Power Spectra of a Constrained Totally Asymmetric Simple Exclusion Process

To synthesize proteins in a cell, an mRNA has to work with a finite pool of ribosomes. When this constraint is included in the modeling by a totally asymmetric simple exclusion process (TASEP), non-trivial consequences emerge. Here, we consider its effects on the power spectrum of the total occupancy, through Monte Carlo simulations and analytical methods. New features, such as dramatic suppressions at low frequencies, are discovered. We formulate a theory based on a linearized Langevin equation with discrete space and time. The good agreement between its predictions and simulation results provides some insight into the effects of finite resoures on a TASEP.Comment: 4 pages, 2 figures v2: formatting change

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

The phenomenon of protein synthesis has been modeled in terms of totally asymmetric simple exclusion processes (TASEP) since 1968. In this article, we provide a tutorial of the biological and mathematical aspects of this approach. We also summarize several new results, concerned with limited resources in the cell and simple estimates for the current (protein production rate) of a TASEP with inhomogeneous hopping rates, reflecting the characteristics of real genes.Comment: 25 pages, 7 figure

New Dates from Submerged Late Pleistocene Sediments in the Southern Sea of Galilee, Israel

From the 17th International Radiocarbon Conference held in Jerusalem, Israel, June 18-23, 2000.Unusual low water levels in the Sea of Galilee (Dead Sea Fault, Israel) have caused the recent exposure of submerged Late Pleistocene prehistoric sites and lacustrine sediments along the southern shores of the lake. The Ohalo II site is a large fisher-hunter-gatherers camp with in-situ brush hut floors, hearths, and a human grave. The site is radiometrically dated by 25 charcoal dates to 19,430 BP (average, uncalibrated). The archaeological remains include quantities of excellently preserved organic remains. These would not have been preserved without a rapid rise of lake level immediately after the occupation, covering the remains with silts and sand. Recently a concentration of eight tree trunks were found about 1.5 km south of Ohalo II, of which five trunks were identified as Salix species and dated as a single accumulation at about 16,100 BP. The trunks, too, had to be submerged quickly together to ensure excellent preservation. The camp and the trunks were found at –212/–213 m, almost 4 m below modern high water levels. We suggest that the finds represent two separate episodes of deposition during low lake levels, almost 3,000 radiocarbon years apart, each followed by an abrupt water rise. It is possible that climatic changes caused the observed fluctuations, though earthquakes (blocking or lowering the Jordan outlet, for example) cannot be ruled out.The Radiocarbon archives are made available by Radiocarbon and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202