Related papers: A Parallel-pulling Protocol for Free-Energy Evalua…
Energy distance is a statistical distance between the distributions of random variables, which characterizes the equality of the distributions. Utilizing the energy distance, we develop a nonparametric test for the diagonal symmetry, which…
Joint Energy-based Model (JEM) is a recently proposed hybrid model that retains strong discriminative power of modern CNN classifiers, while generating samples rivaling the quality of GAN-based approaches. In this paper, we propose a…
We study numerical methods for porous media equation (PME). There are two important characteristics: the finite speed propagation of the free boundary and the potential waiting time, which make the problem not easy to handle. Based on…
Many studies of quantum-size heat engines assume that the dynamics of an internal system is unitary and that the extracted work is equal to the energy loss of the internal system. Both assumptions, however, should be under scrutiny. In the…
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 this paper, we propose an efficient parallelization strategy for boundary element method (BEM) solvers that perform the electromagnetic analysis of structures with lossy conductors. The proposed solver is accelerated with the adaptive…
In this paper, we derive and investigate approaches to dynamically load balance a distributed task parallel application software. The load balancing strategy is based on task migration. Busy processes export parts of their ready task queue…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
We consider the problem of selecting the best variable-value strategy for solving a given problem in constraint programming. We show that the recent Embarrassingly Parallel Search method (EPS) can be used for this purpose. EPS proposes to…
We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation -- a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and…
To design efficient parallel algorithms, some recent papers showed that many sequential iterative algorithms can be directly parallelized but there are still challenges in achieving work-efficiency and high-parallelism. Work-efficiency can…
Understanding and computing the entropic forces exerted by polymer chains under confinement is important for many reasons, from research to applications. However, extracting properties related to the free energy, such as the force (or…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
This paper addresses the problem of scheduling a set of jobs that are released over the time on a set of identical parallel machines, aiming at the minimization of the total weighted completion time. This problem, referred to as $P|r_j|\sum…
Training normalizing flow generative models can be challenging due to the need to calculate computationally expensive determinants of Jacobians. This paper studies the likelihood-free training of flows and proposes the energy objective, an…
Free energies play a central role in many descriptions of equilibrium and non-equilibrium properties of solids. Continuum partial differential equations (PDEs) of atomic transport, phase transformations and mechanics often rely on first and…
A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a…
Software engineers often have to estimate the performance of a software system before having full knowledge of the system parameters, such as workload and operational profile. These uncertain parameters inevitably affect the accuracy of…
A simple zipper model is introduced, representing in a simplified way, e.g., the folded DNA double helix or hairpin structures in RNA. The double stranded hairpin is connected to a heat bath at temperature $T$ and subject to an external…
Key-based workload partitioning is a common strategy used in parallel stream processing engines, enabling effective key-value tuple distribution over worker threads in a logical operator. While randomized hashing on the keys is capable of…