相关论文: Parallel Tempering Algorithm for Conformational St…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Optimizing chemical molecules for desired properties lies at the core of drug development. Despite initial successes made by deep generative models and reinforcement learning methods, these methods were mostly limited by the requirement of…
Quantum machine learning with quantum kernels for classification problems is a growing area of research. Recently, quantum kernel alignment techniques that parameterise the kernel have been developed, allowing the kernel to be trained and…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Coherent control, a central concept in physics and chemistry, has sparked significant interest due to its ability to fine-tune interference effects in atoms and individual molecules for applications ranging from light-harvesting complexes…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
Multi-component polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures,…
Many parallel and distributed computing research results are obtained in simulation, using simulators that mimic real-world executions on some target system. Each such simulator is configured by picking values for parameters that define the…
Parallel tempering is popular method for allowing MCMC algorithms to properly explore a $d$-dimensional multimodal target density. One problem with traditional power-based parallel tempering for multimodal targets is that the proportion of…
We present an algorithm that exploits quantum parallelism to simulate randomness in a quantum system. In our scheme, all possible realizations of the random parameters are encoded quantum mechanically in a superposition state of an…
In this manuscript a method for developing novel filtering algorithms through the parallel concatenation of two Bayesian filters is illustrated. Our description of this method, called turbo filtering, is based on a new graphical model; this…
The tempered Lefschetz thimble method is a parallel-tempering algorithm towards solving the numerical sign problem. It uses the flow time of the gradient flow as a tempering parameter and is expected to tame both the sign and multimodal…
We study the opportunities for parallelism for the simulation of surface reactions. We introduce the concept of a partition and we give new simulation methods based on Cellular Automaton using partitions. We elaborate on the advantages and…
Parallel replica dynamics is a method for accelerating the computation of processes characterized by a sequence of infrequent events. In this work, the processes are governed by the overdamped Langevin equation. Such processes spend much of…
We developed a parallel Bayesian optimization algorithm for large eddy simulations. These simulations challenge optimization methods because they take hours or days to compute, and their objective function contains noise as turbulent…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
In this short note, we show how the parallel adaptive Wang-Landau (PAWL) algorithm of Bornn et al. (2013) can be used to automate and improve simulated tempering algorithms. While Wang-Landau and other stochastic approximation methods have…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…