相关论文: Prototyping Bio-Nanorobots using Molecular Dynamic…

Predicting material properties of 3D printed polymer products is a challenge in additive manufacturing due to the highly localized and complex manufacturing process. The microstructure of such products is fundamentally different from the…

Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…

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…

Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…

Design of robots at the small scale is a trial-and-error based process, which is costly and time-consuming. There are few dynamic simulation tools available to accurately predict the motion or performance of untethered microrobots as they…

Rapid robotic system development sets a demand for multi-disciplinary methods and tools to explore and compare design alternatives. In this paper, we present collaborative modeling that combines discrete-event models of controller software…

Soft-growing robots (i.e., vine robots) are a promising class of soft robots that allow for navigation and growth in tightly confined environments. However, these robots remain challenging to model and control due to the complex interplay…

Robotics simulation has been an integral part of research and development in the robotics area. The simulation eliminates the possibility of harm to sensors, motors, and the physical structure of a real robot by enabling robotics…

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…

Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…

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)…

As robots become increasingly prominent in diverse industrial settings, the desire for an accessible and reliable system has correspondingly increased. Yet, the task of meaningfully assessing the feasibility of introducing a new robotic…

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…

We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…

This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…

Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…

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 simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…

Molecular dynamics (MD) simulations provide crucial insight into molecular interactions and biomolecular function. With interactive MD simulations in VR (iMD-VR), chemists can now interact with these molecular simulations in real-time. Our…

Dynamical systems are ubiquitous within science and engineering, from turbulent flow across aircraft wings to structural variability of proteins. Although some systems are well understood and simulated, scientific imaging often confronts…