Related papers: Complexity and self-organization in Turing
Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our…
The purpose of this paper is two-fold. First we explain the construction of the canonical model of filtered $A_\infty$-algebras given in the authors' book [FOOO]. The canonical model plays a crucial role in the study of Lagrangian Floer…
Chemical transformations depend not only on the identities of the reacting species but also on the catalytic, environmental, and intermediate conditions under which they occur. Classical binary reaction formalisms usually treat such…
The precise nature of chemical-bonding interactions in amorphous, and crystalline, chalcogenides is still unclear due to the complexity arising from the delocalization of bonding, and non-bonding, electrons. Although an increasing degree of…
The diffusion-driven Turing instability is a potential mechanism for spatial pattern formation in numerous biological and chemical systems. However, engineering these patterns and demonstrating that they are produced by this mechanism is…
Book Chapter from "Coarse-Grained Modeling of Biomolecules" part of the submitted "Series in Computational Biophysics"
Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in…
Basic issues of the general model-building framework of the mechanics of complex bodies are discussed. Attention is focused on the representation of the material elements, the conditions for the existence of ground states in conservative…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
Data Science and Machine learning have been growing strong for the past decade. We argue that to make the most of this exciting field we should resist the temptation of assuming that forecasting can be reduced to brute-force data analytics.…
Natural language processing models have emerged that can generate usable software and automate a number of programming tasks with high fidelity. These tools have yet to have an impact on the chemistry community. Yet, our initial testing…
It has been shown recently (Shalygo, 2014) that stationary and dynamic patterns can arise in the proposed one-component model of the analog (continuous state) kinetic automaton, or kinon for short, defined as a reflexive dynamical system…
A Comment on the Letter by M. Rupp et al., Phys. Rev. Lett. 108 058301 (2012).
A brief introduction of the technical approach to model FTUs as an aggregate of cells, whose state transition dynamics are mathematically represented as port-hamiltonians or Differential Algebraic equations is presented. A python library…
This article presents formalistic tool for description of structural and biochemical relations between cells in the course of development of the body of plants. This is flexible formalistic space, based on the Category theory and the Petri…
The spatial character of territorial systems plays a crucial role in the emergence of their complexities. This contribution aims at illustrating to what extent different types of complexities can be exhibited in models of such systems. We…
Based on laboratory based growth of plant-like structures from inorganic materials, we present new theory for the emergence of plant structure at a range of scales dictated by levels of ionization (charge density), which can be traced…
This is an investigation of the role of shuffling and concatenating in the theory of graph drawing. A simple syntactic description of these and related operations is proved complete in the context of finite partial orders, as general as…
The Turing Award is recognized as the most influential and prestigious award in the field of computer science(CS). With the rise of the science of science (SciSci), a large amount of bibliographic data has been analyzed in an attempt to…
Recent uses of differential geometry in materials science are reviewed here, in particular the September issue of the Phil. Trans. Royal Soc., entitled ``Curvature and chemical Structure.''