Related papers: Polyply: a python suite for facilitating simulatio…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to…
Combinatorial group testing reduces screening costs and turnaround time but remains challenging to apply due to design complexity, varying applicability, and lack of implementation tools. Here we present PoolPy, a unified end-to-end…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…
The solutions of a system of polynomials in several variables are often needed, e.g.: in the design of mechanical systems, and in phase-space analyses of nonlinear biological dynamics. Reliable, accurate, and comprehensive numerical…
SkyPy is an open-source Python package for simulating the astrophysical sky. It comprises a library of physical and empirical models across a range of observables and a command-line script to run end-to-end simulations. The library provides…
The growing complexity of Cyber-Physical Systems (CPS), together with increasingly available parallelism provided by multi-core chips, fosters the parallelization of simulation. Simulation speed-ups are expected from co-simulation and…
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…
Multiplex tissue immunostaining is a technology of growing relevance as it can capture in situ the complex interactions existing between the elements of the tumor microenvironment. The existence and availability of large, annotated image…
Polymers are a versatile class of materials with widespread industrial applications. Advanced computational tools could revolutionize their design, but their complex, multi-scale nature poses significant modeling challenges. Conventional…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
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 employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
The lack of freely available (real-life or synthetic) high or ultra-high dimensional, multi-class datasets may hamper the rapidly growing research on feature screening, especially in the field of biometrics, where the usage of such datasets…
High-throughput computational screening of polymers offers a powerful way to address the imbalance between the vast number of polymers synthesised for diverse applications and the relatively small subset that can be studied using atomistic…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…
We present pyroomacoustics, a software package aimed at the rapid development and testing of audio array processing algorithms. The content of the package can be divided into three main components: an intuitive Python object-oriented…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…