Related papers: Building Maps in Collective Variable Space

Multivariate networks are commonly found in real-world data-driven applications. Uncovering and understanding the relations of interest in multivariate networks is not a trivial task. This paper presents a visual analytics workflow for…

The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods…

In survey sampling, calibration is a very popular tool used to make total estimators consistent with known totals of auxiliary variables and to reduce variance. When the number of auxiliary variables is large, calibration on all the…

The use of accelerated sampling methods such as metadynamics has shown significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine, e.g.,…

Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a…

Although jammed granular systems are athermal, several thermodynamic-like descriptions have been proposed which make quantitative predictions about the distribution of volume and stress within a system and provide a corresponding…

Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…

A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…

Finding proper collective variables for complex systems and processes is one of the most challenging tasks in simulations, which limits the interpretation of experimental and simulated data and the application of enhanced sampling…

We obtain exact analytic expressions for a class of functions expressed as integrals over the Haar measure of the unitary group in d dimensions. Based on these general mathematical results, we investigate generic dynamical properties of…

We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

As an important method of handling potential uncertainties in numerical simulations, ensemble simulation has been widely applied in many disciplines. Visualization is a promising and powerful ensemble simulation analysis method. However,…

We have obtained an exact expression for the phase-space volume corresponding to a microcanonical ensemble of systems under center of mass, total linear and angular momenta conservation constraints, and arbitrary constraints on the…

The purpose of this review is to discuss the notion of conservation in hyperbolic systems and how one can formulate it at the discrete level depending on the solution representation of the solution. A general theory is difficult. We discuss…

The study of complex systems is limited by the fact that only few variables are accessible for modeling and sampling, which are not necessarily the most relevant ones to explain the systems behavior. In addition, empirical data typically…

Several aspects of the internal structure of pseudoscalar mesons, accessible through generalized parton distributions in their zero-skewness limit, are examined. These include electromagnetic and gravitational form factors related to charge…

A system of interacting atoms is represented as an union of two subsystems, one of which is the system of atoms, and the other is an auxiliary scalar covariant field, which is equivalent to a given static interatomic potential of general…

We connect the configurational entropy of a liquid to the geometrical properties of its local energy landscape, using a high-temperature expansion. It is proposed that correlations between local structures arises from their overlap and,…

Machine learning force fields (MLFFs) promise to accurately describe the potential energy surface of molecules at the ab initio level of theory with improved computational efficiency. Within MLFFs, equivariant graph neural networks (EQNNs)…