arXiv - PHYS - Biological Physics最新文献_第7页

Effective and efficient modeling of the hydrodynamics for bacterial flagella 细菌鞭毛流体力学的高效建模

arXiv - PHYS - Biological Physics Pub Date : 2024-08-12 DOI: arxiv-2408.06093

Baopi Liu, Lu Chen, Ji Zhang, Xinliang Xu

引用次数: 0

Modeling collagen fibril degradation as a function of matrix microarchitecture 作为基质微结构函数的胶原纤维降解建模

arXiv - PHYS - Biological Physics Pub Date : 2024-08-11 DOI: arxiv-2408.05693

B. Debnath, B. N. Narasimhan, S. I. Fraley, P. Rangamani

{"title":"Modeling collagen fibril degradation as a function of matrix microarchitecture","authors":"B. Debnath, B. N. Narasimhan, S. I. Fraley, P. Rangamani","doi":"arxiv-2408.05693","DOIUrl":"https://doi.org/arxiv-2408.05693","url":null,"abstract":"Collagenolytic degradation is a process fundamental to tissue remodeling. The\u0000microarchitecture of collagen fibril networks changes during development,\u0000aging, and disease. Such changes to microarchitecture are often accompanied by\u0000changes in matrix degradability. In vitro, collagen matrices of the same\u0000concentration but different microarchitectures also vary in degradation rate.\u0000How do different microarchitectures affect matrix degradation? To answer this\u0000question, we developed a computational model of collagen degradation. We first\u0000developed a lattice model that describes collagen degradation at the scale of a\u0000single fibril. We then extended this model to investigate the role of\u0000microarchitecture using Brownian dynamics simulation of enzymes in a\u0000multi-fibril three dimensional matrix to predict its degradability. Our\u0000simulations predict that the distribution of enzymes around the fibrils is\u0000non-uniform and depends on the microarchitecture of the matrix. This\u0000non-uniformity in enzyme distribution can lead to different extents of\u0000degradability for matrices of different microarchitectures. Our model\u0000predictions were tested using in vitro experiments with synthesized collagen\u0000gels of different microarchitectures. Experiments showed that indeed\u0000degradation of collagen depends on the matrix architecture and fibril\u0000thickness. In summary, our study shows that the microarchitecture of the\u0000collagen matrix is an important determinant of its degradability.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213255","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

Dynamic cluster field modeling of collective chemotaxis 集体趋化的动态簇场模型

arXiv - PHYS - Biological Physics Pub Date : 2024-08-08 DOI: arxiv-2408.04748

Aditya Paspunurwar, Adrian Moure, Hector Gomez

{"title":"Dynamic cluster field modeling of collective chemotaxis","authors":"Aditya Paspunurwar, Adrian Moure, Hector Gomez","doi":"arxiv-2408.04748","DOIUrl":"https://doi.org/arxiv-2408.04748","url":null,"abstract":"Collective migration of eukaryotic cells is often guided by chemotaxis, and\u0000is critical in several biological processes, such as cancer metastasis, wound\u0000healing, and embryogenesis. Understanding collective chemotaxis has challenged\u0000experimental, theoretical and computational scientists because cells can sense\u0000very small chemoattractant gradients that are tightly controlled by cell-cell\u0000interactions and the regulation of the chemoattractant distribution by the\u0000cells. Computational models of collective cell migration that offer a\u0000high-fidelity resolution of the cell motion and chemoattractant dynamics in the\u0000extracellular space have been limited to a small number of cells. Here, we\u0000present Dynamic cluster field modeling (DCF), a novel computational method that\u0000enables simulations of collective chemotaxis of cellular systems with O(1000)\u0000cells and high-resolution transport dynamics of the chemoattractant in the\u0000time-evolving extracellular space. We illustrate the efficiency and predictive\u0000capabilities of our approach by comparing our numerical simulations with\u0000experiments in multiple scenarios that involve chemoattractant secretion and\u0000uptake by the migrating cells, regulation of the attractant distribution by\u0000cell motion, and interactions of the chemoattractant with an enzyme. The\u0000proposed algorithm opens new opportunities to address outstanding problems that\u0000involve collective cell migration in the central nervous system, immune\u0000response and cancer metastasis.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141940090","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

Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model 利用 oxRNA 模型对 CCMV 的游离和包封 RNA2 进行分子动力学表征

arXiv - PHYS - Biological Physics Pub Date : 2024-08-07 DOI: arxiv-2408.03662

Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Luca Tubiana, Samuela Pasquali, Raffaello Potestio

{"title":"Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model","authors":"Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Luca Tubiana, Samuela Pasquali, Raffaello Potestio","doi":"arxiv-2408.03662","DOIUrl":"https://doi.org/arxiv-2408.03662","url":null,"abstract":"The cowpea chlorotic mottle virus (CCMV) has emerged as an exemplary model\u0000system to assess the balance between electrostatic and topological features of\u0000ssRNA viruses, specifically in the context of the viral self-assembly process.\u0000Yet, in spite of its biophysical significance, little structural data of the\u0000RNA content of the CCMV virion is currently available. Here, the conformational\u0000dynamics of the RNA2 fragment of CCMV was assessed via coarse-grained molecular\u0000dynamics simulations, employing the oxRNA2 model. The behavior of RNA2 has been\u0000characterized both as a freely-folding molecule and within a mean-field\u0000depiction of a CCMV-like capsid. For the latter, a multi-scale approach was\u0000employed, to derive a radial potential profile of the viral cavity, from\u0000atomistic structures of the CCMV capsid in solution. The conformational\u0000ensembles of the encapsidated RNA2 were significantly altered with respect to\u0000the freely-folding counterparts, as shown by the emergence of long-range motifs\u0000and pseudoknots in the former case. Finally, the role of the N-terminal tails\u0000of the CCMV subunits (and ionic shells thereof) is highlighted as a critical\u0000feature in the construction of a proper electrostatic model of the CCMV capsid.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141939920","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 ubiquitous transfer function links interacting elements to emerging property of complex systems 无处不在的传递函数将相互作用的元素与复杂系统的新特性联系起来

arXiv - PHYS - Biological Physics Pub Date : 2024-08-05 DOI: arxiv-2408.03347

Lina Yan, Jeffrey Huy Khong, Aleksandar Kostadinov, Jerry Ying Hsi Fuh, Chih-Ming Ho

{"title":"A ubiquitous transfer function links interacting elements to emerging property of complex systems","authors":"Lina Yan, Jeffrey Huy Khong, Aleksandar Kostadinov, Jerry Ying Hsi Fuh, Chih-Ming Ho","doi":"arxiv-2408.03347","DOIUrl":"https://doi.org/arxiv-2408.03347","url":null,"abstract":"In the field of complex systems, self-organization magnifies the compounding\u0000effects of element interactions by propagating, modifying, and enhancing\u0000functionality, ultimately leading to emergent system properties. The\u0000intricacies of self-organization make unveiling the elusive link between\u0000element interactions and emergent system properties akin to finding the\u0000proverbial Holy Grail. In the search for identifying a method to predict\u0000system-level properties, we used an inductive approach to bypass the\u0000self-organization. By observing drug interactions within biological complex\u0000system, system property, efficacy, emerged as a smooth response surface in the\u0000multi-dimensional space of drug-system interactions, which can be represented\u0000by the Complex System Response (CSR) function. This CSR function has been\u0000successfully validated across diverse disease models in cell lines, animals,\u0000and clinical trials. Notably, the CSR function reveals that biological complex\u0000systems exhibit second-order non-linearity. In this study, we generalized the\u0000CSR function to physical complex systems, linking maximum compressive yielding\u0000stress to impactful manufacturing parameters of the Selective Laser Melting\u0000(SLM) process. Remarkably though anticipated, the CSR function reveals the\u0000connection between the macroscale system property (compressive yielding stress)\u0000and the microstructure during self-organizing process. In addition, the\u0000second-order non-linear CSR functions ensure a single global optimum in complex\u0000systems.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141939927","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

Intermittent Run Motility of Bacteria in Gels Exhibits Power-Law Distributed Dwell Times 凝胶中细菌的间歇运行运动呈现幂律分布的停留时间

arXiv - PHYS - Biological Physics Pub Date : 2024-08-05 DOI: arxiv-2408.02317

Agniva Datta, Sönke Beier, Veronika Pfeifer, Robert Großmann, Carsten Beta

引用次数: 0

Spontaneous and Induced Oscillations in Confined Epithelia 封闭上皮细胞的自发振荡和诱导振荡

arXiv - PHYS - Biological Physics Pub Date : 2024-08-05 DOI: arxiv-2408.02806

Toshi Parmar, Liam P. Dow, beth L. Pruitt, M. Cristina Marchetti

引用次数: 0

Effect of interleaflet friction on the dynamics of molecular rotors in lipid membranes 小叶间摩擦对脂质膜中分子转子动力学的影响

arXiv - PHYS - Biological Physics Pub Date : 2024-08-02 DOI: arxiv-2408.01280

Naomi Oppenheimer, Vinny C. Suja, Howard A. Stone

引用次数: 0

Extreme-value analysis in nano-biological systems: Applications and Implications 纳米生物系统中的极值分析：应用与影响

arXiv - PHYS - Biological Physics Pub Date : 2024-08-02 DOI: arxiv-2408.01007

Kumiko Hayashi, Nobumichi Takamatsu, Shunki Takaramoto

{"title":"Extreme-value analysis in nano-biological systems: Applications and Implications","authors":"Kumiko Hayashi, Nobumichi Takamatsu, Shunki Takaramoto","doi":"arxiv-2408.01007","DOIUrl":"https://doi.org/arxiv-2408.01007","url":null,"abstract":"Extreme value analysis (EVA) is a statistical method that studies the\u0000properties of extreme values of datasets, crucial for fields like engineering,\u0000meteorology, finance, insurance, and environmental science. EVA models extreme\u0000events using distributions such as Fr'echet, Weibull, or Gumbel, aiding in\u0000risk prediction and management. This review explores EVA's application to\u0000nanoscale biosystems. Traditionally, biological research focuses on average\u0000values from repeated experiments. However, EVA offers insights into molecular\u0000mechanisms by examining extreme data points. We introduce EVA's concepts with\u0000simulations and review its use in studying motor protein movements within\u0000cells, highlighting the importance of in vivo analysis due to the complex\u0000intracellular environment. We suggest EVA as a tool for extracting motor\u0000proteins' physical properties in vivo and discuss its potential in other\u0000biological systems. While EVA's use in nanoscale biological systems is limited,\u0000it holds promise for uncovering hidden properties in extreme data, promoting\u0000its broader application in life sciences.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141940099","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

Propagation of Enzyme-driven Active Fluctuations in Crowded Milieu 拥挤环境中酶驱动活性波动的传播

arXiv - PHYS - Biological Physics Pub Date : 2024-08-01 DOI: arxiv-2408.00578

Rik Chakraborty, Arnab Maiti, Diptangshu Paul, Rajnandan Borthakur, K. R. Jayaprakash, Uddipta Ghosh, Krishna Kanti Dey

引用次数: 0