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Biomolecular condensates have been shown to play a fundamental role in localizing biochemistry in a cell. RNA is a common constituent of condensates, and can determine their biophysical properties. Functions of biomolecular condensates are…
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…
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding…
It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs…
Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species: (i) the number…
In the recent paper of Valleriani {\it et al} [Phys. Rev. E {\bf 83}, 042903 (2011)], a simple model for describing the translation of messenger RNA (mRNA) by ribosomes is presented, and an expression of the translational ratio $r$, defined…
A scheme to control the many-boson tunneling process to open space is derived and demonstrated. The number of ejected particles and their velocities can be controlled by two parameters, the threshold of the potential and the interparticle…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
The control of complex systems is of critical importance in many branches of science, engineering, and industry. Controlling an unsteady fluid flow is particularly important, as flow control is a key enabler for technologies in energy…
The intrinsic stochasticity of gene expression can lead to large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in…
Network control theory has recently emerged as a promising approach for understanding brain function and dynamics. By operationalizing notions of control theory for brain networks, it offers a fundamental explanation for how brain dynamics…
The paper investigates dynamical systems for which the derivative of some positive-definite function along the solutions of this system depends on so-called density function. In turn, such dynamical systems are called density systems. The…
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
A new control method that considers all sources of uncertainty and noises that might affect the time evolutions of quantum physical systems is introduced. Under the proposed approach, the dynamics of quantum systems are characterised by…
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…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…
The 5' UTR, a regulatory region at the beginning of an mRNA molecule, plays a crucial role in regulating the translation process and impacts the protein expression level. Language models have showcased their effectiveness in decoding the…