Dataset Information

Stochastic Dynamics of Gene Switching and Energy Dissipation for Gene Expression.

ABSTRACT: Stochastic dynamics of gene switching and energy dissipation for gene expression are largely unknown, mainly due to the complexity of non-equilibrium mechanisms. Here, based on an important double-deck loop model, the stochastic mechanisms of gene switching and energy dissipation are studied. First, the probability distributions of steady states are calculated theoretically. It is found that the signal can strengthen the choice of gene switching between the "off" and "on" states. Our analysis of energy consumption illustrates that, compared with the synthesis and degradation of proteins, the process of gene switching costs little energy. Our theoretical analysis reveals some interesting insights into the determination of cell state and energy dissipation for gene expression.

SUBMITTER: Liu Q

PROVIDER: S-EPMC7343763 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Stochastic Dynamics of Gene Switching and Energy Dissipation for Gene Expression.

Liu Quan Q Yu FengZhen F Yi Liang L Gao Yijun Y Gui Rong R Yi Ming M Sun Jianqiang J

Frontiers in genetics 20200702

Stochastic dynamics of gene switching and energy dissipation for gene expression are largely unknown, mainly due to the complexity of non-equilibrium mechanisms. Here, based on an important double-deck loop model, the stochastic mechanisms of gene switching and energy dissipation are studied. First, the probability distributions of steady states are calculated theoretically. It is found that the signal can strengthen the choice of gene switching between the "off" and "on" states. Our analysis of ...[more]

PMID: 32714375

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Project description:Many different molecular species have been observed in the interstellar medium. These range from simple diatomic species to saturated organic molecules with several carbon atoms. The latter molecules are assumed to be formed predominantely on the surface of interstellar dust grains. All surface reactions that can proceed under the low interstellar temperatures are exothermic. Their exothermicity can be as high as a few electron volts, which is considerable compared to the thermal energy of the molecules at 10 K. It is postulated that this exothermicity can be used for the desorption of reaction products from the grain. In previous studies, we have shown that translational excitation can lead to desorption, whereas vibrational and rotational excitations are much less efficient in the desorption of surface products. Vibrational excitation is however much more likely upon bond formation than translational excitation. The present study follows energy dissipation upon translational, vibrational, or rotational excitation of admolecules on a surface and its conversion, or lack thereof, to different energy contributions. To this end, thousands of molecular dynamics simulations were performed with an admolecule on top of a surface that received a fixed amount of energy, vibrational, rotational, or translational. Three different surface species have been considered, CO2, H2O, and CH4, spanning a range in binding energies, the number of internal degrees of freedom, and molecular weights. A fast exchange of energy between vibrational stretches is observed, but only very limited exchange to rotational or translation excitation has been found. For the dissipation of energy to the surface, excitation of the surface-admolecule bond is critical. Astrochemical models often assume instantaneous equipartition of energy after a reaction process to estimate the amount of available energy for chemical desorption. Based on the present study, we conclude that this assumption is not justified.

Dataset Information

Stochastic Dynamics of Gene Switching and Energy Dissipation for Gene Expression.

Publications

Stochastic Dynamics of Gene Switching and Energy Dissipation for Gene Expression.

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