Related papers: Exploring High Dimensional Free Energy Landscapes:…
Rare event sampling is a central problem in modern computational chemistry research. Among the existing methods, transition path sampling (TPS) can generate unbiased representations of reaction processes. However, its efficiency depends on…
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…
The theoretical analysis of many problems in physics, astronomy and applied mathematics requires an efficient numerical exploration of multimodal parameter spaces that exhibit broken ergodicity. Monte Carlo methods are widely used to deal…
Metadynamics is an established sampling method aimed at reconstructing the free-energy surface relative to a set of appropriately chosen collective variables. In standard metadynamics the free-energy surface is filled by the addition of…
Action chunking is a widely adopted approach in Learning from Demonstration (LfD). By modeling multi-step action chunks rather than single-step actions, action chunking significantly enhances modeling capabilities for human expert policies.…
Interactive visualizations are crucial in ad hoc data exploration and analysis. However, with the growing number of massive datasets, generating visualizations in interactive timescales is increasingly challenging. One approach for…
Several enhanced sampling methods such as umbrella sampling or metadynamics rely on the identification of an appropriate set of collective variables. Recently two methods have been proposed to alleviate the task of determining efficient…
A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is…
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…
Sampling from discrete distributions with multiple modes and energy barriers is fundamental to machine learning and computational physics. Recent discrete neural samplers like MDNS suffer from mode collapse and fail to sample high-energy…
We study the problem of optimal sampling in an edge-based video analytics system (VAS), where sensor samples collected at a terminal device are offloaded to a back-end server that processes them and generates feedback for a user. Sampling…
Self-supervised learning (SSL) has shown remarkable data representation capabilities across a wide range of datasets. However, when applied to real-world datasets with long-tailed distributions, performance on multiple downstream tasks…
The development of enhanced sampling methods has greatly extended the scope of atomistic simulations, allowing long-time phenomena to be studied with accessible computational resources. Many such methods rely on the identification of an…
Importance sampling is a Monte Carlo method that introduces a proposal distribution to sample the space according to the target distribution. Yet calibration of the proposal distribution is essential to achieving efficiency, thus the resort…
Small-angle scattering (SAS) is a key experimental technique for analyzing nano-scale structures in various materials.In SAS data analysis, selecting an appropriate mathematical model for the scattering intensity is critical, as it…
Wireless sensor networks are often designed to perform two tasks: sensing a physical field and transmitting the data to end-users. A crucial aspect of the design of a WSN is the minimization of the overall energy consumption. Previous…
Attosecond transient-absorption spectroscopy (ATAS) is an established method for exploring electron dynamics on the subfemtosecond time-scale. ATAS spectra contain certain ubiquitous features, such as oscillating fringes, light-induced…
Fast and accurate sampling method is in high demand, in order to bridge the large gaps between molecular dynamic simulations and experimental observations. Recently, integrated tempering enhanced sampling method (ITS) has been proposed and…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the…