Related papers: Physical approaches to the dynamics of genetic cir…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Certain cellular processes take the form of activity pulses that can be interpreted in terms of noise-driven excitable dynamics. Here we present an overview of different gene circuit architectures that exhibit excitable pulses of protein…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
This article describes a numerical procedure designed to tune the parameters of periodically-driven dynamical systems to a state in which they exhibit rich dynamical behavior. This is achieved by maximizing the diversity of subharmonic…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Noisy fluctuations are ubiquitous in complex systems. They play a crucial or delicate role in the dynamical evolution of gene regulation, signal transduction, biochemical reactions, among other systems. Therefore, it is essential to…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
Cellular biology exists embedded in a world dominated by random dynamics and chance. Many vital molecules and pieces of cellular machinery diffuse within cells, moving along random trajectories as they collide with the other biomolecular…
Life is characterized by a myriad of complex dynamic processes allowing organisms to grow, reproduce, and evolve. Physical approaches for describing systems out of thermodynamic equilibrium have been increasingly applied to living systems,…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…