Related papers: Optimizing information flow in small genetic netwo…
Eukaryotic cell development has been optimized by natural selection to obey maximal intracellular flux of messenger proteins. This, in turn, implies maximum Fisher information on angular position about a target nuclear pore complex (NPR).…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
This paper considers distribution systems with a high penetration of distributed, renewable generation and addresses the problem of incorporating the associated uncertainty into the optimal operation of these networks. Joint chance…
Biological neurons have adaptive nature and perform complex computations involving the filtering of redundant information. However, most common neural cell models, including biologically plausible, such as Hodgkin-Huxley or Izhikevich, do…
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,…
This dissertation is a study on the design and analysis of novel, optimal routing and rate control algorithms in wireless, mobile communication networks. Congestion control and routing algorithms upto now have been designed and optimized…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
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…
Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…
Living cells presumably employ optimized information transfer methods, enabling efficient communication even in noisy environments. As expected, the efficiency of chemical communications between cells depends on the properties of the…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
Biological cells are able to accurately sense chemicals with receptors at their surfaces, allowing cells to move towards sources of attractant and away from sources of repellent. The accuracy of sensing chemical concentration is ultimately…
Gene regulation relies on the specificity of transcription factor (TF) - DNA interactions. In equilibrium, limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate…
Numerous biological functions-such as enzymatic catalysis, the immune response system, and the DNA-protein regulatory network-rely on the ability of molecules to specifically recognize target molecules within a large pool of similar…
Regulatory networks (RNs) are a well-accepted modelling formalism in computational systems biology. The control of RNs is currently receiving a lot of attention because it provides a computational basis for cell reprogramming -- an…
We examine deterministic broadcasting on multiple-access channels for a scenario when packets are injected continuously by an adversary to the buffers of the devices at rate $\rho$ packages per round. The aim is to maintain system…
We consider a class of optimal control problems on networks that generically permits a reduction to a universal set of reference problems without differential constraints that may be solved analytically. The derivation shows that input…
Random linear network coding (RLNC) has been shown to efficiently improve the network performance in terms of reducing transmission delays and increasing the throughput in broadcast and multicast communications. However, it can result in…