Related papers: Negative Feedback and Physical Limits of Genes
The design of codes for feedback-enabled communications has been a long-standing open problem. Recent research on non-linear, deep learning-based coding schemes have demonstrated significant improvements in communication reliability over…
The effects of carrying capacity of environment $K$ for degradation (the $K$ effect for short) on the constitutive gene expression and a simple genetic regulation system, are investigated by employing a stochastic Langevin equation combined…
Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells, is, however, a wide open question. We present a…
Spiking neural networks offer low energy consumption due to their event-driven nature. Beyond binary spike outputs, their intrinsic floating-point dynamics merit greater attention. Neuronal threshold levels and reset modes critically…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other, and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we…
Gene expression is inherently a noisy process which manifests as cell-to-cell variability in time evolution of proteins. Consequently, events that trigger at critical threshold levels of regulatory proteins exhibit stochasticity in their…
Appropriate regulation of gene expression is essential to ensure that protein synthesis occurs in a selective manner. The control of transcription is the most dominant type of regulation mediated by a complex of molecules such as…
Studies using assays to quantify the expression of thousands of genes on tens to thousands of cell samples have been carried out for over 20 years. Such assays are based on microarrays, DNA sequencing or other molecular technologies. All…
In many biological networks the responses of individual elements are ambiguous. We consider a scenario in which many sensors respond to a shared signal, each with limited information capacity, and ask that the outputs together convey as…
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show…
Switching controlled dynamics allows for fast, flexible control design methods for quantum stabilization of pure states and subspaces, which naturally include both Hamiltonian and dissipative control actions. A novel approach to…
Electro-optical feedback has many features in common with optical nonlinearities and hence is relevant to the generation of squeezing. First, I discuss theoretical and experimental results for traveling-wave feedback, emphasizing how the…
Over the last several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Though many stochastic effects have been explained, the source of transcriptional bursting (one of the most…
The process that prevents the deposition of cooled gas in cooling flows must rely on feedback in order to maintain gas with short cooling times, while preventing the bulk of the gas from cooling to low temperatures. The primary candidate…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
It is demonstrated, by means of analogue electronic simulation and theoretically, that external noise can markedly change the character of the response of a nonlinear system to a low-frequency periodic field. In general, noise of sufficient…
Expression of cellular genes is regulated by binding of transcription factors to their promoter, either activating or inhibiting transcription of a gene. Particularly interesting is the case when the expressed protein regulates its own…
Gene expression is stochastic and displays variation ("noise") both within and between cells. Intracellular (intrinsic) variance can be distinguished from extracellular (extrinsic) variance by applying the law of total variance to data from…