相关论文: Experimental Free Energy Surface Reconstruction Fr…
The nonequilibrium work relation, or Jarzynski equality, establishes a statistical relationship between a series of nonequilibrium experiments on a system subjected to thermal fluctuations and a hypothetical experiment at thermodynamic…
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…
In thermodynamically characterizing a mixture comprising a finite number of molecules, we consider two kinds of protocol for producing a mixture from a pure substance. The first is a single alchemical operation, whereas the second is a…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
In this Letter we report a simulation study in which we compare the solid-liquid interfacial free energy of NaCl at coexistence, with the value that follows from the height of the homogeneous nucleation barrier. We find that the two…
The Jarzynski equality (JE) is a remarkable statement relating transient irreversible processes to infinite-time free energy differences. Although twenty years old, the JE remains unfamiliar to many; nevertheless it is a robust and powerful…
By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent…
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly exploited. Equilibrium methods such as umbrella sampling,…
The recently proposed Einstein molecule approach is extended to compute the free energy of molecular solids. This method is a variant of the Einstein crystal method of Frenkel and Ladd[J. Chem. Phys. 81,3188 (1984)]. In order to show its…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
Within the statistical multifragmentation model we study modifications of the surface and symmetry energy of primary fragments in the freeze-out volume. The ALADIN experimental data on multifragmentation obtained in reactions induced by…
We propose a continuum model to describe the molecular alignment in thin nematic shells. By contrast with previous accounts, the two-dimensional free energy, aimed at describing the physics of thin films of nematics deposited on curved…
The difference between free surface energy and fracture toughness in amorphous silica is studied via multi-scale simulations. We combine the homogenization of a molecular dynamics fracture model with a phase-field approach to track and…
We present a computational strategy for the evaluation of multidimensional integrals on hyper-rectangles based on Markovian stochastic exploration of the integration domain while the integrand is being morphed by starting from an initial…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
The Jarzynski equality (JE) is known as an exact identity for nonequillibrium systems. The JE was originally formulated for isolated and isothermal systems, while Adib reported an JE extended to an isoenergetic process. In this paper, we…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule…
Hypotheses: To correctly predict the aggregation number and size of wormlike micelles from ionic surfactants, the molecular-thermodynamic theory has to calculate the free energy per molecule in the micelle with accuracy better than 0.01 kT,…
We carry out umbrella sampling Monte Carlo simulations to evaluate the free energy surface of the ST2 model of water as a function two order parameters, the density and a bond-orientational order parameter. We approximate the long-range…