Related papers: PULSEDYN - A dynamical simulation tool for studyin…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
This paper presents a novel approach for propagating uncertainties in dynamical systems building on high-order Taylor expansions of the flow and moment-generating functions (MGFs). Unlike prior methods that focus on Gaussian distributions,…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
We demonstrate that pulses of linear physical systems, weakly perturbed by nonlinear dissipation, exhibit soliton-like behavior in fast collisions. The behavior is demonstrated for linear waveguides with weak cubic loss and for systems…
FluidDyn is a project to foster open-science and open-source in the fluid dynamics community. It is thought of as a research project to channel open-source dynamics, methods and tools to do science. We propose a set of Python packages…
Reachable set computation is an important technique for the verification of safety properties of dynamical systems. In this paper, we investigate reachable set computation for discrete nonlinear systems based on parallelotope bundles. The…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
We propose a novel way of assessing and fusing noisy dynamic data using a Tsetlin Machine. Our approach consists in monitoring how explanations in form of logical clauses that a TM learns changes with possible noise in dynamic data. This…
This article introduces TinyDEM, a lightweight implementation of a full-fledged discrete element method (DEM) solver in 3D. Newton's damped equations of motion are solved explicitly for translations and rotations of a polydisperse ensemble…
We present Bill2d, a modern and efficient C++ package for classical simulations of two-dimensional Hamiltonian systems. Bill2d can be used for various billiard and diffusion problems with one or more charged particles with interactions,…
In this paper, we present a novel research software, called PEGASE, suitable for the design, validation and deployment of advanced control strategies for complex multi-domain energy systems. PEGASE especially features a highly efficient…
Understanding the behavior and evolution of a dynamical many-body system by analyzing patterns in their experimentally captured images is a promising method relevant for a variety of living and non-living self-assembled systems. The arrays…
We show that a pulsed stimulus can be used to generate many-body quantum coherences in light-matter systems of general size. Specifically, we calculate the exact real-time evolution of a driven, generic out-of-equilibrium system comprising…
P-systems are abstract computational models inspired by the phospholipid bilayer membranes generated by biological cells. Illustrated here is a mechanism by which recursive liposome structures (multivesicular liposomes) may be…
Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…
Extensively exploring protein conformational landscapes remains a major challenge in computational biology due to the high computational cost involved in dynamic physics-based simulations. In this work, we propose a novel pipeline, MoDyGAN,…
In this study, the numerical analysis of a specific fluid-solid interaction problem is detailed. The weakly nonlinear Boussinesq system is considered with the addition of a solid object lying on the flat bottom, allowed to move horizontally…
Computational fluid dynamics (CFD) is increasingly used to study blood flows in patient-specific arteries for understanding certain cardiovascular diseases. The techniques work quite well for relatively simple problems, but need…
In this work, we suggest an easy-to-code higher-order finite volume semi-discrete scheme to analyze the nonlinear behavior of the electron-plasma oscillations by solving electron fluid equations numerically. The present method employs a…