Related papers: Translational control of gene expression via inter…

Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore…

An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…

Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…

Cell migration is essential for regulating many biological processes in physiological or pathological conditions, including embryonic development and cancer invasion. In vitro and in silico studies suggest that collective cell migration is…

To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…

Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…

A common approach in robotics is to learn tasks by generalizing from special cases given by a so-called demonstrator. In this paper, we apply this paradigm and present an algorithm that uses a demonstrator (typically given by a trajectory…

Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane…

Feedback loops are known as a versatile tool for controlling transport in small systems, which usually have large intrinsic fluctuations. Here we investigate the control of a temporal correlation function, the waiting time distribution,…

The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…

Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…

Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…

Controlling a dynamical system is the ability of changing its configuration arbitrarily through a suitable choice of inputs. It is a very well studied concept in control theory, with wide ranging applications in medicine, biology, social…

Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…

Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…

Metastasis is a process of cell migration that can be collective and guided by chemical cues. Viewing metastasis in this way, as a physical phenomenon, allows one to draw upon insights from other studies of collective sensing and migration…

Protein mean and variance levels in a simple stochastic gene expression circuit are controlled using proportional integral feedback. It is shown that the protein mean level can be globally and robustly tracked to any desired value using a…

Expression level is known to be a strong determinant of a protein's rate of evolution. But the converse can also be true: evolutionary dynamics can affect expression levels of proteins. Having implications in both directions fosters the…

Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…

The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…