Related papers: ProtoMD: A Prototyping Toolkit for Multiscale Mole…
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
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…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
We present PyAtoms, an interactive open-source software that rapidly simulates atomic-scale scanning tunneling microscopy (STM) and other scanning probe microscopy (SPM) images of two-dimensional (2D) layered materials, moir\'{e} systems,…
AMDAT (Amorphous Molecular Dynamics Analysis Toolkit) is an open-source C++ toolkit for post-processing molecular dynamics trajectories, focused on high-performance static and dynamic analyses of amorphous, glassy, and polymer materials,…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
This paper introduces AcCoRD (Actor-based Communication via Reaction-Diffusion) version 1.0. AcCoRD is a sandbox reaction-diffusion solver designed for the study of molecular communication systems. It uses a hybrid of microscopic and…
Progress in hardware, algorithms, and force fields are pushing the scope of molecular dynamics (MD) simulations towards the length- and time scales of complex biochemical processes. This creates a need for developing advanced analysis…
We previously introduced a conformational sampling method, a multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD), to enhance conformational sampling of a biomolecular system by computer simulations. Here, we present a new…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
This paper presents a rapid-prototype Model Predictive Control (MPC) tool based on the gPROMS platform, with the support for the whole MPC design workflow. The gPROMS-MPC tool can not only directly interact with a first-principle-based…
Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug…
Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
Multimodal approaches that integrate histology and genomics hold strong potential for precision oncology. However, phenotypic and genotypic heterogeneity limits the quality of intra-modal representations and hinders effective inter-modal…