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Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new…
The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic, steric, electron density…
We propose a general stochastic formalism for describing the evolution of chemical reactions involving a finite number of molecules. This approach is consistent with the statistical analysis based on the Chemical Master Equation, and…
In this work we present a reactions module for "Chaos Many-Body Engine" (Grossu et al., 2010 [1]). Following our goal of creating a customizable, object oriented code library, the list of all possible reactions, including the corresponding…
A number of simple chaotic three-dimensional dynamical systems (DSs) with quadratic polynomials on the right-hand sides are reported in the literature, containing exactly 5 or 6 monomials of which only 1 or 2 are quadratic. However, none of…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
Machine learning techniques applied to chemical reactions has a long history. The present contribution discusses applications ranging from small molecule reaction dynamics to platforms for reaction planning. ML-based techniques can be of…
Modeling electronic systems is an important application for quantum computers. In the context of materials science, an important open problem is the computational description of chemical reactions on surfaces. In this work, we outline a…
A first version of a multi-scale, multi-physic hybrid model --called virtual material-- for predictions on Self-Healing Ceramic Matrix Composite's (CMCs) lifetime is presented. The model has a mechanical and a chemical part, which are…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational…
One of the main goals of Artificial Life is to research the conditions for the emergence of life, not necessarily as it is, but as it could be. Artificial Chemistries are one of the most important tools for this purpose because they provide…
In complex materials, numerous intertwined phenomena underlie the overall response at macroscale. These phenomena can pertain to different engineering fields (mechanical , chemical, electrical), occur at different scales, can appear as…
Three-dimensional concrete printing (3DCP) has gained a lot of popularity in recent years. According to many, 3DCP is set to revolutionize the construction industry: yielding unparalleled aesthetics, better quality control, lower cost, and…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
Colloidal particles can create reconfigurable nanomaterials, with applications such as color-changing, self-repairing, and self-regulating materials and reconfigurable drug delivery systems. However, top-down methods for manipulating…
In this paper, we propose a method to build molecular cages designed to capture a specific substrate. We model a cage as a graph of atoms with coordinates in space, and several constraints on their edges (degree, length and angle). We use a…