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Автор: Grafiati
Опубліковано: 6 вересня 2023

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Статті в журналах з теми "Multispecies asymmetric simple exclusion processes"

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Matsui, Chihiro. "Multi-state Asymmetric Simple Exclusion Processes." Journal of Statistical Physics 158, no. 1 (September 27, 2014): 158–91. http://dx.doi.org/10.1007/s10955-014-1121-9.

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2

Karimipour, V. "Multispecies asymmetric simple exclusion process and its relation to traffic flow." Physical Review E 59, no. 1 (January 1, 1999): 205–12. http://dx.doi.org/10.1103/physreve.59.205.

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3

Pronina, Ekaterina, and Anatoly B. Kolomeisky. "Two-channel totally asymmetric simple exclusion processes." Journal of Physics A: Mathematical and General 37, no. 42 (October 7, 2004): 9907–18. http://dx.doi.org/10.1088/0305-4470/37/42/005.

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4

Roy, Dipankar. "The phase diagram for a class of multispecies permissive asymmetric exclusion processes." Journal of Statistical Mechanics: Theory and Experiment 2021, no. 1 (January 6, 2021): 013201. http://dx.doi.org/10.1088/1742-5468/abc7ba.

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5

Cai, Zhong-Pan, Yao-Ming Yuan, Rui Jiang, Mao-Bin Hu, Qing-Song Wu, and Yong-Hong Wu. "Asymmetric coupling in multi-channel simple exclusion processes." Journal of Statistical Mechanics: Theory and Experiment 2008, no. 07 (July 18, 2008): P07016. http://dx.doi.org/10.1088/1742-5468/2008/07/p07016.

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6

XIAO, SONG, MINGZHE LIU, and JING SHANG. "SINGLE ON-RAMP IN ASYMMETRIC SIMPLE EXCLUSION PROCESSES." Modern Physics Letters B 26, no. 06 (March 10, 2012): 1150036. http://dx.doi.org/10.1142/s0217984911500369.

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Анотація:
This paper studies the single on-ramp in a totally asymmetric simple exclusion processes (TASEPs). In our model, particles can only attach irreversibly with rate q to a bulk site k + 1, which is far away from boundaries. The model is investigated under random sequential update and open boundary conditions by using Monte Carlo simulations and mean-field calculations. In the case of hopping rate p = 1, when attachment rate q is fixed and q < 0.5, there are five phases in the system, while when q > 0.5, the system includes only four phases and the LD/LD phase vanishes.
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7

Pronina, Ekaterina, and Anatoly B. Kolomeisky. "Asymmetric coupling in two-channel simple exclusion processes." Physica A: Statistical Mechanics and its Applications 372, no. 1 (December 2006): 12–21. http://dx.doi.org/10.1016/j.physa.2006.05.006.

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8

Landim, C., and H. T. Yau. "Fluctuation-dissipation equation of asymmetric simple exclusion processes." Probability Theory and Related Fields 108, no. 3 (July 16, 1997): 321–56. http://dx.doi.org/10.1007/s004400050112.

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9

Tsekouras, K., and A. B. Kolomeisky. "Inhomogeneous coupling in two-channel asymmetric simple exclusion processes." Journal of Physics A: Mathematical and Theoretical 41, no. 9 (February 19, 2008): 095002. http://dx.doi.org/10.1088/1751-8113/41/9/095002.

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10

Tian, Bo, Rui Jiang, Mao-Bin Hu, Zhong-Jun Ding, and Bin Jia. "Totally asymmetric simple exclusion processes on two intersected lanes." EPL (Europhysics Letters) 128, no. 4 (January 24, 2020): 40005. http://dx.doi.org/10.1209/0295-5075/128/40005.

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Дисертації з теми "Multispecies asymmetric simple exclusion processes"

1

Cook, Larry Jonathan. "Totally Asymmetric Simple Exclusion Processes with Finite Resources." Diss., Virginia Tech, 2009. http://hdl.handle.net/10919/30121.

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Анотація:
In many situations in the world, the amount of resources available for use is limited. This statement is especially true in the cells of living organisms. During the translation process in protein synthesis, ribosomes move along the mRNA strand constructing proteins based on the sequence of codons that form a gene. The totally asymmetric simple exclusion process (TASEP) models well the translation process. However, these genes are constantly competing for ribosomes and other resources in the cell. To see how finite resources and competition affects such a system, we must construct a simple model to account for the limited resources. We consider coupling multiple TASEPs to a finite reservoir of particles where the entry rate of particles into the TASEPs depends on the number of particles left in the reservoir. Starting with a single TASEP connected to the reservoir, we study the system using both Monte Carlo simulations and theoretical approaches. We explore how the average overall density, density profile, and current change as a function of the number of particles initially in the reservoir for various parameters. New features arise not seen in the ordinary TASEP model, even for a single TASEP connected to the pool of particles. These features include a localized shock in the density profile. To explain what is seen in the simulations, we use an appropriately generalized version of a domain wall theory. The dynamics of the TASEPs with finite resources are also studied through the power spectra associated with the total particle occupancy of each TASEP and the reservoir. Again, we find new phenomena not seen in the power spectrum of the ordinary TASEP. For a single constrained TASEP, we find a suppression at low frequencies when compared to the power spectrum of the ordinary TASEP. The severity of this suppression is found to depend on how the entry rate changes with respect to the number of particles in the pool. For two TASEPs of different lengths, we find an enhancement of the power spectrum of the smaller TASEP when compared to the ordinary TASEP's power spectrum. We explain these findings using a linearized Langevin equation. Finally, we model competition between ten genes found in Escherichia coli using a modified version of the TASEP. This modified version includes extended objects and inhomogeneous internal hopping rates. We use the insight gained from the previous studies of finite resources and competition as well as other studies to gain some insight into how competition affects protein production.
Ph. D.
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2

Dong, Jiajia. "Inhomogeneous Totally Asymmetric Simple Exclusion Processes: Simulations, Theory and Application to Protein Synthesis." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/26718.

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Анотація:
In the process of translation, ribosomes, a type of macromolecules, read the genetic code on a messenger RNA template (mRNA) and assemble amino acids into a polypeptide chain which folds into a functioning protein product. The ribosomes perform discrete directed motion that is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. We incorporate the essential components of the translation process: Ribosomes, cognate tRNA concentrations, and mRNA templates correspond to particles (covering ell > 1 sites), hopping rates, and the underlying lattice, respectively. As the hopping rates in an mRNA are given by its sequence (in the unit of codons), we are especially interested in the effects of a finite number of slow codons to the overall stationary current. To study this matter systematically, we first explore the effects of local inhomogeneities, i.e., one or two slow sites of hopping rate q<1 in TASEP for particles of size ell > 1(in the unit of lattice site) using Monte Carlo simulation. We compare the results of ell =1 and ell >1 and notice that the existence of local defects has qualitatively similar effects to the steady state. We focus on the stationary current as well as the density profiles. If there is only a single slow site in the system, we observe a significant dependence of the current on the location of the slow site for both ell =1 and ell >1 cases. In particular, we notice a novel "edge" effect, i.e., the interaction of a single slow codon with the system boundary. When two slow sites are introduced, more intriguing phenomena such as dramatic decreases in the current when the two are close together emerge. We analyze the simulation results using several different levels of mean-field theory. A finite-segment mean-field approximation is especially successful in understanding the "edge effect." If we consider the systems with finite defects as "contrived mRNA's", the real mRNA's are of more biological significance. Inspired by the previous results, we study several mRNA sequences from Escherichia coli. We argue that an effective translation rate including the context of each codon needs to be taken into consideration when seeking an efficient strategy to optimize the protein production.
Ph. D.
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3

Sugden, Kate E. P. "Nonequilibrium statistical physics applied to biophysical cellular processes." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4339.

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Анотація:
The methods of statistical physics are increasingly being employed in a range of interdisciplinary areas. In particular, aspects of complex biological processes have been elucidated by bringing the problems down to the level of simple interactions studied in a statistical sense. In nonequilibrium statistical physics, a one dimensional lattice model known as the totally asymmetric simple exclusion processes (TASEP) has become prominent as a tool for modelling various cellular transport processes. Indeed the context in which the TASEP was first introduced (MacDonald et. al., 1968) was to model ribosome motion along mRNA during protein synthesis. In this work I study a variation of the TASEP in which particles hop along a one dimensional lattice which extends as they reach the end. We introduce this model to describe the unique growth dynamics of filamentous fungi, whereby a narrow fungal filament extends purely from its tip region while being supplied with growth materials from behind the tip. We find that the steady state behaviour of our model reflects that of the TASEP, however there is an additional phase where a dynamic shock is present in the system. I show through Monte Carlo simulation and theoretical analysis that the qualitative behaviour of this model can be predicted with a simple mean-field approximation, while the details of the phase behaviour are accurate only in a refined approximation which takes into account some correlations. I also discuss a further refined mean-field approximation and give a heuristic argument for our results. Next I present an extension of the model which allows the particles to interact with a second lattice, on which they diffuse in either direction. A first order meanfield continuum approximation suggests that the steady states of this system will exhibit some novel behaviour. Through Monte Carlo simulation I discuss the qualitative changes that arise due to the on-off dynamics. Finally I study a model for a second biological phenomenon: the length fluctuations of microtubules. The model describes stochastic polymerisation events at the tip of a microtubule. Using a mean-field theory, we find a transition between regimes where the microtubule grows on average, and where the length remains finite. For low rates of polymerisation and depolymerisation, the transition is in good agreement with Monte Carlo simulation.
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4

Pronina, Ekaterina. "Theoretical investigation of biological transport: Asymmetric simple exclusion processes in two-channel systems." Thesis, 2007. http://hdl.handle.net/1911/20634.

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Анотація:
Multi-particle non-equilibrium dynamics in two-channel biological transport systems is investigated theoretically within the framework of asymmetric simple exclusion processes (ASEP). In exclusion processes particles move along the lattice by hopping between neighboring sites that are vacant. We consider the systems with open boundaries, where particles enter the lattice on the entrance site and leave from the exit site with given rates. Four different ASEP models are studied. The first two models investigate interchannel coupling between parallel channels in a one-way transport system. The third model considers junction of two parallel tracks, while the last model investigates two-way transport system with narrow entrances with coupling on the boundaries. Theoretical investigation of these non-equilibrium systems reveal many interesting phenomena, such as unusual phase diagrams that contain up to seven stationary-state phases, localization of the domain wall in the bulk of the system, symmetry-breaking and strong interparticle correlation. Stationary phase diagrams, particle currents and bulk values of densities are calculated in a mean-field approximation for the systems in the thermodynamic limit. In addition, exact matrix product ansatz method and phenomenological domain-wall theory are applied to analyze dynamic properties. For several systems nearest-neighbour correlation and density distribution functions are computed and size-scaling effects are analyzed. Extensive Monte Carlo computer simulations are carried out for all systems to test predictions and they verify our theoretical results.
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Книги з теми "Multispecies asymmetric simple exclusion processes"

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Majumdar, Satya N. Random growth models. Edited by Gernot Akemann, Jinho Baik, and Philippe Di Francesco. Oxford University Press, 2018. http://dx.doi.org/10.1093/oxfordhb/9780198744191.013.38.

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This article discusses the connection between a particular class of growth processes and random matrices. It first provides an overview of growth model, focusing on the TASEP (totally asymmetric simple exclusion process) with parallel updating, before explaining how random matrices appear. It then describes multi-matrix models and line ensembles, noting that for curved initial data the spatial statistics for large time t is identical to the family of largest eigenvalues in a Gaussian Unitary Ensemble (GUE multi-matrix model. It also considers the link between the line ensemble and Brownian motion, and whether this persists on Gaussian Orthogonal Ensemble (GOE) matrices by comparing the line ensembles at fixed position for the flat polynuclear growth model (PNG) and at fixed time for GOE Brownian motions. Finally, it examines (directed) last passage percolation and random tiling in relation to growth models.
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Тези доповідей конференцій з теми "Multispecies asymmetric simple exclusion processes"

1

Song, Xiao, Cai Jiu-ju, Wang Ruo-hui, and Liu Fei. "Totally asymmetric simple exclusion processes apply in traffic system." In 2009 IEEE International Conference on Granular Computing (GRC). IEEE, 2009. http://dx.doi.org/10.1109/grc.2009.5255048.

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