相关论文: A "fast growth" method of computing free energy di…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
The formally exact framework of equilibrium Density Functional Theory (DFT) is capable of simultaneously and consistently describing thermodynamic and structural properties of interacting many-body systems in arbitrary external potentials.…
In this thesis we examine methodologies for determining free energy differences (FEDs) of phases via Monte Carlo simulation. We identify and address three generic issues that arise in FED calculations; the choice of representation, the…
Existing methods to determine the stability of a power system to small perturbations are based on eigenvalue analysis and focus on the asymptotic (long-term) behavior of the power grid. During the preasymptotic (short-term) transient,…
Large parameter studies of fluid dynamic instabilities can crucially be simplified, if the user does not need to specify the simulation time. For this purpose, a steady state detection is implemented in the CFD library OpenFOAM. It…
Results for the kinetics of vapor-liquid transitions, following temperature quenches with different densities, are presented from the molecular dynamics simulations of a Lennard-Jones system. For critical density, bicontinuous liquid and…
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the availability of only a finite number of data values, N. In…
We present a finite-size scaling analysis of the droplet condensation-evaporation transition of a lattice gas (in two and three dimensions) and a Lennard-Jones gas (in three dimensions) at fixed density. Parallel multicanonical simulations…
We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts…
We propose a method to compute free-energy differences from nonadiabatic alchemical transformations using flow-based generative models. The method, nonadiabatic force matching, hinges on estimating the dissipation along an alchemical…
We derive the optimal estimates of the free energies of an arbitrary number of thermodynamic states from nonequilibrium work measurements; the work data are collected from forward and reverse switching processes and obey a fluctuation…
During reactive transport modeling, the computational cost associated with chemical reaction calculations is often 10-100 times higher than that of transport calculations. Most of these costs results from chemical equilibrium calculations…
Diffusive dynamics abound in nature and have been especially studied in physical, biological, and financial systems. These dynamics are characterised by a linear growth of the mean squared displacement (MSD) with time. Often, the conditions…
Mechanical models for tumor growth have been used extensively in recent years for the analysis of medical observations and for the prediction of cancer evolution based on imaging analysis. This work deals with the numerical approximation of…
Computer simulations and scaling theory are used to investigate the damping of oscillations during epitaxial growth on high-symmetry surfaces. The crossover from smooth to rough growth takes place after the deposition of (D/F)^\delta…
We present a new and exploratory approach to determine the $\Delta\beta(\beta)$-shift in the $O(3)$ nonlinear $\sigma$-model. The method is based on a scaling hypothesis for a free energy difference, which is assumed to be valid in a…
According to the Jarzynski theorem, equilibrium free energy differences can be calculated from the statistics of work carried out during non-equilibrium transformations. Although exact, this approach can be plagued by large statistical…
We propose a formulation of adaptive computation of free energy differences, in the ABF or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows to present a truly…
Kinetics of separation between the low and high density phases in a single component Lennard-Jones model has been studied via molecular dynamics simulations, at a very low temperature, in the space dimension $d=2$. For densities close to…
We present a system that enables rapid model experimentation for tera-scale machine learning with trillions of non-zero features, billions of training examples, and millions of parameters. Our contribution to the literature is a new method…