Biology🧬 + Physics🔭

Transcription Networks - Basic Concepts The cell continuously monitors its environment and calculates the amount of each protein that is needed. The rate of production is controlled by transcription networks. To represent environmental states, cells use special proteins called transcription factors as symbols. Transcription factors are molecules that can rapidly switch between active and inactive molecular states, with rates determined by environmental factors. Transcription factors bind to DNA and regulate read-rate of genes. Transcription factors regulate their target genes to mobilize the appropriate protein response in each case. flowchart LR genes --transcribed--> mRNA --translated--> proteins; proteins--modify-->environment; environment --what?--> genes E. coli: has an internal representation of about 300 degrees of freedom. Hence, it has 300 transcription factors. ...

Bacterial chemotaxis signal response: allows bacteria to navigate. Chemicals are either attractants or repellants. Common attractants: sugars and amino acids serene and aspartate, and repellents such as certain metal ions and amino acid leucine. bacteria can detect concentration gradients as small as a change of one molecule per cell volume across the cell length. They detect such gradients over background concentrations spanning five orders of magnitude. (no reference) Biased random walk: walk straight for 1sec and then tumbes in about 0.1 sec. Ecoli keeps track of the gradient and then adjusts the tumbling frequency accordingly. ...

Langevin Model: Theory and Units by Yatharth Bhasin (version 2) This article explains the basic set of equations governing the Langevin model simulation of an FCS process. Further, it includes a thorough discussion on the units conversions needed for the simulation. Implementation is also briefly discussed. The last section details a conversion case study. Langevin Equation The Langevin equation simulates Brownian motion of particles. The equation can be solved to simulate non-equilibrium systems. ...