arXiv - QuanBio - Molecular Networks最新文献

Multi-variable control to mitigate loads in CRISPRa networks 多变量控制减轻 CRISPRa 网络的负载

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-11 DOI: arxiv-2409.07384

Krishna Manoj, Theodore W. Grunberg, Domitilla Del Vecchio

引用次数: 0

Some bounds on positive equilibria in mass action networks 大规模行动网络中正均衡的一些界限

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-10 DOI: arxiv-2409.06877

Murad Banaji

引用次数: 0

Limits on the computational expressivity of non-equilibrium biophysical processes 非平衡生物物理过程计算表达能力的限制

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-09 DOI: arxiv-2409.05827

Carlos Floyd, Aaron R. Dinner, Arvind Murugan, Suriyanarayanan Vaikuntanathan

{"title":"Limits on the computational expressivity of non-equilibrium biophysical processes","authors":"Carlos Floyd, Aaron R. Dinner, Arvind Murugan, Suriyanarayanan Vaikuntanathan","doi":"arxiv-2409.05827","DOIUrl":"https://doi.org/arxiv-2409.05827","url":null,"abstract":"Many biological decision-making processes can be viewed as performing a\u0000classification task over a set of inputs, using various chemical and physical\u0000processes as \"biological hardware.\" In this context, it is important to\u0000understand the inherent limitations on the computational expressivity of\u0000classification functions instantiated in biophysical media. Here, we model\u0000biochemical networks as Markov jump processes and train them to perform\u0000classification tasks, allowing us to investigate their computational\u0000expressivity. We reveal several unanticipated limitations on the input-output\u0000functions of these systems, which we further show can be lifted using\u0000biochemical mechanisms like promiscuous binding. We analyze the flexibility and\u0000sharpness of decision boundaries as well as the classification capacity of\u0000these networks. Additionally, we identify distinctive signatures of networks\u0000trained for classification, including the emergence of correlated subsets of\u0000spanning trees and a creased \"energy landscape\" with multiple basins. Our\u0000findings have implications for understanding and designing physical computing\u0000systems in both biological and synthetic chemical settings.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206275","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

When lowering temperature, the in vivo circadian clock in cyanobacteria follows and surpasses the in vitro protein clock trough the Hopf bifurcation 当温度降低时，蓝藻体内的昼夜节律遵循并超越体外蛋白质时钟的霍普夫分岔曲线

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-09 DOI: arxiv-2409.05537

I. Mihalcescu, H. Kaji, H. Maruyama, J. Giraud, M. Van-Melle Gateau, B. Houchmandzadeh, H. Ito

{"title":"When lowering temperature, the in vivo circadian clock in cyanobacteria follows and surpasses the in vitro protein clock trough the Hopf bifurcation","authors":"I. Mihalcescu, H. Kaji, H. Maruyama, J. Giraud, M. Van-Melle Gateau, B. Houchmandzadeh, H. Ito","doi":"arxiv-2409.05537","DOIUrl":"https://doi.org/arxiv-2409.05537","url":null,"abstract":"The in vivo circadian clock in single cyanobacteria is studied here by\u0000time-lapse fluorescence microscopy when the temperature is lowered below\u000025{deg}C . We first disentangle the circadian clock behavior from the\u0000bacterial cold shock response by identifying a sequence of \"death steps\" based\u0000on cellular indicators. By analyzing only \"alive\" tracks, we show that the\u0000dynamic response of individual oscillatory tracks to a step-down temperature\u0000signal is described by a simple Stuart-Landau oscillator model. The same\u0000dynamical analysis applied to in vitro data (KaiC phosphorylation level\u0000following a temperature step-down) allows for extracting and comparing both\u0000clock's responses to a temperature step down. It appears, therefore, that both\u0000oscillators go through a similar supercritical Hopf bifurcation. Finally, to\u0000quantitatively describe the temperature dependence of the resulting in vivo and\u0000in vitro Stuart-Landau parameters $mu(T)$ and $omega_c(T)$, we propose two\u0000simplified analytical models: temperature-dependent positive feedback or\u0000time-delayed negative feedback that is temperature compensated. Our results\u0000provide strong constraints for future models and emphasize the importance of\u0000studying transitory regimes along temperature effects in circadian systems.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206279","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

Non-explosivity of endotactic stochastic reaction systems 内向随机反应系统的非爆炸性

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-09 DOI: arxiv-2409.05340

Chuang Xu

引用次数: 0

Irreversibility in Bacterial Regulatory Networks 细菌调控网络中的不可逆性

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-06 DOI: arxiv-2409.04513

Yi Zhao, Thomas P. Wytock, Kimberly A. Reynolds, Adilson E. Motter

引用次数: 0

A Molecular Communication Perspective of Alzheimer's Disease: Impact of Amyloid Beta Oligomers on Glutamate Diffusion in the Synaptic Cleft 阿尔茨海默病的分子通讯视角：淀粉样β寡聚体对突触裂隙中谷氨酸扩散的影响

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-05 DOI: arxiv-2409.03396

Nayereh FallahBagheri, Ozgur B. Akan

{"title":"A Molecular Communication Perspective of Alzheimer's Disease: Impact of Amyloid Beta Oligomers on Glutamate Diffusion in the Synaptic Cleft","authors":"Nayereh FallahBagheri, Ozgur B. Akan","doi":"arxiv-2409.03396","DOIUrl":"https://doi.org/arxiv-2409.03396","url":null,"abstract":"Molecular communication (MC) within the synaptic cleft is vital for\u0000neurotransmitter diffusion, a process critical to cognitive functions. In\u0000Alzheimer's Disease (AD), beta-amyloid oligomers (A$beta$os) disrupt this\u0000communication, leading to synaptic dysfunction. This paper investigates the\u0000molecular interactions between glutamate, a key neurotransmitter, and\u0000A$beta$os within the synaptic cleft, aiming to elucidate the underlying\u0000mechanisms of this disruption. Through stochastic modeling, we simulate the\u0000dynamics of A$beta$os and their impact on glutamate diffusion. The findings,\u0000validated by comparing simulated results with existing experimental data,\u0000demonstrate that A$beta$os serve as physical obstacles, hindering glutamate\u0000movement and increasing collision frequency. This impairment of synaptic\u0000transmission and long-term potentiation (LTP) by binding to receptors on the\u0000postsynaptic membrane is further validated against known molecular interaction\u0000behaviors observed in similar neurodegenerative contexts. The study also\u0000explores potential therapeutic strategies to mitigate these disruptions. By\u0000enhancing our understanding of these molecular interactions, this research\u0000contributes to the development of more effective treatments for AD, with the\u0000ultimate goal of alleviating synaptic impairments associated with the disease.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206276","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

Exact first passage time distribution for second-order reactions in chemical networks 化学网络中二阶反应的精确首过时间分布

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-04 DOI: arxiv-2409.02698

Changqian Rao, David Waxman, Wei Lin, Zhuoyi Song

{"title":"Exact first passage time distribution for second-order reactions in chemical networks","authors":"Changqian Rao, David Waxman, Wei Lin, Zhuoyi Song","doi":"arxiv-2409.02698","DOIUrl":"https://doi.org/arxiv-2409.02698","url":null,"abstract":"The first passage time (FPT) is a generic measure that quantifies when a\u0000random quantity reaches a specific state. We consider the FTP distribution in\u0000nonlinear stochastic biochemical networks, where obtaining exact solutions of\u0000the distribution is a challenging problem. Even simple two-particle collisions\u0000cause strong nonlinearities that hinder the theoretical determination of the\u0000full FPT distribution. Previous research has either focused on analyzing the\u0000mean FPT, which provides limited information about a system, or has considered\u0000time-consuming stochastic simulations that do not clearly expose causal\u0000relationships between parameters and the system's dynamics. This paper presents\u0000the first exact theoretical solution of the full FPT distribution in a broad\u0000class of chemical reaction networks involving $A + B rightarrow C$ type of\u0000second-order reactions. Our exact theoretical method outperforms stochastic\u0000simulations, in terms of computational efficiency, and deviates from\u0000approximate analytical solutions. Given the prevalence of bimolecular reactions\u0000in biochemical systems, our approach has the potential to enhance the\u0000understanding of real-world biochemical processes.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206277","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

Waveform distortion for temperature compensation and synchronization in circadian rhythms: An approach based on the renormalization group method 用于温度补偿和昼夜节律同步的波形失真：基于重正化群法的方法

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-04 DOI: arxiv-2409.02526

Shingo Gibo, Teiji Kunihiro, Tetsuo Hatsuda, Gen Kurosawa

{"title":"Waveform distortion for temperature compensation and synchronization in circadian rhythms: An approach based on the renormalization group method","authors":"Shingo Gibo, Teiji Kunihiro, Tetsuo Hatsuda, Gen Kurosawa","doi":"arxiv-2409.02526","DOIUrl":"https://doi.org/arxiv-2409.02526","url":null,"abstract":"Numerous biological processes accelerate as temperatures increase, but the\u0000period of circadian rhythms remains constant, known as temperature\u0000compensation, while synchronizing with the 24h light-dark cycle. We\u0000theoretically explores the possible relevance of waveform distortions in\u0000circadian gene-protein dynamics to the temperature compensation and\u0000synchronization. Our analysis of the Goodwin model provides a coherent\u0000explanation of most of temperature compensation hypotheses. Using the\u0000renormalization group method, we analytically demonstrate that the decreasing\u0000phase of circadian protein oscillations should lengthen with increasing\u0000temperature, leading to waveform distortions to maintain a stable period. This\u0000waveform-period correlation also occurs in other oscillators like\u0000Lotka-Volterra and van der Pol models. A reanalysis of known data nicely\u0000confirms our findings on waveform distortion and its impact on synchronization\u0000range. Thus we conclude that circadian rhythm waveforms are fundamental to both\u0000temperature compensation and synchronization.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"183 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206278","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

Exact computation of Transfer Entropy with Path Weight Sampling 利用路径权重采样精确计算转移熵

arXiv - QuanBio - Molecular Networks Pub Date : 2024-09-03 DOI: arxiv-2409.01650

Avishek Das, Pieter Rein ten Wolde

引用次数: 0