Related papers: Collective Variables for Crystallization Simulatio…
Collective variables (CVs) play a crucial role in capturing rare events in high-dimensional systems, motivating the continual search for principled approaches to their design. In this work, we revisit the framework of quantitative coarse…
The Collaborative Analysis Versioning Environment System (CAVES) project concentrates on the interactions between users performing data and/or computing intensive analyses on large data sets, as encountered in many contemporary scientific…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
We present a coarse molecular-dynamics (CMD) approach for the study of stress-induced structural transformations in crystals at finite temperatures. The method relies on proper choice of a coarse variable (order parameter, observable),…
Unsupervised machine learning methods are used to identify structural changes using the melting point transition in classical molecular dynamics simulations as an example application of the approach. Dimensionality reduction and clustering…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
Monte Carlo simulations are widely used to simulate complex molecular systems, but standard approaches suffer from metastability. Lately, the use of non-local proposal updates in a collective-variable (CV) space has been proposed in several…
Relevant methods of variable selection have been proposed in model-based clustering and classification. These methods are making use of backward or forward procedures to define the roles of the variables. Unfortunately, these stepwise…
Crystalline alloys and related mixed systems make up a large family of materials with high tunability which have been proposed as the solution to a large number of energy related materials design problems. Due to the presence of chemical…
Background: Virtual Machine (VM) consolidation is an effective technique to improve resource utilization and reduce energy footprint in cloud data centers. It can be implemented in a centralized or a distributed fashion. Distributed VM…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (4He and Ne), molecular solids (H2 and CH4), and some ionic (LiH), covalent (graphite), and…
Electron microscopy has enabled many scientific breakthroughs across multiple fields. A key challenge is the tuning of microscope parameters based on images to overcome optical aberrations that deteriorate image quality. This calibration…
Electrochemical processes play a crucial role in energy storage and conversion systems, yet their computational modeling remains a significant challenge. Accurately incorporating the effects of electric potential has been a central focus in…
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…
Isomerization, i.e. the rearrangement between distinct molecular configurations, is a fundamental process in chemistry. Here we demonstrate that two-dimensional Coulomb crystals can emulate molecular isomerization and be used to…