arXiv - PHYS - Biological Physics最新文献_第9页

Predicting the Progression of Cancerous Tumors in Mice: A Machine and Deep Learning Intuition 预测小鼠癌症肿瘤的进展：一种机器和深度学习直觉

arXiv - PHYS - Biological Physics Pub Date : 2024-07-27 DOI: arxiv-2407.19277

Amit K Chattopadhyay, Aimee Pascaline N Unkundiye, Gillian Pearce, Steven Russell

{"title":"Predicting the Progression of Cancerous Tumors in Mice: A Machine and Deep Learning Intuition","authors":"Amit K Chattopadhyay, Aimee Pascaline N Unkundiye, Gillian Pearce, Steven Russell","doi":"arxiv-2407.19277","DOIUrl":"https://doi.org/arxiv-2407.19277","url":null,"abstract":"The study explores Artificial Intelligence (AI) powered modeling to predict\u0000the evolution of cancer tumor cells in mice under different forms of treatment.\u0000The AI models are analyzed against varying ambient and systemic parameters,\u0000e.g. drug dosage, volume of the cancer cell mass, and time taken to destroy the\u0000cancer cell mass. The data required for the analysis have been synthetically\u0000extracted from plots available in both published and unpublished literature\u0000(primarily using a Matlab architecture called \"Grabit\"), that are then\u0000statistically standardized around the same baseline for comparison. Three forms\u0000of treatment are considered - saline (multiple concentrations used), magnetic\u0000nanoparticles (mNPs) and fluorodeoxyglycose iron oxide magnetic nanoparticles\u0000(mNP-FDGs) - analyzed using three Machine Learning (ML) algorithms, Decision\u0000Tree (DT), Random Forest (RF), Multilinear Regression (MLR), and a Deep\u0000Learning (DL) module, the Adaptive Neural Network (ANN). The AI models are\u0000trained on 60-80% data, the rest used for validation. Assessed over all three\u0000forms of treatment, ANN consistently outperforms other predictive models. Our\u0000models predict mNP-FDG as the most potent treatment regime that kills the\u0000cancerous tumor completely in ca 13 days from the start of treatment. The\u0000models can be generalized to other forms of cancer treatment regimens.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141867141","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

Dimensional reduction and adaptation-development-evolution relation in evolved biological systems 进化生物系统中的降维与适应-发展-进化关系

arXiv - PHYS - Biological Physics Pub Date : 2024-07-27 DOI: arxiv-2407.19168

Kunihiko Kaneko

{"title":"Dimensional reduction and adaptation-development-evolution relation in evolved biological systems","authors":"Kunihiko Kaneko","doi":"arxiv-2407.19168","DOIUrl":"https://doi.org/arxiv-2407.19168","url":null,"abstract":"Life systems are complex and hierarchical, with diverse components at\u0000different scales, yet they sustain themselves, grow, and evolve over time. How\u0000can a theory of such complex biological states be developed? Here we note that\u0000for a hierarchical biological system to be robust, it must achieve consistency\u0000between micro-scale (e.g. molecular) and macro-scale (e.g. cellular) phenomena.\u0000This allows for a universal theory of adaptive change in cells based on\u0000biological robustness and consistency between cellular growth and molecular\u0000replication. Here, we show how adaptive changes in high-dimensional phenotypes\u0000(biological states) are constrained to low-dimensional space, leading to the\u0000derivation of a macroscopic law for cellular states. The theory is then\u0000extended to evolution, leading to proportionality between evolutionary and\u0000environmental responses, as well as proportionality between phenotypic\u0000variances due to noise and due to genetic changes. The universality of the\u0000results across several models and experiments is demonstrated. Then, by further\u0000extending the theory of evolutionary dimensional reduction to multicellular\u0000systems, the relationship between multicellular development and evolution, in\u0000particular the developmental hourglass, is demonstrated. Finally, the\u0000possibility of collapse of dimensional reduction under nutrient limitation is\u0000discussed.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141867121","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

Locomotion of Active Polymerlike Worms in Porous Media 活性聚合物状蠕虫在多孔介质中的运动

arXiv - PHYS - Biological Physics Pub Date : 2024-07-26 DOI: arxiv-2407.18805

Rosa Sinaasappel, Mohammad Fazelzadeh, Twan Hooijschuur, Sara Jabbari-Farouji, Antoine Deblais

引用次数: 0

Tutorial for the growth and development of Myxococcus xanthus as a Model System at the Intersection of Biology and Physics 作为生物学和物理学交叉模型系统的黄肉霉菌的生长和发育教程

arXiv - PHYS - Biological Physics Pub Date : 2024-07-26 DOI: arxiv-2407.18714

Jesus Manuel Antúnez Domínguez, Laura Pérez García, Natsuko Rivera-Yoshida, Jasmin Di Franco, David Steiner, Alejandro V. Arzola, Mariana Benítez, Charlotte Hamngren Blomqvist, Roberto Cerbino, Caroline Beck Adiels, Giovanni Volpe

引用次数: 0

Passive wing deployment and retraction in beetles and flapping microrobots 甲虫和拍打式微型机器人的被动展翅和缩翅

arXiv - PHYS - Biological Physics Pub Date : 2024-07-25 DOI: arxiv-2407.18180

Hoang-Vu Phan, Hoon Cheol Park, Dario Floreano

{"title":"Passive wing deployment and retraction in beetles and flapping microrobots","authors":"Hoang-Vu Phan, Hoon Cheol Park, Dario Floreano","doi":"arxiv-2407.18180","DOIUrl":"https://doi.org/arxiv-2407.18180","url":null,"abstract":"Birds, bats and many insects can tuck their wings against their bodies at\u0000rest and deploy them to power flight. Whereas birds and bats use well-developed\u0000pectoral and wing muscles and tendons, how insects control these movements\u0000remains unclear, as mechanisms of wing deployment and retraction vary among\u0000insect species. Beetles (Coleoptera) display one of the most complex wing\u0000mechanisms. For example, in rhinoceros beetles, the wing deployment initiates\u0000by fully opening the elytra and partially releasing the hindwings from the\u0000abdomen. Subsequently, the beetle starts flapping, elevates the hindwings at\u0000the bases, and unfolds the wingtips in an origami-like fashion. Whilst the\u0000origami-like fold have been extensively explored, limited attention has been\u0000given to the hindwing base deployment and retraction, which are believed to be\u0000driven by thoracic muscles. Using high-speed cameras and robotic flapping-wing\u0000models, here we demonstrate that rhinoceros beetles can effortlessly elevate\u0000the hindwings to flight position without the need for muscular activity. We\u0000show that opening the elytra triggers a spring-like partial release of the\u0000hindwings from the body, allowing the clearance needed for subsequent flapping\u0000motion that brings the hindwings into flight position. The results also show\u0000that after flight, beetles can leverage the elytra to push the hindwings back\u0000into the resting position, further strengthening the hypothesis of a passive\u0000deployment mechanism. Finally, we validate the hypothesis with a flapping\u0000microrobot that passively deploys its wings for stable controlled flight and\u0000retracts them neatly upon landing, which offers a simple yet effective approach\u0000to the design of insect-like flying micromachines.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782912","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

Chemically reactive and aging macromolecular mixtures II: Phase separation and coarsening 化学反应和老化大分子混合物 II：相分离和粗化

arXiv - PHYS - Biological Physics Pub Date : 2024-07-25 DOI: arxiv-2407.18171

Ruoyao Zhang, Sheng Mao, Mikko P. Haataja

{"title":"Chemically reactive and aging macromolecular mixtures II: Phase separation and coarsening","authors":"Ruoyao Zhang, Sheng Mao, Mikko P. Haataja","doi":"arxiv-2407.18171","DOIUrl":"https://doi.org/arxiv-2407.18171","url":null,"abstract":"In a companion paper, we put forth a thermodynamic model for complex\u0000formation via a chemical reaction involving multiple macromolecular species,\u0000which may subsequently undergo liquid-liquid phase separation and a further\u0000transition into a gel-like state. In the present work, we formulate a\u0000thermodynamically consistent kinetic framework to study the interplay between\u0000phase separation, chemical reaction and aging in spatially inhomogeneous\u0000macromolecular mixtures. A numerical algorithm is also proposed to simulate\u0000domain growth from collisions of liquid and gel domains via passive Brownian\u0000motion in both two and three spatial dimensions. Our results show that the\u0000coarsening behavior is significantly influenced by the degree of gelation and\u0000Brownian motion. The presence of a gel phase inside condensates strongly limits\u0000the diffusive transport processes, and Brownian motion coalescence controls the\u0000coarsening process in systems with high area/volume fractions of gel-like\u0000condensates, leading to formation of interconnected domains with atypical\u0000domain growth rates controlled by size-dependent translational and rotational\u0000diffusivities.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782983","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

The Bifurcation Growth Rate for the Robust Pattern Formation in the Reaction-Diffusion System on the Growing Domain 增长域上反应-扩散系统中稳健模式形成的分岔增长率

arXiv - PHYS - Biological Physics Pub Date : 2024-07-24 DOI: arxiv-2407.17217

Shin Nishihara, Toru Ohira

{"title":"The Bifurcation Growth Rate for the Robust Pattern Formation in the Reaction-Diffusion System on the Growing Domain","authors":"Shin Nishihara, Toru Ohira","doi":"arxiv-2407.17217","DOIUrl":"https://doi.org/arxiv-2407.17217","url":null,"abstract":"Among living organisms, there are species that change their patterns on their\u0000body surface during their growth process and those that maintain their\u0000patterns. Theoretically, it has been shown that large-scale species do not form\u0000distinct patterns. However, exceptionally, even large-scale species like\u0000giraffes form and maintain patterns, and previous studies have shown that the\u0000growth plays a crucial role in pattern formation and transition. Here we show\u0000how the growth of the domain contributes to Turing bifurcation based on the\u0000reaction-diffusion system by applying the Gray-Scott model to the reaction\u0000terms, both analytically and numerically, focusing on the phenomenon of pattern\u0000formation and maintenance in large species like giraffes, where melanocytes are\u0000widely distributed. After analytically identifying the Turing bifurcation\u0000related to the growth rate, we numerically verify the pattern formation and\u0000maintenance in response to the finite-amplitude perturbations of the blue state\u0000specific to the Gray-Scott model near the bifurcation. Furthermore, among pairs\u0000of the parameters that form Turing patterns in a reaction-diffusion system on a\u0000fixed domain, we determine a pair of the parameters that maximizes the growth\u0000rate for the Turing bifurcation in a reaction-diffusion system on a\u0000time-dependently growing domain. Specifically, we conduct a numerical analysis\u0000to pursue the pair of the parameters in the Turing space that can be the most\u0000robust in maintaining the patterns formed on the fixed domain, even as the\u0000domain grows. This study may contribute to specifically reaffirming the\u0000importance of growth rate in pattern formation and understanding patterns that\u0000are easy to maintain even during growth.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782913","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 Knots are Plectonemes 当绳结成为折线

arXiv - PHYS - Biological Physics Pub Date : 2024-07-23 DOI: arxiv-2407.16290

Fei Zheng, Antonio Suma, Christopher Maffeo, Kaikai Chen, Mohammed Alawami, Jingjie Sha, Aleksei Aksimentiev, Cristian Micheletti, Ulrich F Keyser

{"title":"When Knots are Plectonemes","authors":"Fei Zheng, Antonio Suma, Christopher Maffeo, Kaikai Chen, Mohammed Alawami, Jingjie Sha, Aleksei Aksimentiev, Cristian Micheletti, Ulrich F Keyser","doi":"arxiv-2407.16290","DOIUrl":"https://doi.org/arxiv-2407.16290","url":null,"abstract":"The transport of DNA polymers through nanoscale pores is central to many\u0000biological processes, from bacterial gene exchange to viral infection. In\u0000single-molecule nanopore sensing, the detection of nucleic acid and protein\u0000analytes relies on the passage of a long biopolymer through a nanoscale\u0000aperture. Understanding the dynamics of polymer translocation through\u0000nanopores, especially the relation between ionic current signal and polymer\u0000conformations is thus essential for the successful identification of targets.\u0000Here, by analyzing ionic current traces of dsDNA translocation, we reveal that\u0000features up to now uniquely associated with knots are instead different\u0000structural motifs: plectonemes. By combining experiments and simulations, we\u0000demonstrate that such plectonemes form because of the solvent flow that induces\u0000rotation of the helical DNA fragment in the nanopore, causing torsion\u0000propagation outwards from the pore. Molecular dynamic simulations reveal that\u0000plectoneme initialization is dominated by the applied torque while the\u0000translocation time and size of the plectonemes depend on the coupling of torque\u0000and pulling force, a mechanism that might also be relevant for in vivo DNA\u0000organization. Experiments with nicked DNA constructs show that the number of\u0000plectonemes depends on the rotational constraints of the translocating\u0000molecules. Thus, our work introduces plectonemes as essential structural\u0000features that must be considered for accurate analysis of polymer transport in\u0000the nanopore.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782915","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

Pre-oligomerisation stochastic dynamics of prions driven by water molecules 水分子驱动的朊病毒聚合前随机动力学

arXiv - PHYS - Biological Physics Pub Date : 2024-07-23 DOI: arxiv-2407.16250

Mairembam Kelvin Singh, R. K. Brojen Singh, Moirangthem Shubhakanta Singh

引用次数: 0

New Theoretical Insights Unraveling Color Pattern in the Flowers of Passiflora incarnata 揭示西番莲花色图案的新理论见解

arXiv - PHYS - Biological Physics Pub Date : 2024-07-23 DOI: arxiv-2407.18979

Ishaan Misra, V. Ramanathan

引用次数: 0