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By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…

Populations and Evolution · Quantitative Biology 2025-10-01 Kevin Hudnall , Raissa D'Souza

Aleatory architectures explore new approaches and concepts at the intersection of granular materials research and architecture/structural engineering. It explicitly includes stochastic (re-) configuration of individual structural elements…

Soft Condensed Matter · Physics 2015-10-21 Sean Keller , Heinrich Jaeger

The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…

Biomolecules · Quantitative Biology 2013-08-06 Ruth Nussinov

The mechanics of crawling cells on a substrate is investigated by using a minimal model that satisfies the force-free condition. A cell is described by two subcellular elements connected by a linear actuator that changes the length of the…

Soft Condensed Matter · Physics 2018-04-18 Mitsusuke Tarama , Ryoichi Yamamoto

Given that observational and numerical climate data are being produced at ever more prodigious rates, increasingly sophisticated and automated analysis techniques have become essential. Deep learning is quickly becoming a standard approach…

Fluid Dynamics · Physics 2017-09-12 A. Rupe , J. P. Crutchfield , K. Kashinath , Prabhat

We study convex subsets of buildings, discuss some structural features and derive several characterizations of buildings.

Metric Geometry · Mathematics 2007-05-23 Andreas Balser , Alexander Lytchak

This chapter reviews four notions of system structure, three of which are contextual and classic (i.e. the complete computational structure linked to a state space model, the sparsity pattern of a transfer function, and the interconnection…

Systems and Control · Computer Science 2014-06-10 Vasu Chetty , Sean Warnick

In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…

Biological Physics · Physics 2019-11-12 Lautaro Vassallo , David Hansmann , Lidia A. Braunstein

This dissertation builds a compositional cyber-physical systems theory to develop concrete semantics relating the above diverse views necessary for safety and security assurance. In this sense, composition can take two forms. The first is…

Logic in Computer Science · Computer Science 2021-09-13 Georgios Bakirtzis

The innumerable shapes of plant leaves present a challenge to the explanatory power of biophysical theory. A model is needed that can produce these shapes with a small set of parameters. This paper presents a simple model of leaf shape…

Tissues and Organs · Quantitative Biology 2010-04-27 David A. Young

Here I describe a view of the evolution of cellular automata that allows to operate on larger structures. Instead of calculating the next state of all cells in one step, the method here developed uses a time slice that can proceed at…

Cellular Automata and Lattice Gases · Physics 2010-07-20 Markus Redeker

Software architecture is receiving increasingly attention as a critical design level for software systems. As software architecture design resources (in the form of architectural specifications) are going to be accumulated, the development…

Software Engineering · Computer Science 2009-09-25 Jianjun Zhao

We perform a comprehensive study of the formation of three dimensional (pyramidal) structures in a large range of conditions, including the possible evaporation of adatoms from the surface and the presence of surface defects. We compare our…

Materials Science · Physics 2016-08-16 Pablo Jensen , Hernán Larralde , Muriel Meunier , Alberto Pimpinelli

The shape of buildings plays a critical role in the energy efficiency, lifestyles, land use and infrastructure systems of cities. Thus, as most of the world's cities continue to grow and develop, understanding the interplay between the…

Physics and Society · Physics 2015-12-04 Markus Schläpfer , Joey Lee , Luís M. A. Bettencourt

The accumulation of adaptations in an open-ended manner during lifetime learning is a holy grail in reinforcement learning, intrinsic motivation, artificial curiosity, and developmental robotics. We present a specification for a cognitive…

Artificial Intelligence · Computer Science 2013-03-29 Chrisantha Fernando , Vera Vasas

Starting from the working hypothesis that both physics and the corresponding mathematics have to be described by means of discrete concepts on the Planck scale, one of the many problems one has to face in this enterprise is to find the…

High Energy Physics - Theory · Physics 2008-11-26 Manfred Requardt

We describe a percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Tissues are considered as structures made of regular healthy,…

Statistical Mechanics · Physics 2016-01-28 Vladimir Privman , Vyacheslav Gorshkov , Sergiy Libert

The covering approximation space evolves in time due to the explosion of the information, and the characteristic matrixes of coverings viewed as an effective approach to approximating the concept should update with time for knowledge…

Information Theory · Computer Science 2015-03-13 Guangming Lang , Qingguo Li , Lankun Guo , Chunyong Wang

This paper describes an agent-based model of a finite group of agents in a single population who each choose which convention to advocate, and which convention to practice. Influences or dependencies in agents choice exists in the form of…

Physics and Society · Physics 2009-09-30 A. K. M. Azhar , W. A. T. Wan Abdullah , M. Ruzlan

The first step in the construction of a regression model or a data-driven analysis, aiming to predict or elucidate the relationship between the atomic scale structure of matter and its properties, involves transforming the Cartesian…