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Drug development is time and cost-consuming: It takes in average 10 years and 1 billion euros to move from a therapeutic target to a new drug. To speedup this process and reduce its cost, numerical simulation are massively used.…

We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…

Electronic structure simulation (ESS) has been used for decades to provide quantitative scientific insights on an atomistic scale, enabling advances in chemistry, biology, and materials science, among other disciplines. Following standard…

Arrays of gate-defined semiconductor quantum dots are among the leading candidates for building scalable quantum processors. High-fidelity initialization, control, and readout of spin qubit registers require exquisite and targeted control…

Masked diffusion language models (MDLMs) have recently emerged as a new paradigm in language modeling, offering flexible generation dynamics and enabling efficient parallel decoding. However, existing decoding strategies for pre-trained…

Molecular dynamics (MD) simulations are essential for understanding atomic-scale behaviors in materials science, yet writing LAMMPS scripts remains highly specialized and time-consuming tasks. Although LLMs show promise in code generation…

Computational fluid dynamics (CFD) has been the main workhorse of computational physics. Yet its steep learning curve and fragmented, multi-stage workflow create significant barriers. To address these challenges, we present Foam-Agent, a…

Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…

The Fusion Synthesis Engine (FUSE) is a state-of-the-art software suite designed to revolutionize fusion power plant design. FUSE integrates first-principle models, machine learning, and reduced models into a unified framework, enabling…

In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…

Generating precise 3D molecular geometries is crucial for drug discovery and material science. While prior efforts leverage 1D representations like SELFIES to ensure molecular validity, they fail to fully exploit the rich chemical knowledge…

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

OpenFMO framework, an open-source software (OSS) platform for Fragment Molecular Orbital (FMO) method, is extended to multi-physics simulations (MPS). After reviewing the several FMO implementations on distributed computer environments, the…

Computational Fluid Dynamics (CFD) serves as a powerful tool for simulating fluid flow across diverse industries. High-resolution CFD simulations offer valuable insights into fluid behavior and flow patterns, aiding in optimizing design…

Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…

We present the basic idea, implementation, measured performance and performance model of FDPS (Framework for developing particle simulators). FDPS is an application-development framework which helps the researchers to develop particle-based…

For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…

We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…

Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…

Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resulting in difficulties in spectral identification. Open Modification Search (OMS)…