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pro vyhledávání: '"James Holehouse"'
Autor:
James Holehouse
Publikováno v:
Entropy, Vol 25, Iss 7, p 996 (2023)
Understanding how systems relax to equilibrium is a core theme of statistical physics, especially in economics, where systems are known to be subject to extrinsic noise not included in simple agent-based models. In models of binary choice—ones not
Externí odkaz:
https://doaj.org/article/5a42449a0860455682df6e5cafb35e08
Autor:
James Holehouse, Hector Pollitt
Publikováno v:
PLoS ONE, Vol 17, Iss 5, p e0267083 (2022)
We solve the binary decision model of Brock and Durlauf (2001) in time using a method reliant on the resolvent of the master operator of the stochastic process. Our solution is valid when not at equilibrium and can be used to exemplify path-dependent
Externí odkaz:
https://doaj.org/article/41e16368749642f5bc82567c0c9d0e0d
Publikováno v:
Biophys J
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic parameters of the m
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8b065639a510234912512b6abae5bc44
https://doi.org/10.1016/j.bpj.2020.02.016
https://doi.org/10.1016/j.bpj.2020.02.016
Autor:
James Holehouse, José Moran
We provide a generic method to find full dynamical solutions to binary decision models with interactions. In these models, agents follow a stochastic evolution where they must choose between two possible choices by taking into account the choices of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3874bbb8bbae0991dacfc58a92621535
Publikováno v:
Braichenko, S, Holehouse, J & Grima, R 2021, ' Distinguishing between models of mammalian gene expression : Telegraph-like models versus mechanistic models ', Journal of The Royal Society Interface, vol. 18, no. 183 . https://doi.org/10.1098/rsif.2021.0510
Journal of the Royal Society Interface
Journal of the Royal Society Interface
Funding Information: S.B. and R.G. were supported by a Leverhulme Trust grant no. (RPG-2018-423). J.H. was supported by a BBSRC EASTBIO PhD studentship. Two-state models (telegraph-like models) have a successful history of predicting distributions of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f6a9b6f1b9954dab140f4bcdb0339274
https://www.pure.ed.ac.uk/ws/files/235779750/rsif.2021.0510.pdf
https://www.pure.ed.ac.uk/ws/files/235779750/rsif.2021.0510.pdf
Revisiting the Reduction of Stochastic Models of Genetic Feedback Loops with Fast Promoter Switching
Autor:
Ramon Grima, James Holehouse
Publikováno v:
Biophys J
Holehouse, J & Grima, R 2019, ' Revisiting the reduction of stochastic models of genetic feedback loops with fast promoter switching ', Biophysical Journal . https://doi.org/10.1016/j.bpj.2019.08.021
Holehouse, J & Grima, R 2019, ' Revisiting the reduction of stochastic models of genetic feedback loops with fast promoter switching ', Biophysical Journal . https://doi.org/10.1016/j.bpj.2019.08.021
Propensity functions of the Hill-type are commonly used to model transcriptional regulation in stochastic models of gene expression. This leads to an effective reduced master equation for the mRNA and protein dynamics only. Based on deterministic con
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eb73dc02e28885af674cc7f308682aa6
https://doi.org/10.1016/j.bpj.2019.08.021
https://doi.org/10.1016/j.bpj.2019.08.021
Publikováno v:
Holehouse, J, Gupta, A & Grima, R 2020, ' Steady-state fluctuations of a genetic feedback loop with fluctuating rate parameters using the unified colored noise approximation ', Journal of Physics A: Mathematical and Theoretical, vol. 53, 405601 . https://doi.org/10.1088/1751-8121/aba4d0
A common model of stochastic auto-regulatory gene expression describes promoter switching via cooperative protein binding, effective protein production in the active state and dilution of proteins. Here we consider an extension of this model whereby
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eae66c6324ce55477fd07de442782e20
https://hdl.handle.net/20.500.11820/c265a6fb-8ea0-4f5e-8744-58f71035717b
https://hdl.handle.net/20.500.11820/c265a6fb-8ea0-4f5e-8744-58f71035717b
Publikováno v:
Holehouse, J, Sukys, A & Grima, R 2020, ' Stochastic time-dependent enzyme kinetics : Closed-form solution and transient bimodality ', The Journal of Chemical Physics, vol. 153, no. 16, 164113 . https://doi.org/10.1063/5.0017573
We derive an approximate closed-form solution to the chemical master equation describing the Michaelis-Menten reaction mechanism of enzyme action. In particular, assuming that the probability of a complex dissociating into enzyme and substrate is sig
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34985c3e5dd8c57397a891e6b6fc6e13
https://doi.org/10.1063/5.0017573
https://doi.org/10.1063/5.0017573