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Polymers-macromolecular systems composed of repeating chemical units-constitute the molecular foundation of living organisms, while their synthetic counterparts drive transformative advances across medicine, consumer products, and energy…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…
The Institute for Solid State Physics (ISSP) at The University of Tokyo has been carrying out a software development project named ``the Project for Advancement of Software Usability in Materials Science (PASUMS)". Since the launch of…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
We present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple…
Visual programming has the potential of providing novice programmers with a low-code experience to build customized processing pipelines. Existing systems typically require users to build pipelines from scratch, implying that novice users…
Text-to-image generative models can be tremendously valuable in supporting creative tasks by providing inspirations and enabling quick exploration of different design ideas. However, one common challenge is that users may still not be able…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
In this paper, we present pomdp_py, a general purpose Partially Observable Markov Decision Process (POMDP) library written in Python and Cython. Existing POMDP libraries often hinder accessibility and efficient prototyping due to the…
On-demand Polymer discovery is essential for various industries, ranging from biomedical to reinforcement materials. Experiments with polymers have a long trial-and-error process, leading to use of extensive resources. For these processes,…
We introduce TorchSim, an open-source atomistic simulation engine tailored for the Machine Learned Interatomic Potential (MLIP) era. By rewriting core atomistic simulation primitives in PyTorch, TorchSim can achieve orders of magnitude…
We present release 2.0 of the ALPS (Algorithms and Libraries for Physics Simulations) project, an open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models…
mlpack is an open-source C++ machine learning library with an emphasis on speed and flexibility. Since its original inception in 2007, it has grown to be a large project implementing a wide variety of machine learning algorithms, from…
Magpy is a C++ accelerated Python package for modelling and simulating the magnetic dynamics of nano-sized particles. Nanoparticles are modelled as a system of three-dimensional macrospins and simulated with a set of coupled stochastic…
Novice learners find motion as a continuous process of change challenging to understand. In this paper, we present a pedagogical approach based on agent-based, visual programming to address this issue. Integrating Logo programming with…
As the atomistic simulations of materials science move from traditional potentials to machine learning interatomic potential (MLIP), the field is entering the second phase focused on discovering and explaining new material phenomena. While…
We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract in- terface to common molecular dynamics codes, enabling rapid and portable development of…
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric…