Related papers: A "fast growth" method of computing free energy di…
We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach -- based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a…
We analyze a modification of the Richards growth model by introducing a time-dependent perturbation in the growth rate. This modification becomes effective at a special switching time, which represents the first-crossing-time of the…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
We study the problem of stabilization for a class of evolution systems with fractional-damping. After writing the equations as an augmented system we prove in this article first that the problem is well posed. Second, using the LaSalle's…
Adiabatic processes are important for studying the dynamics of a time-dependent system. Conventionally, the adiabatic processes can only be achieved by varying the system slowly. We speed up both classical and quantum adiabatic processes by…
Generative models are a promising tool to address the sampling problem in multi-body and condensed-matter systems in the framework of statistical mechanics. In this work, we show that normalizing flows can be used to learn a transformation…
We propose a new method to efficiently compute load-flows (the steady-state of the power-grid for given productions, consumptions and grid topology), substituting conventional simulators based on differential equation solvers. We use a deep…
We analyse a non-local parabolic integro-differential equation modelling the evolutionary dynamics of a phenotypically-structured population in a changing environment. Such models arise in a variety of contexts from climate change to…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
In this paper, we propose a tumor growth model to incorporate and investigate the spatial effects of autophagy. The cells are classified into two phases: normal cells and autophagic cells, whose dynamics are also coupled with the nutrients.…
Predicting turbulent flame speed (the large time front speed) is a fundamental problem in turbulent combustion theory. Several models have been proposed to study the turbulent flame speed, such as the G-equations, the F-equations…
We performed molecular dynamics simulations to study relaxation phenomena during vapor-liquid transitions in a single component Lennard-Jones system. Results from two different overall densities are presented; one in the neighborhood of the…
Via a combination of molecular dynamics (MD) simulations and finite-size scaling (FSS) analysis, we study dynamic critical phenomena for the vapor-liquid transition in a three dimensional Lennard-Jones system. The phase behavior of the…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
The work fluctuations of an oscillator in contact with a heat reservoir and driven out of equilibrium by an external force are studied experimentally. The oscillator dynamics is modeled by a Langevin equation. We find both experimentally…
We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular…
The ability to separate and analyze chemical species with high resolution, sensitivity, and throughput is central to the development of microfluidics systems. Deterministic lateral displacement (DLD) is a continuous separation method based…
We discuss the problem of counting the maximum number of distinct states that an isolated physical system can pass through in a given period of time---its maximum speed of dynamical evolution. Previous analyses have given bounds in terms of…
Motivated by a series of experiments that revealed a temperature dependence of the dynamic scaling regime of growing surfaces, we investigate theoretically how a nonequilibrium growth process reacts to a sudden change of system parameters.…
We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…