Related papers: Polyply: a python suite for facilitating simulatio…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been…
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…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…
Nonlinearities and instabilities in mechanical structures have shown great promise for embedding advanced functionalities. However, simulating structures subject to nonlinearities can be challenging due to the complexity of their behavior,…
The advances in materials and biological sciences have necessitated the use of molecular simulations to study polymers. The Markov chain Monte Carlo simulations enable the sampling of relevant microstates of polymeric systems by traversing…
This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used…
RidePy enables fast computer simulations of on-demand mobility modes such as ridehailing or ridepooling. It strongly focuses on modeling the mobility service itself, rather than its customers or the environment. Through a combination of…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
We present FlowPM, a Particle-Mesh (PM) cosmological N-body code implemented in Mesh-TensorFlow for GPU-accelerated, distributed, and differentiable simulations. We implement and validate the accuracy of a novel multi-grid scheme based on…
Existing Python libraries and tools lack the ability to efficiently compute statistical test results for large datasets in the presence of missing values. This presents an issue as soon as constraints on runtime and memory availability…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
Due to the complex specifications of current electronic systems, design decisions need to be explored automatically. However, the exploration process is a complex task given the plethora of design choices such as the selection of…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step…
We present a "multipatch" infrastructure for numerical simulation of fluid problems in which sub-regions require different gridscales, different grid geometries, different physical equations, or different reference frames. Its key element…
Abstract polymer models are systems of weighted objects, called polymers, equipped with an incompatibility relation. An important quantity associated with such models is the partition function, which is the weighted sum over all sets of…