Related papers: Physical approaches to the dynamics of genetic cir…
Dynamic gene-regulatory networks are complex since the number of potential components involved in the system is very large. Estimating dynamic networks is an important task because they compromise valuable information about interactions…
Understanding computational capabilities of simple biological circuits, such as the regulatory circuits of single-cell organisms, remains an active area of research. Recent theoretical work has shown that a simple regulatory architecture…
Experiments performed on a wide range of glassy materials display many interesting phenomena, such as aging behavior. In recent years, a large body of experiments probed this nonequilibrium glassy dynamics through elaborate protocols, in…
The work is devoted to the analysis of cell population dynamics where cells make a choice between differentiation and apoptosis. This choice is based on the values of intracellular proteins whose concentrations are described by a system of…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
The whole complex process to obtain a protein encoded by a gene is difficult to include in a mathematical model. There are many models for describing different aspects of a genetic network. Finding a better model is one of the most…
Many natural systems are organized as networks, in which the nodes (be they cells, individuals or populations) interact in a time-dependent fashion. The dynamic behavior of these networks depends on how these nodes are connected, which can…
Quantum circuits -- built from local unitary gates and local measurements -- are a new playground for quantum many-body physics and a tractable setting to explore universal collective phenomena far-from-equilibrium. These models have shed…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
Many real-world scientific processes are governed by complex nonlinear dynamic systems that can be represented by differential equations. Recently, there has been increased interest in learning, or discovering, the forms of the equations…
This chapter revisits the concept of excitability, a basic system property of neurons. The focus is on excitable systems regarded as behaviors rather than dynamical systems. By this we mean open systems modulated by specific interconnection…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…
Habituation - a phenomenon in which a dynamical system exhibits a diminishing response to repeated stimulations that eventually recovers when the stimulus is withheld - is universally observed in living systems from animals to unicellular…
The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…
A wide range of organisms use circadian clocks to keep internal sense of daily time and regulate their behavior accordingly. Most of these clocks use intracellular genetic networks based on positive and negative regulatory elements. The…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…