Related papers: Non-equilibrium, stochastic model for tRNA binding…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
A detailed stochastic model of single-gene auto-regulation is established and its solutions are explored when mRNA dynamics is fast compared with protein dynamics and in the opposite regime. The model includes all the sources of randomness…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a…
Transcription factors (TFs) interact with a multitude of binding sites on DNA and partner proteins inside cells. We investigate how nonspecific binding/unbinding to such decoy binding sites affects the magnitude and time-scale of random…
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…
This paper investigates the stochastic fluctuations of the number of copies of a given protein in a cell. This problem has already been addressed in the past and closed-form expressions of the mean and variance have been obtained for a…
During the initiation stage of protein synthesis, a ribosomal initiation complex (IC) is assembled on a messenger RNA (mRNA) template. In bacteria, the speed and accuracy of this assembly process are regulated by the complementary…
In order to express specific genes at the right time, the transcription of genes is regulated by the presence and absence of transcription factor molecules. With transcription factor concentrations undergoing constant changes, gene…
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000 - 16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of…
Determining the mechanism by which transfer RNAs (tRNAs) rapidly and precisely transit through the ribosomal A, P and E sites during translation remains a major goal in the study of protein synthesis. Here, we report the real-time dynamics…
Using the dynamic mean-field approximation of the totally asymmetric simple exclusion process (TASEP), we investigate the effect of small changes in the initiation, exit, and elongation rates along the mRNA strand on the steady state…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
To double the cellular population of ribosomes, a fraction of the active ribosomes is allocated to synthesize ribosomal proteins. Subsequently, these ribosomal proteins enter the ribosome self-assembly process, synthesizing new ribosomes…
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…
We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects (RFMEO). This model encapsulates many realistic features of translation including…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising…