相关论文: From Byte to Bench to Bedside: Molecular Dynamics …
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…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
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…
Clinical trials are an indispensable part of the drug development process, bridging the gap between basic research and clinical application. During the development of new drugs, clinical trials are used not only to evaluate the safety and…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
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…
Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force field accuracy. Notwithstanding this, MD will still be in the…
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)…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
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…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Controlled drug delivery (CDD), the controlled release and delivery of therapeutic drugs inside the human body, is a promising approach to increase the efficacy of drug administration and reduce harmful side effects to the body. CDD has…
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…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
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…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
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…