Related papers: Adaptation and regulation with signal detection im…
We consider adaptive control problem in presence of nonlinear parametrization of uncertainties in the model. It is shown that despite traditional approaches require for domination in the control loop during adaptation, it is not often…
During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially or simultaneously. These growth patterns are manifested in all types of bacteria and yeasts. The ubiquity of these growth…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
Determining mechanistic models of gene regulation, especially underlying phenotypic variation, is a central goal of both mathematical biology and modern evolutionary biology. However, several challenges, involving both common…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative…
A system made up of N interacting species is considered. Self-reaction terms are assumed of the logistic type. Pairwise interactions take place among species according to different modalities, thus yielding a complex asymmetric disordered…
Identifiability conditions for single or multiple modules in a dynamic network specify under which conditions the considered modules can be uniquely recovered from the second-order statistical properties of the measured signals. Conditions…
In this paper, we study the problem of detecting multiple hidden submatrices in a large Gaussian random matrix when the planted signal is inhomogeneous across entries. Under the null hypothesis, the observed matrix has independent and…
Chemotaxis is the process by which cells behave in a way that follows the chemical gradient. Applications to bacteria growth, tissue inflammation, and vascular tumors provide a focus on optimization strategies. Experiments can characterize…
This paper presents a new parameter estimation algorithm for the adaptive control of a class of time-varying plants. The main feature of this algorithm is a matrix of time-varying learning rates, which enables parameter estimation error…
Biological organisms are adaptive, able to function in unpredictably changing environments. Drawing on recent nonequilibrium physics, we show that in adaptation, fitness has two components parameterized by observable coordinates: a static…
An important feature of many complex systems, both natural and artificial, is the structure and organization of their interaction networks with interesting properties. Here we present a theory of self-organization by evolutionary adaptation…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
We consider a physical system in which the description of states and measurements follow the usual quantum mechanical rules. We also assume that the dynamics is linear, but may not be fully quantum (i.e unitary). We show that in such a…
The process of diagnosis involves learning about the state of a system from various observations of symptoms or findings about the system. Sophisticated Bayesian (and other) algorithms have been developed to revise and maintain beliefs…
This paper formulates a framework for the analysis and distributed control of interconnected systems from the behavioural perspective. The discussions are carried out from the viewpoint of set theory and the results are completely…
A variety of physical, social and biological systems generate complex fluctuations with correlations across multiple time scales. In physiologic systems, these long-range correlations are altered with disease and aging. Such correlated…
The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…