Related papers: Control systems for synthetic biology and a case-s…
In this paper, we consider the problem of optimal exogenous control of gene regulatory networks. Our approach consists in adapting an established reinforcement learning algorithm called the fitted Q iteration. This algorithm infers the…
A challenge in global change biology is to predict how species will respond to future environmental change and to manage these responses. To make such predictions and management actions robust to novel futures, we need to accurately…
Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first genetic circuits -- the repressilator and the toggle switch -- were designed and implemented, many advances have been made in this area of research.…
Living cells need a constant availability of certain resources to have a sustained gene expression process. Limited availability of cellular resources for gene expression, like ribosomes, along with a variation of resource affinity,…
Very high dimensional nonlinear systems arise in many engineering problems due to semi-discretization of the governing partial differential equations, e.g. through finite element methods. The complexity of these systems present…
The performance, reliability, cost, size and energy usage of computing systems can be improved by one or more orders of magnitude by the systematic use of modern control and optimization methods. Computing systems rely on the use of…
We consider the problem of approximating discrete-time plants with finite-valued sensors and actu- ators by deterministic finite memory systems for the purpose of certified-by-design controller synthesis. Building on ideas from robust…
The concepts and methods of Systems Biology are being extended to neuropharmacology, to test and design drugs against neurological and psychiatric disorders. Computational modeling by integrating compartmental neural modeling technique and…
The integral control of positive systems using nonnegative control input is an important problem arising, among others, in biochemistry, epidemiology and ecology. An immediate solution is to use an ON-OFF nonlinearity between the controller…
Genetic algorithms, as implemented in optimal control strategies, are currently successfully exploited in a wide range of problems in molecular physics. In this context, laser control of molecular alignment and orientation remains a very…
The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
Controlling an evolving population is an important task in modern molecular genetics, including directed evolution for improving the activity of molecules and enzymes, in breeding experiments in animals and in plants, and in devising public…
The event-triggered control with intermittent output can reduce the communication burden between the controller and plant side over the network. It has been exploited for adaptive output feedback control of uncertain nonlinear systems in…
The application of systems and control theory to membrane physiology is presented here. Modeling efforts have focused on describing those physiologically realistic mechanisms which govern the regulation of membrane permeability in nerve.…
We present the epithelial-to-mesenchymal transition (EMT) from two perspectives: experimental/technological and theoretical. We review the state of the current understanding of the regulatory networks that underlie EMT in three…
Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
The process of programmed cell death, namely apoptosis, is a natural mechanism that regulates healthy tissue, multicellular structures, and homeostasis. An improved understanding of apoptosis can significantly enhance our knowledge of…