Related papers: A Set of Tutorials for the LAMMPS Simulation Packa…
Molecular dynamics (MD) simulations are essential for understanding biomolecular systems but remain challenging to automate. Recent advances in large language models (LLM) have demonstrated success in automating complex scientific tasks…
The promise of AI-driven scientific discovery hinges on whether AI agents can autonomously design and execute the computational workflows that underpin modern science. Molecular dynamics (MD) simulation presents a natural test bed to…
Numerical simulations are a powerful tool to study quantum systems beyond exactly solvable systems lacking an analytic expression. For one-dimensional entangled quantum systems, tensor network methods, amongst them Matrix Product States…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
A new open source tool for fluid simulation of multi-component plasmas is presented, based on a flexible software design that is applicable to scientific simulations in a wide range of fields. This design enables the same code to be…
Traditional force-fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab-initio accuracy at low…
Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting…
Machine learning interatomic potentials (MLIPs) enables molecular dynamics (MD) simulations with ab initio accuracy and has been applied to various fields of physical science. However, the performance and transferability of MLIPs are…
In this work, methods are presented to automatically generate a fully atomistic LAMMPS models of arbitrary linear multiblock polyurethane copolymers. The routine detailed here receives as parameters the number of repeat units per hard…
The integration of large language models (LLMs) into materials science offers a transformative opportunity to streamline computational workflows, yet current agentic systems remain constrained by rigid, carefully crafted domain-specific…
The Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of…
Simulation studies are computer experiments that involve creating data by pseudorandom sampling. The key strength of simulation studies is the ability to understand the behaviour of statistical methods because some 'truth' (usually some…
Engineers widely rely on simulation platforms like COMSOL or ANSYS to model and optimise processes. However, setting up such simulations requires expertise in defining geometry, generating meshes, establishing boundary conditions, and…
Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…
Large Language Models (LLMs) demonstrate remarkable performance in semantic understanding and generation, yet accurately assessing their output reliability remains a significant challenge. While numerous studies have explored calibration…
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…
Running complex sets of machine learning experiments is challenging and time-consuming due to the lack of a unified framework. This leaves researchers forced to spend time implementing necessary features such as parallelization, caching,…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
After many years of development of the basic tools, quantum simulation with ultracold atoms has now reached the level of maturity where it can be used to investigate complex quantum processes. Planning of new experiments and upgrading…
Argon molecular dynamics (MD) simulations are performed with a newly developed MD program, Easy M(1)odular M(2)olecular M(3)echanics (EM3). The program was developed in an object-oriented fashion containing classes for each critical part of…