相关论文: ExTASY: Scalable and Flexible Coupling of MD Simul…

There is a growing number of tasks that work directly on point clouds. As the size of the point cloud grows, so do the computational demands of these tasks. A possible solution is to sample the point cloud first. Classic sampling…

Many processes in chemistry and physics take place on timescales that cannot be explored using standard molecular dynamics simulations. This renders the use of enhanced sampling mandatory. Here we introduce an enhanced sampling method that…

We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…

To quantify the complexity of a system, entropy-based methods have received considerable critical attentions in real-world data analysis. Among numerous entropy algorithms, amplitude-based formulas, represented by Sample Entropy, suffer…

The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…

Despite the increasing adoption of Field-Programmable Gate Arrays (FPGAs) in compute clouds, there remains a significant gap in programming tools and abstractions which can leverage network-connected, cloud-scale, multi-die FPGAs to…

The study of multiphase flows in porous media is fundamental to various fields, including oil recovery, CO2 sequestration, hydrogeology, and others. Accurate predictions of fluid behavior in these systems can enhance process efficiency…

Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…

The growing gap between processor and memory speeds results in complex memory hierarchies as processors evolve to mitigate such divergence by taking advantage of the locality of reference. In this direction, the BSC performance analysis…

Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…

Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of…

We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…

Determinantal point processes (DPPs) are specific probability distributions over clouds of points that are used as models and computational tools across physics, probability, statistics, and more recently machine learning. Sampling from…

ExaScale systems will be a key driver for simulations that are essential for advance of science and economic growth. We aim to present a new concept of microprocessor for floating-point computations useful for being a basic building block…

Sampling-based model predictive control (MPC) offers strong performance in nonlinear and contact-rich robotic tasks, yet often suffers from poor exploration due to locally greedy sampling schemes. We propose \emph{Model Tensor Planning}…

Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite…

The growing complexity of Cyber-Physical Systems (CPS), together with increasingly available parallelism provided by multi-core chips, fosters the parallelization of simulation. Simulation speed-ups are expected from co-simulation and…

Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…