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Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various…
Many interesting phenomena are characterized by the complex interaction of different physical processes, each often best modeled numerically via a specific approach. In this paper, we present the design and implementation of an…
This article proposes a universal simulation platform for simulating systems undergoing duress. In other words, this paper introduces a total simulation package which includes a number of methods of simulating the flexibility of a given…
Underwater exploration offers critical insights into our planet and attracts increasing attention for its broader applications in resource exploration, national security, etc. We study the underwater scene understanding methods, which aim…
We explore using the Suggested Upper Merged Ontology (SUMO) to develop a semantic simulation. We provide two proof-of-concept demonstrations modeling transitions in a simulated gasoline engine using a general-purpose programming language.…
Recent research in materials science opens exciting perspectives to design novel quantum materials and devices, but it calls for quantitative predictions of properties which are not accessible in standard first principles packages. PAOFLOW…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…
This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the…
The Geant4 toolkit is the leading software for the simulation of particle transport through matter, widely used in nuclear physics, high-energy physics, and medical physics. However, the initial learning curve for new developers can be…
A liquid can be used to represent signals, actuate mechanical computing devices and to modify signals via chemical reactions. We give a brief overview of liquid based computing devices developed over hundreds of years. These include…
We describe NIMBLE, a system for programming statistical algorithms for general model structures within R. NIMBLE is designed to meet three challenges: flexible model specification, a language for programming algorithms that can use…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
This report presents the development and results of an advanced SPH (Smoothed Particle Hydrodynamics) simulation framework, designed for high fidelity fluid dynamics modeling. Our framework, accessible at…
This paper presents Non-Axiomatic Term Logic (NATL) as a theoretical computational framework of humanlike symbolic reasoning in artificial intelligence. NATL unites a discrete syntactic system inspired from Aristotle's term logic and a…
Cosmological field-level inference requires differentiable forward models that solve the challenging dynamics of gas and dark matter under hydrodynamics and gravity. We propose a hybrid approach where gravitational forces are computed using…
Cognitive BASIC is a minimal, BASIC-style prompting language and in-model interpreter that structures large language model (LLM) reasoning into explicit, stepwise execution traces. Inspired by the simplicity of retro BASIC, we repurpose…
Existing deep learning-based surrogate models facilitate efficient data generation, but fall short in uncertainty quantification, efficient parameter space exploration, and reverse prediction. In our work, we introduce SurroFlow, a novel…
FiniteFlow is a public framework for defining and executing numerical algorithms over finite fields and reconstructing multivariate rational functions. The framework allows to build complex algorithms by combining basic building blocks into…
An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…