arXiv - QuanBio - Molecular Networks最新文献_第3页

Optimal Frequency in Second Messenger Signaling Quantifying cAMP Information Transmission in Bacteria 量化细菌中 cAMP 信息传递的第二信使信号的最佳频率

arXiv - QuanBio - Molecular Networks Pub Date : 2024-08-09 DOI: arxiv-2408.04988

Jiarui Xiong, Liang Wang, Jialun Lin, Lei Ni, Rongrong Zhang, Shuai Yang, Yajia Huang, Jun Chu, Fan Jin

引用次数: 0

Multiple Notch ligands in the synchronization of the segmentation clock 分割时钟同步过程中的多种 Notch 配体

arXiv - QuanBio - Molecular Networks Pub Date : 2024-08-07 DOI: arxiv-2408.04027

Marcos Wappner, Koichiro Uriu, Andrew C. Oates, Luis G. Morelli

{"title":"Multiple Notch ligands in the synchronization of the segmentation clock","authors":"Marcos Wappner, Koichiro Uriu, Andrew C. Oates, Luis G. Morelli","doi":"arxiv-2408.04027","DOIUrl":"https://doi.org/arxiv-2408.04027","url":null,"abstract":"Notch signaling is a ubiquitous and versatile intercellular signaling system\u0000that drives collective behaviors and pattern formation in biological tissues.\u0000During embryonic development, Notch is involved in generation of collective\u0000biochemical oscillations that form the vertebrate body segments, and its\u0000failure results in embryonic defects. Notch ligands of the Delta family are key\u0000components of this collective rhythm, but it is unclear how different Delta\u0000ligands with distinct properties contribute to relaying information among\u0000cells. Motivated by the zebrafish segmentation clock, in this work we propose a\u0000theory describing interactions between biochemical oscillators, where Notch\u0000receptor is bound by both oscillatory and nonoscillatory Delta ligands. Based\u0000on previous in vitro binding studies, we first consider Notch activation by\u0000Delta dimers. This hypothesis is consistent with experimental observations in\u0000conditions of perturbed Notch signaling. Then we test an alternative hypothesis\u0000where Delta monomers directly bind and activate Notch, and show that this\u0000second model can also describe the experimental observations. We show that\u0000these two hypotheses assign different roles for a non-oscillatory ligand, as a\u0000binding partner or as a baseline signal. Finally, we discuss experiments to\u0000distinguish between the two scenarios. Broadly, this work highlights how a\u0000multiplicity of ligands may be harnessed by a signaling system to generate\u0000versatile responses.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141942697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Thermodynamic Space of Chemical Reaction Networks 化学反应网络的热力学空间

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-16 DOI: arxiv-2407.11498

Shiling Liang, Paolo De Los Rios, Daniel Maria Busiello

{"title":"Thermodynamic Space of Chemical Reaction Networks","authors":"Shiling Liang, Paolo De Los Rios, Daniel Maria Busiello","doi":"arxiv-2407.11498","DOIUrl":"https://doi.org/arxiv-2407.11498","url":null,"abstract":"Living systems are usually maintained out of equilibrium and exhibit complex\u0000dynamical behaviors. The external energy supply often comes from chemical\u0000fluxes that can keep some species concentrations constant. Furthermore, the\u0000properties of the underlying chemical reaction networks (CRNs) are also\u0000instrumental in establishing robust biological functioning. Hence, capturing\u0000the emergent complexity of living systems and the role of their non-equilibrium\u0000nature is fundamental to uncover constraints and properties of the CRNs\u0000underpinning their functions. In particular, while kinetics plays a key role in\u0000shaping detailed dynamical phenomena, the range of operations of any CRN must\u0000be fundamentally constrained by thermodynamics, as they necessarily operate\u0000with a given energy budget. Here, we derive universal thermodynamic upper and\u0000lower bounds for the accessible space of species concentrations in a generic\u0000CRN. The resulting region determines the \"thermodynamic space\" of the CRN, a\u0000concept we introduce in this work. Moreover, we obtain similar bounds also for\u0000the affinities, shedding light on how global thermodynamic properties can limit\u0000local non-equilibrium quantities. We illustrate our results in two paradigmatic\u0000examples, the Schl\"ogl model for bistability and a minimal self-assembly\u0000process, demonstrating how the onset of complex behaviors is intimately tangled\u0000with the presence of non-equilibrium driving. In summary, our work unveils the\u0000exact form of the accessible space in which a CRN must work as a function of\u0000its energy budget, shedding light on the non-equilibrium origin of a variety of\u0000phenomena, from amplification to pattern formation. Ultimately, by providing a\u0000general tool for analyzing CRNs, the presented framework constitutes a stepping\u0000stone to deepen our ability to predict complex out-of-equilibrium behaviors and\u0000design artificial chemical reaction systems.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"121 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141719497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Boundary-induced slow mixing for Markov chains and its application to stochastic reaction networks 马尔可夫链的边界诱导缓慢混合及其在随机反应网络中的应用

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-16 DOI: arxiv-2407.12166

Wai-TongLouis, Fan, Jinsu Kim, Chaojie Yuan

{"title":"Boundary-induced slow mixing for Markov chains and its application to stochastic reaction networks","authors":"Wai-TongLouis, Fan, Jinsu Kim, Chaojie Yuan","doi":"arxiv-2407.12166","DOIUrl":"https://doi.org/arxiv-2407.12166","url":null,"abstract":"Markov chains on the non-negative quadrant of dimension $d$ are often used to\u0000model the stochastic dynamics of the number of $d$ entities, such as $d$\u0000chemical species in stochastic reaction networks. The infinite state space\u0000poses technical challenges, and the boundary of the quadrant can have a\u0000dramatic effect on the long term behavior of these Markov chains. For instance,\u0000the boundary can slow down the convergence speed of an ergodic Markov chain\u0000towards its stationary distribution due to the extinction or the lack of an\u0000entity. In this paper, we quantify this slow-down for a class of stochastic\u0000reaction networks and for more general Markov chains on the non-negative\u0000quadrant. We establish general criteria for such a Markov chain to exhibit a\u0000power-law lower bound for its mixing time. The lower bound is of order\u0000$|x|^theta$ for all initial state $x$ on a boundary face of the quadrant,\u0000where $theta$ is characterized by the local behavior of the Markov chain near\u0000the boundary of the quadrant. A better understanding of how these lower bounds\u0000arise leads to insights into how the structure of chemical reaction networks\u0000contributes to slow-mixing.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Refining Boolean models with the partial most permissive scheme 用部分最允许方案完善布尔模型

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-13 DOI: arxiv-2407.09954

Nadine Ben Boina, Brigitte Mossé, Anaïs Baudot, Élisabeth Remy

引用次数: 0

Lomics: Generation of Pathways and Gene Sets using Large Language Models for Transcriptomic Analysis Lomics：使用大型语言模型生成通路和基因组，用于转录组分析

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-12 DOI: arxiv-2407.09089

Chun-Ka Wong, Ali Choo, Eugene C. C. Cheng, Wing-Chun San, Kelvin Chak-Kong Cheng, Yee-Man Lau, Minqing Lin, Fei Li, Wei-Hao Liang, Song-Yan Liao, Kwong-Man Ng, Ivan Fan-Ngai Hung, Hung-Fat Tse, Jason Wing-Hon Wong

{"title":"Lomics: Generation of Pathways and Gene Sets using Large Language Models for Transcriptomic Analysis","authors":"Chun-Ka Wong, Ali Choo, Eugene C. C. Cheng, Wing-Chun San, Kelvin Chak-Kong Cheng, Yee-Man Lau, Minqing Lin, Fei Li, Wei-Hao Liang, Song-Yan Liao, Kwong-Man Ng, Ivan Fan-Ngai Hung, Hung-Fat Tse, Jason Wing-Hon Wong","doi":"arxiv-2407.09089","DOIUrl":"https://doi.org/arxiv-2407.09089","url":null,"abstract":"Interrogation of biological pathways is an integral part of omics data\u0000analysis. Large language models (LLMs) enable the generation of custom pathways\u0000and gene sets tailored to specific scientific questions. These targeted sets\u0000are significantly smaller than traditional pathway enrichment analysis\u0000libraries, reducing multiple hypothesis testing and potentially enhancing\u0000statistical power. Lomics (Large Language Models for Omics Studies) v1.0 is a\u0000python-based bioinformatics toolkit that streamlines the generation of pathways\u0000and gene sets for transcriptomic analysis. It operates in three steps: 1)\u0000deriving relevant pathways based on the researcher's scientific question, 2)\u0000generating valid gene sets for each pathway, and 3) outputting the results as\u0000.GMX files. Lomics also provides explanations for pathway selections.\u0000Consistency and accuracy are ensured through iterative processes, JSON format\u0000validation, and HUGO Gene Nomenclature Committee (HGNC) gene symbol\u0000verification. Lomics serves as a foundation for integrating LLMs into omics\u0000research, potentially improving the specificity and efficiency of pathway\u0000analysis.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141719517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nonequilibrium Thermodynamics of Non-Ideal Reaction-Diffusion Systems: Implications for Active Self-Organization 非理想反应-扩散系统的非平衡热力学：主动自组织的意义

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-12 DOI: arxiv-2407.09128

Francesco Avanzini, Timur Aslyamov, Étienne Fodor, Massimiliano Esposito

{"title":"Nonequilibrium Thermodynamics of Non-Ideal Reaction-Diffusion Systems: Implications for Active Self-Organization","authors":"Francesco Avanzini, Timur Aslyamov, Étienne Fodor, Massimiliano Esposito","doi":"arxiv-2407.09128","DOIUrl":"https://doi.org/arxiv-2407.09128","url":null,"abstract":"We develop a framework describing the dynamics and thermodynamics of open\u0000non-ideal reaction-diffusion systems, which embodies Flory-Huggins theories of\u0000mixtures and chemical reaction network theories. Our theory elucidates the\u0000mechanisms underpinning the emergence of self-organized dissipative structures\u0000in these systems. It evaluates the dissipation needed to sustain and control\u0000them, discriminating the contributions from each reaction and diffusion process\u0000with spatial resolution. It also reveals the role of the reaction network in\u0000powering and shaping these structures. We identify particular classes of\u0000networks in which diffusion processes always equilibrate within the structures,\u0000while dissipation occurs solely due to chemical reactions. The spatial\u0000configurations resulting from these processes can be derived by minimizing a\u0000kinetic potential, contrasting with the minimization of the thermodynamic free\u0000energy in passive systems. This framework opens the way to investigating the\u0000energetic cost of phenomena such as liquid-liquid phase separation,\u0000coacervation, and the formation of biomolecular condensates.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141722239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A deep graph model for the signed interaction prediction in biological network 用于预测生物网络中签名交互作用的深度图模型

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-10 DOI: arxiv-2407.07357

Shuyi Jin, Mengji Zhang, Meijie Wang, Lun Yu

引用次数: 0

Flexibility in noisy cell-to-cell information dynamics 细胞间嘈杂信息动态的灵活性

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-09 DOI: arxiv-2407.06556

Ismail Qunbar, Michael Vennettilli, Amir Erez

引用次数: 0

Theory of epigenetic switching due to stochastic histone mark loss during DNA replication DNA 复制过程中随机组蛋白标记丢失导致的表观遗传学转换理论

arXiv - QuanBio - Molecular Networks Pub Date : 2024-07-08 DOI: arxiv-2407.06019

Ander Movilla Miangolarra, Martin Howard

引用次数: 0