Carlo method for estimating the density of states, from which the macroscopic properties of a closed system can be calculated. They demonstrated their algorithm by…
The decomposition kinetics of a solid-solution into separate phases are analyzed with an equation of motion initially developed to account for dissipative processes in quantum systems. This equation and the steepest-entropy-ascent quantum…
The Steepest Entropy Ascent (SEA) ansatz, recently recognized as the fourth law of thermodynamics, governs the irreversible evolution of a system from a non-equilibrium state toward a unique maximum-entropy equilibrium. SEA builds upon the…
In experiments and in simulations, the free energy of a state of a system can be determined from the probability that the state is occupied. However, it is often necessary to impose a biasing potential on the system so that high energy…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of…
The Jarzynski identity can be applied to instances when a microscopic system is pulled repeatedly but quickly along some coordinate, allowing the calculation of an equilibrium free energy profile along the pulling coordinate from a set of…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
In our original article (Phys. Chem. Chem. Phys., 2012, 14, 60446053) a convergence problem resulted in an averaging error in computing the entropy from a set of Wang-Landau Monte-Carlo simulations. Here we report corrected results for the…
The Hagedorn regime of string theory is usually understood as an equilibrium limiting phenomenon: the exponential growth of the density of states makes the canonical partition function singular at the Hagedorn temperature, while in the…
Efficient sampling from ensembles of Hamiltonian cycles is critical for predicting the thermodynamic properties of compact polymers, with applications including modeling protein and RNA folding and designing soft materials. Although…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
Monte Carlo algorithms such as the Wang-Landau algorithm and similar `entropic' methods are able to accurately sample the density of states of model systems and thereby give access to thermal equilibrium properties at any temperature.…
Soft porous crystals are flexible metal-organic frameworks that respond to physical stimuli such as temperature, pressure, and gas adsorption by large changes in their structure and unit cell volume. While they have attracted a lot of…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
In order to better understand the occurrence of phase transitions, we adopt an approach based on the study of energy landscapes: The relation between stationary points of the potential energy landscape of a classical many-particle system…