Related papers: MDcraft -- a modern molecular dynamics simulation …
Molecular dynamics (MD) simulations play an important role in understanding and engineering heat transport properties of complex materials. An essential requirement for reliably predicting heat transport properties is the use of accurate…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Multiparticle collision dynamics (MPCD) is a relatively new algorithm of fluid flow simulations that has been applied mostly to flows around simple objects. One might ask how it behaves in more complex flows. Therefore, we extend MPCD to…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…
Recent advances in (scanning) transmission electron microscopy have enabled routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for…
Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…
Automatic differentiation represents a paradigm shift in scientific programming, where evaluating both functions and their derivatives is required for most applications. By removing the need to explicitly derive expressions for gradients,…
This master thesis introduces the idea of dynamic cutoffs in molecular dynamics simulations, based on the distance between particles and the interface, and presents a solution for detecting interfaces in real-time. Our dynamic cutoff method…
Scientific Machine Learning (SciML) has advanced recently across many different areas in computational science and engineering. The objective is to integrate data and physics seamlessly without the need of employing elaborate and…
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…
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…
Advancements in scientific instrument sensors and connected devices provide unprecedented insight into ongoing experiments and present new opportunities for control, optimization, and steering. However, the diversity of sensors and…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…