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The study of molecular dynamics simulations is largely facilitated by analysis and visualization toolsets. However, these toolsets are often designed for specific use cases and those only, while scripting extensions to such toolsets is…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
In recent years, cell-based assays have been frequently used in molecular interaction analysis. Cell-based assays complement traditional biochemical and biophysical methods, as they allow for molecular interaction analysis, mode of action…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Additive manufacturing (AM) techniques have been used to enhance the design and fabrication of complex components for various applications in the medical, aerospace, energy, and consumer products industries. A defining feature for many AM…
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like…
We present a multi-modal dialog system to assist online shoppers in visually browsing through large catalogs. Visual browsing is different from visual search in that it allows the user to explore the wide range of products in a catalog,…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
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…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…
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…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
Existing machine learning methods for molecular (e.g., gene) embeddings are restricted to specific tasks or data modalities, limiting their effectiveness within narrow domains. As a result, they fail to capture the full breadth of gene…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Molecular dynamics (MD) simulations have been widely applied to study macromolecules including proteins. However, high-dimensionality of the datasets produced by simulations makes it difficult for thorough analysis, and further hinders a…