Desire of God: an Exchange

Derrida, Jacques; Caputo, John D.; Kearney, Richard

doi:10.5422/fso/9780823225316.003.0020

Cited by 10 publications

(20 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Examples of such lattice models are the well known asymmetric simple exclusion process (ASEP) as well as its variants [25][26][27], the Katz-Lebowitz-Spohn (KLS) model [28,29], the zero range process [14,30], as well as its numerous variants [15,[31][32][33], etc.…”

Section: A Stochastic Driven Lattice Modelsmentioning

confidence: 99%

“…Even though a drive dependence of the stationary distribution is generically expected [47,59], one can nevertheless find nonequilibrium models whose stationary solution is not affected by the drive (and is thus equal to the equilibrium one). This is, for instance, the case for the asymmetric simple exclusion process (ASEP) on a ring in one dimension [27], or for the zero range process [14]. For this specific subclass of nonequilibrium systems, no shift in stationary densities is expected to be observed when the drives are switched on.…”

Section: Relation Between µ Cont and µ Eqmentioning

confidence: 99%

“…Indeed, even if a general procedure to define a nonequilibrium free energy is not yet established, one can sometimes, but rarely, directly compute the nonequilibrium stationary distribution which brings directly an "out-of-equilibrium partition function" different from the equilibrium one. Some examples are the zero range process and its extensions [14,15,30,32,33], the simple exclusion processes [26,27], etc.…”

Section: Relation Between µ Cont and µ Isomentioning

confidence: 99%

“…This model has been chosen over more standard lattice models [14,24,25,28,29] because its steady-state distribution can be determined exactly and it depends on the nonequilibrium driving force, a generic property according to, for instance, the McLennan expansion [57]. In contrast, standard models like the zero range process (ZRP) [14,24,25] or the asymmetric simple exclusion process (ASEP) [25,27] with periodic boundary conditions have a steady-state distribution that is independent of the drive. Other models, like the KLS model [28,29], are expected to have a steady-state distribution that depends on the drive, but this distribution is not known exactly.…”

Section: Explicit Examples Of Lattice Gas Models In Contactmentioning

confidence: 99%

See 3 more Smart Citations

Nonequilibrium chemical potentials of steady-state lattice gas models in contact: A large-deviation approach

Guioth

Bertin

2019

Phys. Rev. E

View full text Add to dashboard Cite

We introduce a general framework to describe the stationary state of two driven systems exchanging particles or mass through a contact, in a slow exchange limit. The definition of chemical potentials for the systems in contact requires that the large-deviations function describing the repartition of mass between the two systems is additive, in the sense of being a sum of contributions from each system. We show that this additivity property does not hold for an arbitrary contact dynamics, but is satisfied on condition that a macroscopic detailed balance condition holds at contact, and that the coarse-grained contact dynamics satisfies a factorization property. However, the nonequilibrium chemical potentials of the systems in contact keep track of the contact dynamics, and thus do not obey an equation of state. These nonequilibrium chemical potentials can be related either to the equilibrium chemical potential, or to the nonequilibrium chemical potential of the isolated systems. Results are applied both to an exactly solvable driven lattice gas model, and to the Katz-Lebowitz-Spohn model using a numerical procedure to evaluate the chemical potential. The breaking of the additivity property is also illustrated on the exactly solvable model. arXiv:1909.00432v2 [cond-mat.stat-mech] 2 Dec 2019with (∆N A ) c referring to the sum over configurations C A , C B that, respectively, contain N (C A ) = ρ A V A + ∆N A and N (C B ) = ρ B V B − ∆N A particles (the second sum being exactly the same with ∆N A = 0).

show abstract

Section: A Stochastic Driven Lattice Modelsmentioning

confidence: 99%

Section: Relation Between µ Cont and µ Eqmentioning

confidence: 99%

Section: Relation Between µ Cont and µ Isomentioning

confidence: 99%

Section: Explicit Examples Of Lattice Gas Models In Contactmentioning

confidence: 99%

See 2 more Smart Citations

Nonequilibrium chemical potentials of steady-state lattice gas models in contact: A large-deviation approach

Guioth

Bertin

2019

Phys. Rev. E

View full text Add to dashboard Cite

show abstract

“…The asymmetric simple exclusion process (TASEP) [1][2][3][4][5] is the simplest model of interacting self-propelled particles. In its simplest version, under open boundary conditions, particles enter from one end of a one-dimensional lattice and exit from the other end after traversing the distance between the two ends by a sequence of hops from one lattice site to the next; however, a successful hop is allowed if, and only if, the target site is not already occupied by another particle.…”

Section: Introductionmentioning

confidence: 99%

Biologically motivated three-species exclusion model: Effects of leaky scanning and overlapping genes on initiation of protein synthesis

Mishra

Chowdhury

2019

Phys. Rev. E

View full text Add to dashboard Cite

Totally asymmetric simple exclusion process (TASEP) was originally introduced as a model for the traffic-like collective movement of ribosomes on a messenger RNA (mRNA) that serves as the track for the motor-like forward stepping of individual ribosomes. In each step, a ribosome elongates a protein by a single unit using the track also as a template for protein synthesis. But, prefabricated, functionally competent, ribosomes are not available to begin synthesis of protein; a subunit directionally scans the mRNA in search of the pre-designated site where it is supposed to bind with the other subunit and begin the synthesis of the corresponding protein. However, because of 'leaky' scanning, a fraction of the scanning subunits miss the target site and continue their search beyond the first target. Sometimes such scanners successfully identify the site that marks the site for initiation of the synthesis of a different protein. In this paper, we develop an exclusion model, with three interconvertible species of hard rods, to capture some of the key features of these biological phenomena and study the effects of the interference of the flow of the different species of rods on the same lattice. More specifically, we identify the meantime for the initiation of protein synthesis as appropriate mean first-passage time that we calculate analytically using the formalism of backward master equations. In spite of the approximations made, our analytical predictions are in reasonably good agreement with the numerical data that we obtain by performing Monte Carlo simulations. We also compare our results with a few experimental facts reported in the literature and propose new experiments for testing some of our new quantitative predictions. arXiv:1812.10143v2 [cond-mat.stat-mech]

show abstract

Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript

Sharma

Chowdhury

2011

Journal of Theoretical Biology

View full text Add to dashboard Cite

The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called translation. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the track. Often several ribosomes may translate the same (mRNA) simultaneously. The ribosomes bound simultaneously to a single mRNA transcript are the members of a polyribosome (or, simply, polysome). Experimentally measured polysome profile gives the distribution of polysome sizes. Recently a breakthrough in determining the instantaneous positions of the ribosomes on a given mRNA track has been achieved and the technique is called ribosome profiling [1,2]. Motivated by the success of these techniques, we have studied the spatio-temporal organization of ribosomes by extending a theoretical model that we have reported elsewhere [3]. This extended version of our model incorporates not only (i) mechano-chemical cycle of individual ribomes, and (ii) their steric interactions, but also (iii) the effects of (a) kinetic proofreading, (b) translational infidelity, (c) ribosome recycling, and (d) sequence inhomogeneities. The theoretical framework developed here will serve in guiding further experiments and in analyzing the data to gain deep insight into various kinetic processes involved in translation.

show abstract

Desire of God: an Exchange

Cited by 10 publications

References 0 publications

Nonequilibrium chemical potentials of steady-state lattice gas models in contact: A large-deviation approach

Nonequilibrium chemical potentials of steady-state lattice gas models in contact: A large-deviation approach

Biologically motivated three-species exclusion model: Effects of leaky scanning and overlapping genes on initiation of protein synthesis

Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript

Contact Info

Product

Resources

About