Stochastic kinetics of ribosomes: single motor properties and collective behavior

Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an {\it exact} analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a ``Michaelis-Menten-like'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechano-chemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes simultaneously move on the same mRNA track, while each synthesizes a copy of the same protein. We extend the model of a single ribosome by incorporating steric exclusion of different individuals on the same track. We draw the phase diagram of this model of ribosome traffic in 3-dimensional spaces spanned by experimentally controllable parameters. We suggest new experimental tests of our theoretical predictions.Comment: Final published versio

Flow properties of driven-diffusive lattice gases: theory and computer simulation

We develop n-cluster mean-field theories (0 < n < 5) for calculating the flow properties of the non-equilibrium steady-states of the Katz-Lebowitz-Spohn model of the driven diffusive lattice gas, with attractive and repulsive inter-particle interactions, in both one and two dimensions for arbitrary particle densities, temperature as well as the driving field. We compare our theoretical results with the corresponding numerical data we have obtained from the computer simulations to demonstrate the level of accuracy of our theoretical predictions. We also compare our results with those for some other prototype models, notably particle-hopping models of vehicular traffic, to demonstrate the novel qualitative features we have observed in the Katz-Lebowitz-Spohn model, emphasizing, in particular, the consequences of repulsive inter-particle interactions.Comment: 12 RevTex page

Cluster formation and anomalous fundamental diagram in an ant trail model

A recently proposed stochastic cellular automaton model ({\it J. Phys. A 35, L573 (2002)}), motivated by the motions of ants in a trail, is investigated in detail in this paper. The flux of ants in this model is sensitive to the probability of evaporation of pheromone, and the average speed of the ants varies non-monotonically with their density. This remarkable property is analyzed here using phenomenological and microscopic approximations thereby elucidating the nature of the spatio-temporal organization of the ants. We find that the observations can be understood by the formation of loose clusters, i.e. space regions of enhanced, but not maximal, density.Comment: 11 pages, REVTEX, with 11 embedded EPS file

Asymmetric rolling of interstitial-free steel using differential roll diameters. Part II : microstructure and annealing effects

The effects of annealing on the microstructure, texture, tensile properties, and R value evolution of an IF steel sheet after room-temperature symmetric and asymmetric rolling were examined. Simulations were carried out to obtain R values from the experimental textures using the viscoplastic self-consistent polycrystal plasticity model. The investigation revealed the variations in the textures due to annealing and symmetric/asymmetric rolling and showed that the R values correlate strongly with the evolution of the texture. An optimum heat treatment for the balance of strength, ductility, and deep drawability was found to be at 873 K (600 _C) for 30 minutes

Facile control of nanoporosity in Cellulose Acetate using Nickel(II) nitrate additive and water pressure treatment for highly efficient battery gel separators

We succeed in fabricating nearly straight nanopores in cellulose acetate (CA) polymers for use as battery gel separators by utilizing an inorganic hexahydrate (Ni(NO3)2??6H2O) complex and isostatic water pressure treatment. The continuous nanopores are generated when the polymer film is exposed to isostatic water pressure after complexing the nickel(II) nitrate hexahydrate (Ni(NO3)2??6H2O) with the CA. These results can be attributed to the manner in which the polymer chains are weakened because of the plasticization effect of the Ni(NO3)2??6H2O that is incorporated into the CA. Furthermore, we performed extensive molecular dynamics simulation for confirming the interaction between electrolyte and CA separator. The well controlled CA membrane after water pressure treatment enables fabrication of highly reliable cell by utilizing 2032-type coin cell structure. The resulting cell performance exhibits not only the effect of the physical morphology of CA separator, but also the chemical interaction of electrolyte with CA polymer which facilitates the Li-ion in the cell.ope

A High Throughput Aqueous Passivation Testing Methodology for Compositionally Complex Alloys using Scanning Droplet Cell

Compositionally complex alloy systems containing more than five principal elements allow exploring a wide range of compositions, processing, and structural variables with the hope for identifying unique properties. Such opportunities also apply to designing materials for improved corrosion resistance, regulated by a self-healing passive film. Such a rich landscape in reactivity and protectivity demands the search for high-throughput experimental testing workflows to uncover key metrics, indicative of superior properties. In this communication, one such methodology is demonstrated for evaluating passivation performance of a combinatorial library of Al0.7-x-yCoxCryFe0.15Ni0.15 thin film alloys in deaerated 0.1 mol/L H2SO4(aq), using a scanning droplet cell

On Fuglede's conjecture for three intervals

In this paper we prove the "Tiling implies Spectral" part of Fuglede's paper for the case of three intervals. Then we prove the "Spectral implies Tiling" part of the conjecture for the case of three equal intervals as also when the intervals have lengths 1/2, 1/4, 1/4. For the general case we change our approach to get information on the structure of the spectrum for the n-interval case. Finally, we use symbolic computations on Mathematica, and prove this part of the conjecture with an additional assumption on the spectrum.Comment: 21 page

Farmer Participatory Problem Identification: a case study of Karnal District, Haryana

Adequate food grain production (212 million tonnes) along with sufficient buffer stock (70 million tonnes) is a testimony of an effective agricultural research and extension system in India. This success can be attributed to the relentless efforts made by the scientists, extensionists, farmers and development agencies towards agricultural development. The ultimate goal of the National Agricultural Research System in India is to develop the most suitable technologies for the end-users through its multi-location research. Further, technological advancement in agriculture is aimed at increasing production efficiency with higher returns to the Indian farmer

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry