Related papers: PLUMED 2: New feathers for an old bird
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
Molecular dynamics (MD) enables the study of physical systems with excellent spatiotemporal resolution but suffers from severe time-scale limitations. To address this, enhanced sampling methods have been developed to improve exploration of…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
We present a framework for efficiently performing Monte Carlo wave-function simulations in cavity QED with moving particles. It relies heavily on the object-oriented programming paradigm as realised in C++, and is extensible and applicable…
The significant increase in software production, driven by the acceleration of development cycles over the past two decades, has led to a steady rise in software vulnerabilities, as shown by statistics published yearly by the CVE program.…
Getting the best performance from the ever-increasing number of hardware platforms has been a recurring challenge for data processing systems. In recent years, the advent of data science with its increasingly numerous and complex types of…
Recent advancements in reasoning-based Large Language Models (LLMs), particularly their potential through test-time scaling, have created significant opportunities for distillation in code generation and critique. However, progress in both…
Graphic Processing Units (GPUs) have become ubiquitous in scientific computing. However, writing efficient GPU kernels can be challenging due to the need for careful code tuning. To automatically explore the kernel optimization space,…
Version 2.10 of the Distributed and Unified Numerics Environment DUNE introduces a range of enhancements across its core and extension modules, with a continued emphasis on modern C++ integration and improved usability. This release extends…
There is a pressing need for better development methods and tools to keep up with the growing demand and increasing complexity of new software systems. New types of user interfaces, the need for intelligent components, sustainability…
Multimodal Large Language Models (MLLMs) achieve versatility by reformulating diverse tasks into a unified instruction-following framework via instruction tuning. However, real-world deployment requires continuous adaptation to emerging…
The purpose of this paper is to introduce Condensed-Matter-Laboratory (CML) application for simulating solids and nanostructures and calculating different properties of them by density functional theory and using Green's function theory in…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
Despite impressive advancements in recent multimodal reasoning approaches, they are still limited in flexibility and efficiency, as these models typically process only a few fixed modality inputs and require updates to numerous parameters.…
The rapid growth of deep learning has driven exponential increases in model parameters and computational demands. NVIDIA GPUs and their CUDA-based software ecosystem provide robust support for parallel computing, significantly alleviating…
Probabilistic Programming Languages (PPLs) are a powerful tool in machine learning, allowing highly expressive generative models to be expressed succinctly. They couple complex inference algorithms, implemented by the language, with an…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…
The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without…