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This paper presents `chipfiring`, a comprehensive Python package for the mathematical analysis of chip-firing games on finite graphs. The package provides a robust toolkit for defining graphs and chip configurations (divisors), performing…
ergodicity is an open-source Python library for computational work on stochastic dynamics, with particular emphasis on non-ergodicity, time-average behavior, heavy-tailed processes, and decision making under uncertainty. The package brings…
We consider the stability and the input-output analysis problems of a class of large-scale hybrid systems composed of continuous dynamics coupled with discrete dynamics defined over finite alphabets, e.g., deterministic finite state…
The self consistent version of the density functional theory (DFT) is presented, which allows to calculate the ground state and dynamic properties of finite multi-electron systems such as atoms, molecules and clusters. The exact functional…
Misconceptions about program execution hinder many novice programmers. We introduce SimpliPy, a notional machine designed around a carefully chosen Python subset to clarify core control flow and scoping concepts. Its foundation is a precise…
Dynamic Binary Instrumentation (DBI) is the set of techniques that enable instrumentation of programs at run-time, making it possible to monitor and modify the execution of compiled binaries or entire systems. DBI is used for countless…
In this work, we present a software package in Python for high-throughput first-principles calculations of thermodynamic properties at finite temperatures, which we refer to as DFTTK (Density Functional Theory Tool Kit). DFTTK is based on…
Density functional theory (DFT) serves as the basis for computational discovery in materials science and chemistry, yet each calculation demands extensive human effort: adjusting algorithms when convergence stalls, revising plans when…
We introduce giotto-tda, a Python library that integrates high-performance topological data analysis with machine learning via a scikit-learn-compatible API and state-of-the-art C++ implementations. The library's ability to handle various…
Evolutionary Game Theory (EGT) simulations are used to model populations undergoing biological and cultural evolution in a range of fields, from biology to economics to linguistics. In this paper we present DyPy, an open source Python…
In this paper, the author aims to establish a mathematical model for a mimic computer. To this end, a novel automaton is proposed. First, a one-dimensional cellular automaton is used for expressing some dynamic changes in the structure of a…
SfePy (Simple finite elements in Python) is a software for solving various kinds of problems described by partial differential equations in one, two or three spatial dimensions by the finite element method. Its source code is mostly (85\%)…
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…
Cellular automata are often used to model systems in physics, social sciences, biology that are inherently asynchronous. Over the past 20 years, studies have demonstrated that the behavior of cellular automata drastically changed under…
The Besicovitch pseudo-metric is a shift-invariant pseudo-metric on the set of infinite sequences, that enjoys interesting properties and is suitable for studying the dynamics of cellular automata. They correspond to the asymptotic behavior…
Programs written in dynamic languages make heavy use of features --- run-time type tests, value-indexed dictionaries, polymorphism, and higher-order functions --- that are beyond the reach of type systems that employ either purely syntactic…
Dynamical density functional theory (DDFT) is a powerful variational framework to study the nonequilibrium properties of colloids by only considering a time-dependent one-body number density. Despite the large number of recent successes,…
Combined modeling and verification of dynamic systems and the data they operate on has gained momentum in AI and in several application domains. We investigate the expressive yet concise framework of data-aware dynamic systems (DDS),…
A new class of exclusion type processes acting in continuum with synchronous updating is introduced and studied. Ergodic averages of particle velocities are obtained and their connections to other statistical quantities, in particular to…
In this paper, we study infinite dimensional stochastic systems having both unbounded control and observation operators. First of all, using a semigroup approach, we give another take of the well-posedness of such systems treated in [SIAM…