Related papers: RiD-kit: Software package designed to do enhanced …
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics…
This paper demonstrates the integration model-based design approaches or vehicle control, with validation in a freely available open-source simulator. Continued interest in autonomous vehicles and their deployment is driven by the potential…
The Kilobot is a widely used platform for investigation of swarm robotics. Physical Kilobots are slow moving and require frequent recalibration and charging, which significantly slows down the development cycle. Simulators can speed up the…
Embedded systems have proliferated in various consumer and industrial applications with the evolution of Cyber-Physical Systems and the Internet of Things. These systems are subjected to stringent constraints so that embedded software must…
Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements,…
Enhanced sampling methods typically require predefined collective variables (CVs) that presuppose knowledge of reaction coordinates, restricting the discovery of unanticipated transition mechanisms or intermediates. Here, we show that a…
Large-scale datasets have been pivotal to the advancements of deep learning models in recent years, but training on such large datasets invariably incurs substantial storage and computational overhead. Meanwhile, real-world datasets often…
Randomized controlled trials (RCTs) are the gold standard for assessing drug safety and efficacy. However, RCTs have some drawbacks which have led to the use of single-arm studies to make certain internal drug development and regulatory…
We present KinetiX, a software toolkit to generate computationally efficient fuel-specific routines for the chemical source term, thermodynamic and mixture-averaged transport properties for use in combustion simulation codes. The C++…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Cloud computing provides engineers or scientists a place to run complex computing tasks. Finding a workflow's deployment configuration in a cloud environment is not easy. Traditional workflow scheduling algorithms were based on some…
I describe an approach to compiling common idioms in R code directly to native machine code and illustrate it with several examples. Not only can this yield significant performance gains, but it allows us to use new approaches to computing…
In order to find the most likely failure scenarios which may occur under certain given operation domain, critical-scenario-based test is supposed as an effective and widely used method, which gives suggestions for designers to improve the…
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective…
Many video workflows benefit from a mixture of user controls with varying granularity, from exact 4D object trajectories and camera paths to coarse text prompts, while existing video generative models are typically trained for fixed input…
Collective variable (CV) or order parameter based enhanced sampling algorithms have achieved great success due to their ability to efficiently explore the rough potential energy landscapes of complex systems. However, the degeneracy of…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Hybrid systems are increasingly used in critical applications such as medical devices, infrastructure systems, and autonomous vehicles. Lince is an academic tool for specifying and simulating such systems using a C-like language with…
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics.…