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A systemic approach to analyze integrated energy system modeling tools: A review of national models.

ABSTRACT: We reviewed the literature focusing on nineteen integrated Energy System Models (ESMs) to: (i) identify the capabilities and shortcomings of current ESMs to analyze adequately the transition towards a low-carbon energy system; (ii) assess the performance of the selected models by means of the derived criteria, and (iii) discuss some potential solutions to address the ESM gaps. This paper delivers three main outcomes. First, we identify key criteria for analyzing current ESMs and we describe seven current and future low-carbon energy system modeling challenges: the increasing need for flexibility, further electrification, emergence of new technologies, technological learning and efficiency improvements, decentralization, macroeconomic interactions, and the role of social behavior in the energy system transition. These criteria are then translated into required modeling capabilities such as the need for hourly temporal resolution, sectoral coupling technologies (e.g., P2X), technological learning, flexibility technologies, stakeholder behavior, cross border trade, and linking with macroeconomic models. Second, a Multi-Criteria Analysis (MCA) is used as a framework to identify modeling gaps while clarifying high modeling capabilities of MARKAL, TIMES, REMix, PRIMES, and METIS. Third, to bridge major energy modeling gaps, two conceptual modeling suites are suggested, based on both optimization and simulation methodologies, in which the integrated ESM is hard-linked with a regional model and an energy market model and soft-linked with a macroeconomic model.

SUBMITTER: Fattahi A

PROVIDER: S-EPMC7452863 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement).We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We generalize the notion of codon preference index (CPI) to overlapping coding regions, and use RNAsampleCDS to generate control sequences required in the computation of CPI for the Gag-Pol overlapping coding region of HIV-1. These applications show that RNAsampleCDS constitutes a unique tool in the software arsenal now available to evolutionary biologists.Source code for the programs and additional data are available at http://bioinformatics.bc.edu/clotelab/RNAsampleCDS/ .

Project description:Phytohormones, especially jasmonates, are known to be mediators of the plant responses to wounding and herbivore feeding. Their role in such stress responses has been largely studied locally in treated leaves. However, less is known about the induced systemic distribution of phytohormone signals upon these kinds of stresses. Here, a holistic approach was performed in order to investigate the systemic phytohormone pattern in the rosette of Arabidopsis thaliana after herbivore-related wounding. Levels of different stress-related phytohormones such as jasmonates, abscisic acid, and salicylic acid were analyzed in individual leaves. We demonstrate that the typically used sampling method, where leaves are first cut and immediately frozen, causes false-positive results since cutting already induces systemic jasmonate elevations within less than 1.6 min. Therefore, this approach is not suitable to study systemic phytohormone changes in the whole plant. By developing a new method where leaves are frozen first and subsequently cut, sampling-induced phytohormone elevations could be reduced. Using this new method, we show that jasmonic acid and its active isoleucine conjugate (jasmonoyl-isoleucine) are involved in the fast systemic wound response of Arabidopsis. A systemic induction of the jasmonates' precursor, 12-oxo-phytodienoic acid, was not observed throughout our treatments. The systemic phytohormone distribution pattern is strongly linked to the vascular connections between the leaves, providing further evidence that the vascular system is used for long distance-signaling in Arabidopsis. Besides already known vascular connections, we also demonstrate that the systemic distribution of jasmonate signals can be extended to distant leaves, which are systemically but indirectly connected via another vascularly connected leaf. This holistic approach covering almost the whole Arabidopsis rosette introduces a method to overcome false-positive results in systemic phytohormone determinations and demonstrates that wounding-induced long-distance signaling includes fast changes in jasmonate levels in systemic, non-treated leaves.

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A systemic approach to analyze integrated energy system modeling tools: A review of national models.

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