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Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…

Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…

Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…

A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…

The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…

Dielectric structures composed of many inclusions that manipulate light in ways the bulk materials cannot are commonly seen in the field of metamaterials. In these structures, each inclusion depends on a set of parameters such as location…

In this paper we propose a new class of Dynamic Mixture Models (DAMMs) being able to sequentially adapt the mixture components as well as the mixture composition using information coming from the data. The information driven nature of the…

Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…

Computer experiments are pivotal for modeling complex real-world systems. Maximizing information extraction and ensuring accurate surrogate modeling necessitates space-filling designs, where design points extensively cover the input domain.…

Flexible elastic structures, such as beams, rods, ribbons, plates, and shells, exhibit complex nonlinear dynamical behaviors that are central to a wide range of engineering and scientific applications, including soft robotics, deployable…

The full optimization of the design and operation of instruments whose functioning relies on the interaction of radiation with matter is a super-human task, given the large dimensionality of the space of possible choices for geometry,…

Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale…

Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of…

We present a scalable, robust approach to creating quantum programs of arbitrary size and complexity. The approach is based on the true abstraction of the problem. The quantum program is expressed in terms of a high-level model together…

Computational micromagnetics requires numerical solution of partial differential equations to resolve complex interactions in magnetic nanomaterials. The Virtual Micromagnetics project described here provides virtual machine simulation…

Advanced materials and their applications have become a key field of research, and it looks like this trend is not going to change soon. For that reason, the need for systematic and efficient methods for organizing knowledge in the field…

All simulation approaches eventually face limits in computational scalability when applied to large spatiotemporal domains. This challenge becomes especially apparent in molecular-level particle simulations, where high spatial and temporal…

Machine Learning tools are nowadays widely applied extensively to the prediction of the properties of molecular materials, using datasets extracted from high-throughput computational models. In several cases of scientific and technological…

We have presented some practical consequences on the molecular-dynamics simulations arising from the numerical algorithm published recently in paper Int. J. Mod. Phys. C 16, 413 (2005). The algorithm is not a finite-difference method and…

Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…