Related papers: Controllability analysis and control synthesis for…
Synthetic biology is an interdisciplinary field aiming to design biochemical systems with desired behaviors. To this end, molecular controllers have been developed which, when embedded into a pre-existing ambient biochemical network,…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited,…
The control of complex systems is an ongoing challenge of complexity research. Recent advances using concepts of structural control deduce a wide range of control related properties from the network representation of complex systems. Here,…
TASEP modeling was shown to offer a parsimonious explanation for the experimentally confirmed ability of a single upstream Open Reading Frames (uORFs) to upregulate downstream translation during the integrated stress response. As revealed…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…
With the advantages of high modeling accuracy and large bandwidth, recurrent neural network (RNN) based inversion model control has been proposed for output tracking. However, some issues still need to be addressed when using the RNN-based…
Coherent control of bound state processes via the interfering overlapping resonances scenario [Christopher et al., J. Chem. Phys. 123, 064313 (2006)] is developed to control intramolecular vibrational redistribution (IVR). The approach is…
Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare…
In this paper, we use the framework of infinitesimal homeostasis to study general design principles for the occurrence of homeostasis in gene regulatory networks. We assume that the dynamics of the genes explicitly includes both…
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription…
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.…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
In $\textit{Escherichia coli}$ bacterium, the molecular compounds involved in protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked intracellular localization patterns. Yet a quantitative understanding of the physical…