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Keywords = Langevin point kinetic model

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14 pages, 993 KB  
Article
A New Model for the Stochastic Point Reactor: Development and Comparison with Available Models
by Alamir Elsayed, Mohamed El-Beltagy, Amnah Al-Juhani and Shorooq Al-Qahtani
Energies 2021, 14(4), 955; https://doi.org/10.3390/en14040955 - 11 Feb 2021
Cited by 3 | Viewed by 2086
Abstract
The point kinetic model is a system of differential equations that enables analysis of reactor dynamics without the need to solve coupled space-time system of partial differential equations (PDEs). The random variations, especially during the startup and shutdown, may become severe and hence [...] Read more.
The point kinetic model is a system of differential equations that enables analysis of reactor dynamics without the need to solve coupled space-time system of partial differential equations (PDEs). The random variations, especially during the startup and shutdown, may become severe and hence should be accounted for in the reactor model. There are two well-known stochastic models for the point reactor that can be used to estimate the mean and variance of the neutron and precursor populations. In this paper, we reintroduce a new stochastic model for the point reactor, which we named the Langevin point kinetic model (LPK). The new LPK model combines the advantages, accuracy, and efficiency of the available models. The derivation of the LPK model is outlined in detail, and many test cases are analyzed to investigate the new model compared with the results in the literature. Full article
(This article belongs to the Special Issue Advances in Modelling for Nuclear Science and Engineering)
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19 pages, 2888 KB  
Review
Computational Methods for Modeling Aptamers and Designing Riboswitches
by Sha Gong, Yanli Wang, Zhen Wang and Wenbing Zhang
Int. J. Mol. Sci. 2017, 18(11), 2442; https://doi.org/10.3390/ijms18112442 - 17 Nov 2017
Cited by 32 | Viewed by 7711
Abstract
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic “switches”, regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the [...] Read more.
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic “switches”, regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers. As structural changes in aptamers must be achieved within the certain time window for effective regulation, kinetics is another key point for understanding aptamer function in riboswitch-mediated gene regulation. The coarse-grained self-organized polymer (SOP) model using Langevin dynamics simulation has been successfully developed to investigate folding kinetics of aptamers, while their co-transcriptional folding kinetics can be modeled by the helix-based computational method and BarMap approach. Based on the known aptamers, the web server Riboswitch Calculator and other theoretical methods provide a new tool to design synthetic riboswitches. This review will represent an overview of these computational methods for modeling structure and kinetics of riboswitch aptamers and for designing riboswitches. Full article
(This article belongs to the Special Issue Aptamers)
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