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Molecular dynamics (MD) simulations of successive collision cascades within the same simulation domain were performed using two different inter-atomic potentials (IAP) in tungsten, one EAM based and the other a `quantum accurate' machine…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
Robotics simulation has been an integral part of research and development in the robotics area. The simulation eliminates the possibility of harm to sensors, motors, and the physical structure of a real robot by enabling robotics…
While molecular dynamics (MD) is a very useful computational method for atomistic simulations, modeling the interatomic interactions for reliable MD simulations of real materials has been a long-standing challenge. In 2007, Behler and…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Artificial intelligence (AI) and machine learning (ML) models in materials science are predominantly trained on ideal bulk crystals, limiting their transferability to real-world applications where surfaces, interfaces, and defects dominate.…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
One of the most promising applications in nanoscience is the design of new materials to improve water permeability and selectivity of nanoporous membranes. Understanding the molecular architecture behind these fascinating structures and how…
Rendering huge biological scenes with atomistic detail presents a significant challenge in molecular visualization due to the memory limitations inherent in traditional rendering approaches. In this paper, we propose a novel method for the…
Physical interactive robotics, ranging from wearable devices to collaborative humanoid robots, require close coordination between mechanical design and control. However, evaluating interactive dynamics is challenging due to complex human…
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…
Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…
A thin plate or slab, prepared so that opposite faces have different surface stresses, will bend as a result of the stress difference. We have developed a classical molecular dynamics (MD) formulation where (similar in spirit to…
While there have been many developments in computational probes of both strongly-correlated molecular systems and machine-learning accelerated molecular dynamics, there remains a significant gap in capabilities in simulating accurate…
Dynamical systems are ubiquitous within science and engineering, from turbulent flow across aircraft wings to structural variability of proteins. Although some systems are well understood and simulated, scientific imaging often confronts…
Learning-based methods have made significant progress in physics simulation, typically approximating dynamics with a monolithic end-to-end optimized neural network. Although these models offer an effective way to simulation, they may lose…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Scientists often explore and analyze large-scale scientific simulation data by leveraging two- and three-dimensional visualizations. The data and tasks can be complex and therefore best supported using myriad display technologies, from…