Related papers: A Parallel-pulling Protocol for Free-Energy Evalua…
When a system deviates from equilibrium, it is possible to manipulate and control it to drive it towards equilibrium within a finite time $t_f$, even reducing its natural relaxation time scale $\tau_{relax}$. Although numerous theoretical…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Parallel applications often rely on work stealing schedulers in combination with fine-grained tasking to achieve high performance and scalability. However, reducing the total energy consumption in the context of work stealing runtimes is…
The pseudopotential and free energy models are two popular extensions of the lattice Boltzmann method for multiphase flows. Until now, they have been developed apart from each other in the literature. However, important questions about…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
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…
Confidence estimation infers a probability for whether each model output is correct or not. While predicting such binary correctness is sensible for tasks with exact answers, free-form generation tasks are often more nuanced, with output…
An electrostatic gyrokinetic-based model is applied to simulate parallel plasma transport in the scrape-off layer to a divertor plate. The authors focus on a test problem that has been studied previously, using parameters chosen to model a…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
This paper introduces the \emph{serial-parallel decision problem}. Consider an online scheduler that receives a series of tasks, where each task has both a parallel and a serial implementation. The parallel implementation has the advantage…
We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors…
Dissipation and adhesion are important in many areas of materials science, including friction and lubrication, cold spray deposition, and micro-electromechanical systems (MEMS). Another interesting problem is the adhesion of mineral grains…
The nonequilibrium free energy theorems show how distributions of work along nonequilibrium paths are related to free energy differences between the equilibrium states at the end points of these paths. In this paper we develop a natural way…
Recently, task-based programming models have emerged as a prominent alternative among shared-memory parallel programming paradigms. Inherently asynchronous, these models provide native support for dynamic load balancing and incorporate data…
We consider the problem of sampling a high dimensional multimodal target probability measure. We assume that a good proposal kernel to move only a subset of the degrees of freedoms (also known as collective variables) is known a priori.…
There are two halves to RL systems: experience collection time and policy learning time. For a large number of samples in rollouts, experience collection time is the major bottleneck. Thus, it is necessary to speed up the rollout generation…
We evaluate the grand potential of a cluster of two molecular species, equivalent to its free energy of formation from a binary vapour phase, using a nonequilibrium molecular dynamics technique where guide particles, each tethered to a…