Related papers: Polyply: a python suite for facilitating simulatio…
We present a method for differentiable simulation of soft articulated bodies. Our work enables the integration of differentiable physical dynamics into gradient-based pipelines. We develop a top-down matrix assembly algorithm within…
We describe a novel, interdisciplinary, computational methods course that uses Python and associated numerical and visualization libraries to enable students to implement simulations for a number of different course modules. Problems in…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
Field-theoretical method is efficient in predicting the assembling structures of polymeric systems. However, for the polymer/nanoparticle mixture, the continuous density description is not suitable to capture the realistic assembly of…
Crystalline interfaces are of highly importance in many practical applications. To conduct effective simulation and analysis for coincident site lattice (CSL) interfaces, effective programmes are of high demand in building their CSL…
This thesis details a Python-based software designed to calculate the Jones polynomial, a vital mathematical tool from Knot Theory used for characterizing the topological and geometrical complexity of curves in \( \mathbb{R}^3 \), which is…
A variety of problems in device and materials design require the rapid forward modeling of Maxwell's equations in complex micro-structured materials. By combining high-order accurate integral equation methods with classical multiple…
In this paper, a new python package (optipoly) is described that solves box-constrained optimization problem over multivariate polynomial cost functions. The principle of the algorithm is described before its performance is compared to…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We discuss in detail a recently proposed hybrid particle-continuum scheme for complex fluids and evaluate it at the example of a confined homopolymer solution in slit geometry. The hybrid scheme treats polymer chains near the impenetrable…
We present the Python package CELL, which provides a modular approach to the cluster expansion (CE) method. CELL can treat a wide variety of substitutional systems, including one-, two-, and three-dimensional alloys, in a general…
As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…
Polyhedral nanocrystals are building blocks for nanostructured materials that find applications in catalysis and plasmonics. Synthesis efforts and self-assembly experiments have been assisted by computer simulations that predict phase…
Machine learning has rapidly advanced the design and discovery of new materials with targeted applications in various systems. First-principles calculations and other computer experiments have been integrated into material design pipelines…
BondGraphTools is a Python library for scripted modelling of complex multi-physics systems. In contrast to existing modelling solutions, BondGraphTools is based upon the well established bond graph methodology, provides a programming…
Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…
This article describes lcpy, an open-source python package that allows for advanced parametric Life Cycle Assessment (LCA) and Life Cycle Costing (LCC) analysis. The package is designed to allow the user to model a process with a flexible,…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
We introduce GenPhylo, a Python module that simulates nucleotide sequence data along a phylogeny avoiding the restriction of continuous-time Markov processes. GenPhylo uses directly a general Markov model and therefore naturally…