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Microscopy techniques have played vital roles in materials science, biology, and nanotechnology, offering high-resolution imaging and detailed insights into properties at nanoscale and atomic level. The automation of microscopy experiments,…
Rapid and accurate simulations of fluid dynamics around complicated geometric bodies are critical in a variety of engineering and scientific applications, including aerodynamics and biomedical flows. However, while scientific machine…
To accurately study chemical reactions in the condensed phase or within enzymes, both a quantum-mechanical description and sufficient configurational sampling is required to reach converged estimates. Here, quantum mechanics/molecular…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…
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…
Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Polymers are a versatile class of materials with widespread industrial applications. Advanced computational tools could revolutionize their design, but their complex, multi-scale nature poses significant modeling challenges. Conventional…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective…
In this paper, we present ScalarFlow, a first large-scale data set of reconstructions of real-world smoke plumes. We additionally propose a framework for accurate physics-based reconstructions from a small number of video streams. Central…
Cryo-electron tomography (cryo-ET) provides a unique window into molecular organization in cellular environments (in situ). However, the interpretation of molecular structural information is complicated by several intrinsic properties of…
MLMOD is a software package for incorporating machine learning approaches and models into simulations of microscale mechanics and molecular dynamics in LAMMPS. Recent machine learning approaches provide promising data-driven approaches for…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic, steric, electron density…