Related papers: A Parallel-pulling Protocol for Free-Energy Evalua…
Buildings rarely perform as designed/simulated and and there are numerous tangible benefits if this gap is reconciled. A new scientific yet pragmatic methodology - called Enhanced Parameter Estimation (EPE) - is proposed that allows…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
The TREE method has been widely used for long-range interaction {\it N}-body problems. We have developed a parallel TREE code for two-component classical plasmas with open boundary conditions and highly non-uniform charge distributions. The…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
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…
We apply the general procedure presented by Jarzynski in [1] to the problem of dissipation in a voltage-driven single-electron box. We obtain the expression of dissipated work, and find its relation to the dissipation Q obtained in [2]. We…
Most natural and engineered processes, such as biomolecular reactions, protein folding, and population dynamics, occur far from equilibrium and, therefore, cannot be treated within the framework of classical equilibrium thermodynamics. The…
Classical list scheduling is a very popular and efficient technique for scheduling jobs in parallel and distributed platforms. It is inherently centralized. However, with the increasing number of processors, the cost for managing a single…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
The athermal quasistatic deformation method provides an elegant solution to overcome the limitation of short time spans in molecular simulations. It provides overdamped conditions, allowing for the extraction of purely structural responses…
Due to their versatility in investigating phenomena in microscopic scales, optical tweezers have been an excellent platform for studying stochastic thermodynamics. In this context, this work presents experimental measurements of the…
Non-equilibrium Monte Carlo simulations based on Jarzynski's equality are a well-understood method to compute differences in free energy and also to sample from a target probability distribution without the need to thermalize the system…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
A parallel computer system is a collection of processing elements that communicate and cooperate to solve large computational problems efficiently. To achieve this, at first the large computational problem is partitioned into several tasks…
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,…
To keep pace with Moore's law, chip designers have focused on increasing the number of cores per chip rather than single core performance. In turn, modern jobs are often designed to run on any number of cores. However, to effectively…
We describe an embarrassingly parallel, anytime Monte Carlo method for likelihood-free models. The algorithm starts with the view that the stochasticity of the pseudo-samples generated by the simulator can be controlled externally by a…