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Abstract Despite the advances in discovering new nuclei, modeling microscopic nuclear structure, nuclear reactors, and stellar nucleosynthesis, we still lack a systemic tool, such as a network approach, to understand the structure and dynamics of over 70 thousands reactions compiled in JINA REACLIB. To this end, we develop an analysis framework, under which it is simple to know which reactions generally are possible and which are not, by counting neutrons and protons incoming to and outgoing from any target nucleus. Specifically, we assemble here a nuclear reaction network in which a node represents a nuclide, and a link represents a direct reaction between nuclides. Interestingly, the degree distribution of nuclear network exhibits a bimodal distribution that significantly deviates from the common power-law distribution of scale-free networks and Poisson distribution of random networks. Based on the dynamics from the cross section parameterizations in REACLIB, we surprisingly find that the distribution is universal for reactions with a rate below the threshold, λ < e − T γ , where T is the temperature and γ ≈ 1.05. Moreover, we discover three rules that govern the structure pattern of nuclear reaction network: (i) reaction-type is determined by linking choices, (ii) network distances between the reacting nuclides on 2D grid of Z vs N of nuclides are short, and (iii) each node in- and out-degrees are close to each other. By incorporating these three rules, our model universally unveils the underlying nuclear reaction patterns hidden in a large and dense nuclear reaction network regardless of nuclide chart expansions. It enables us to predict missing links that represent possible new nuclear reactions not yet discovered.
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Diffusive search and trajectories on tubular networks: a propagator approach
Abstract Several organelles in eukaryotic cells, including mitochondria and the endoplasmic reticulum, form interconnected tubule networks extending throughout the cell. These tubular networks host many biochemical pathways that rely on proteins diffusively searching through the network to encounter binding partners or localized target regions. Predicting the behavior of such pathways requires a quantitative understanding of how confinement to a reticulated structure modulates reaction kinetics. In this work, we develop both exact analytical methods to compute mean first passage times and efficient kinetic Monte Carlo algorithms to simulate trajectories of particles diffusing in a tubular network. Our approach leverages exact propagator functions for the distribution of transition times between network nodes and allows large simulation time steps determined by the network structure. The methodology is applied to both synthetic planar networks and organelle network structures, demonstrating key general features such as the heterogeneity of search times in different network regions and the functional advantage of broadly distributing target sites throughout the network. The proposed algorithms pave the way for future exploration of the interrelationship between tubular network structure and biomolecular reaction kinetics. Graphic Abstract
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- PAR ID:
- 10252397
- Date Published:
- Journal Name:
- The European Physical Journal E
- Volume:
- 44
- Issue:
- 6
- ISSN:
- 1292-8941
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1140/epje/s10189-021-00083-0
