亚细胞过程
A model of the dynamics of natural rotifer populations is described as a discrete nonlinear map depending on three parameters, which reflect characteristics of the population and environment. Model dynamics and their change by variation of…
We address the controversial hot question concerning the validity of the loose coupling versus the lever-arm theories in the actomyosin dynamics by re-interpreting and extending the phenomenological washboard potential model proposed by…
During division it is of primary importance for a cell to correctly determine the site of cleavage. The bacterium Escherichia coli divides in the center, producing two daughter cells of equal size. Selection of the center as the correct…
It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders of magnitude faster than the maximal one calculated from the diffusion--limited theory. It was therefore commonly assumed that…
We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…
The stationary states of systems with many molecular motors are studied theoretically for uniaxial and centered (aster-like) arrangements of cytoskeletal filaments using Monte Carlo simulations and a two-state model. Mutual exclusion of…
We investigate the translocation of a single stranded DNA (ssDNA) through a pore, which fluctuates between two conformations, by using coupled master equations (ME). The probability density function (PDF) of the first passage times (FPT) of…
The motility of certain gram-negative bacteria is mediated by retraction of type IV pili surface filaments, which are essential for infectivity. The retraction is powered by a strong molecular motor protein, PilT, producing very high forces…
In E. coli the determination of the middle of the cell and the proper placement of the septum is essential to the division of the cell. This step depends on the proteins MinC, MinD, and MinE. Exposure to a constant external field e.g., an…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…
The internal cell wall structure of the bacterium Lactobacillus helveticus has been observed in situ in aqueous solution using an atomic force microscope (AFM). The AFM tip was used not only for imaging but presumably to remove mechanically…
Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong…
In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…
Models of the mind are based on the possibility of computing in brain microtubules. From this point of view, information processing is the fundamental issue for understanding the brain mechanisms that produce consciousness. The cytoskeleton…
A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of…
We investigate a mechanism for the polar localization of proteins in bacteria. We focus on the MinCD/DivIVA system regulating division site placement in the rod-shaped bacterium Bacillus subtilis. Our model relies on a combination of…
Position determination in biological systems is often achieved through protein concentration gradients. Measuring the local concentration of such a protein with a spatially-varying distribution allows the measurement of position within the…
Transcription regulation typically involves the binding of proteins over long distances on multiple DNA sites that are brought close to each other by the formation of DNA loops. The inherent complexity of the assembly of regulatory…