Related papers: MDsrv -- visual sharing and analysis of molecular …
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
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…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Microbiomes are a vital part of the human body, engaging in tasks like food digestion and immune defense. Their structure and function must be understood in order to promote host health and facilitate swift recovery during disease. Due to…
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) simulation is widely used to analyze the properties of molecules and materials. Most practical applications, such as comparison with experimental measurements, designing drug molecules, or optimizing materials, rely…
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…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this,…
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…
We present a method for producing documentary-style content using real-time scientific visualization. We produce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology. We employ scalable methods…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…
Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for…
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…
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…
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…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
The molecular dynamics (MD) simulation technique has been widely used in complex systems, but the accessible time scale is limited due to the requirement of small integration timesteps. Here, we propose a novel method, named Exploratory…