Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

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

Doping Dependence of Thermal Oxidation on n-type 4H-SiC

The doping dependence of dry thermal oxidation rates in n-type 4H-SiC was investigated. The oxidation was performed in the temperature range 1000C to 1200C for samples with nitrogen doping in the range of 6.5e15/cm3 to 9.3e18/cm3, showing a clear doping dependence. Samples with higher doping concentrations displayed higher oxidation rates. The results were interpreted using a modified Deal-Grove model. Linear and parabolic rate constants and activation energies were extracted. Increasing nitrogen led to an increase in linear rate constant pre-exponential factor from 10-6m/s to 10-2m/s and the parabolic rate constant pre-exponential factor from 10e9m2/s to 10e6m2/s. The increase in linear rate constant was attributed to defects from doping-induced lattice mismatch, which tend to be more reactive than bulk crystal regions. The increase in the diffusion-limited parabolic rate constant was attributed to degradation in oxide quality originating from the doping-induced lattice mismatch. This degradation was confirmed by the observation of a decrease in optical density of the grown oxide films from 1.4 to 1.24. The linear activation energy varied from 1.6eV to 2.8eV, while the parabolic activation energy varied from 2.7eV to 3.3eV, increasing with doping concentration. These increased activation energies were attributed to higher nitrogen content, leading to an increase in effective bond energy stemming from the difference in C-Si (2.82eV) and Si-N (4.26eV) binding energies. This work provides crucial information in the engineering of SiO2 dielectrics for SiC MOS structures, which typically involve regions of very different doping concentrations, and suggests that thermal oxidation at high doping concentrations in SiC may be defect mediated.Comment: 13 pages. 9 figures, accepted as a transiction in IEEE electron device. TED MS#8035

Collective traffic-like movement of ants on a trail: dynamical phases and phase transitions

The traffic-like collective movement of ants on a trail can be described by a stochastic cellular automaton model. We have earlier investigated its unusual flow-density relation by using various mean field approximations and computer simulations. In this paper, we study the model following an alternative approach based on the analogy with the zero range process, which is one of the few known exactly solvable stochastic dynamical models. We show that our theory can quantitatively account for the unusual non-monotonic dependence of the average speed of the ants on their density for finite lattices with periodic boundary conditions. Moreover, we argue that the model exhibits a continuous phase transition at the critial density only in a limiting case. Furthermore, we investigate the phase diagram of the model by replacing the periodic boundary conditions by open boundary conditions.Comment: 8 pages, 6 figure

Optimizing 3d printed metallic object’s postprocessing : a case of gamma‐tial alloys

Gamma‐TiAl (γ‐TiAl) alloys can be used in high‐end products relevant to the aerospace, defense, biomedical, and marine industries. Fabricating objects made of γ‐TiAl alloys needs an additive manufacturing process called Electron Beam Melting (EBM) or other similar processes because these alloys are difficult‐to‐cut materials. An object fabricated by EBM exhibits poor surface finish and must undergo postprocessing. In this study, cylindrical specimens were fabricated by EBM and post‐processed by turning at different cutting conditions (cutting speed, depth of cut, feed rate, insert radius, and coolant flowrate). The EBM conditions were as follows: average powder size 110 μm, acceleration voltage 60 kV, beam current 10 mA, beam scanning speed 2200 mm/s, and beam focus offset 0.20 mm. The surface roughness and cutting force were recorded for each set of cutting conditions. The values of the cutting conditions were set by the L36 Design of Experiment approach. The effects of the cutting conditions on surface roughness and cutting force are elucidated by constructing the possibility distributions (triangular fuzzy numbers) from the experimental data. Finally, the optimal cutting conditions to improve the surface finish of specimens made of γ‐TiAl alloys are determined using the possibility distributions. Thus, this study’s outcomes can be used to develop intelligent systems for optimizing additive manufacturing processes. © 2021 by the authors. Licensee MDPI, Basel, Switzerland