Amit K Chattopadhyay, Aimee Pascaline N Unkundiye, Gillian Pearce, Steven Russell
The study explores Artificial Intelligence (AI) powered modeling to predict the evolution of cancer tumor cells in mice under different forms of treatment. The AI models are analyzed against varying ambient and systemic parameters, e.g. drug dosage, volume of the cancer cell mass, and time taken to destroy the cancer cell mass. The data required for the analysis have been synthetically extracted from plots available in both published and unpublished literature (primarily using a Matlab architecture called "Grabit"), that are then statistically standardized around the same baseline for comparison. Three forms of treatment are considered - saline (multiple concentrations used), magnetic nanoparticles (mNPs) and fluorodeoxyglycose iron oxide magnetic nanoparticles (mNP-FDGs) - analyzed using three Machine Learning (ML) algorithms, Decision Tree (DT), Random Forest (RF), Multilinear Regression (MLR), and a Deep Learning (DL) module, the Adaptive Neural Network (ANN). The AI models are trained on 60-80% data, the rest used for validation. Assessed over all three forms of treatment, ANN consistently outperforms other predictive models. Our models predict mNP-FDG as the most potent treatment regime that kills the cancerous tumor completely in ca 13 days from the start of treatment. The models can be generalized to other forms of cancer treatment regimens.
{"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 The data required for the analysis have been synthetically\u0000extracted from plots available in both published and unpublished literature\u0000(primarily using a Matlab architecture called \"Grabit\"), that are then\u0000statistically standardized around the same baseline for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":"15 1","pages":""},"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}
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a hierarchical biological system to be robust, it must achieve consistency between micro-scale (e.g. molecular) and macro-scale (e.g. cellular) phenomena. This allows for a universal theory of adaptive change in cells based on biological robustness and consistency between cellular growth and molecular replication. Here, we show how adaptive changes in high-dimensional phenotypes (biological states) are constrained to low-dimensional space, leading to the derivation of a macroscopic law for cellular states. The theory is then extended to evolution, leading to proportionality between evolutionary and environmental responses, as well as proportionality between phenotypic variances due to noise and due to genetic changes. The universality of the results across several models and experiments is demonstrated. Then, by further extending the theory of evolutionary dimensional reduction to multicellular systems, the relationship between multicellular development and evolution, in particular the developmental hourglass, is demonstrated. Finally, the possibility of collapse of dimensional reduction under nutrient limitation is discussed.
{"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":"10 1","pages":""},"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}
Rosa Sinaasappel, Mohammad Fazelzadeh, Twan Hooijschuur, Sara Jabbari-Farouji, Antoine Deblais
We investigate the locomotion of thin, living textit{T.~Tubifex} worms, which display active polymerlike behavior, within quasi-2D arrays of pillars with different spatial arrangements and densities. These active worms spread in crowded environments, with a dynamics dependent on both the concentration and arrangement of obstacles. In contrast to passive polymers, our results reveal that in disordered configurations, increasing the pillar density enhances the long-time diffusion of our active polymer-like worms, while we observe the opposite trend in ordered pillar arrays. We found that in disordered media, living worms reptate through available curvilinear tubes, whereas they become trapped within pores of ordered media. Intriguingly, we show that reducing the worm's activity significantly boosts its spread, enabling passive sorting of worms by activity level. Our experimental observations are corroborated through simulations of the tangentially-driven polymer model.
{"title":"Locomotion of Active Polymerlike Worms in Porous Media","authors":"Rosa Sinaasappel, Mohammad Fazelzadeh, Twan Hooijschuur, Sara Jabbari-Farouji, Antoine Deblais","doi":"arxiv-2407.18805","DOIUrl":"https://doi.org/arxiv-2407.18805","url":null,"abstract":"We investigate the locomotion of thin, living textit{T.~Tubifex} worms,\u0000which display active polymerlike behavior, within quasi-2D arrays of pillars\u0000with different spatial arrangements and densities. These active worms spread in\u0000crowded environments, with a dynamics dependent on both the concentration and\u0000arrangement of obstacles. In contrast to passive polymers, our results reveal\u0000that in disordered configurations, increasing the pillar density enhances the\u0000long-time diffusion of our active polymer-like worms, while we observe the\u0000opposite trend in ordered pillar arrays. We found that in disordered media,\u0000living worms reptate through available curvilinear tubes, whereas they become\u0000trapped within pores of ordered media. Intriguingly, we show that reducing the\u0000worm's activity significantly boosts its spread, enabling passive sorting of\u0000worms by activity level. Our experimental observations are corroborated through\u0000simulations of the tangentially-driven polymer model.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141867145","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}
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
Myxococcus xanthus is a unicellular organism whose cells possess the ability to move and communicate, leading to the emergence of complex collective properties and behaviours. This has made it an ideal model system to study the emergence of collective behaviours in interdisciplinary research efforts lying at the intersection of biology and physics, especially in the growing field of active matter research. Often, challenges arise when setting up reliable and reproducible culturing protocols. This tutorial provides a clear and comprehensive guide on the culture, growth, development, and experimental sample preparation of textit{M. xanthus}. Additionally, it includes some representative examples of experiments that can be conducted using these samples, namely motility assays, fruiting body formation, predation, and elasticotaxis.
{"title":"Tutorial for the growth and development of Myxococcus xanthus as a Model System at the Intersection of Biology and Physics","authors":"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","doi":"arxiv-2407.18714","DOIUrl":"https://doi.org/arxiv-2407.18714","url":null,"abstract":"Myxococcus xanthus is a unicellular organism whose cells possess the ability\u0000to move and communicate, leading to the emergence of complex collective\u0000properties and behaviours. This has made it an ideal model system to study the\u0000emergence of collective behaviours in interdisciplinary research efforts lying\u0000at the intersection of biology and physics, especially in the growing field of\u0000active matter research. Often, challenges arise when setting up reliable and\u0000reproducible culturing protocols. This tutorial provides a clear and\u0000comprehensive guide on the culture, growth, development, and experimental\u0000sample preparation of textit{M. xanthus}. Additionally, it includes some\u0000representative examples of experiments that can be conducted using these\u0000samples, namely motility assays, fruiting body formation, predation, and\u0000elasticotaxis.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"86 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141867144","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}
Birds, bats and many insects can tuck their wings against their bodies at rest and deploy them to power flight. Whereas birds and bats use well-developed pectoral and wing muscles and tendons, how insects control these movements remains unclear, as mechanisms of wing deployment and retraction vary among insect species. Beetles (Coleoptera) display one of the most complex wing mechanisms. For example, in rhinoceros beetles, the wing deployment initiates by fully opening the elytra and partially releasing the hindwings from the abdomen. Subsequently, the beetle starts flapping, elevates the hindwings at the bases, and unfolds the wingtips in an origami-like fashion. Whilst the origami-like fold have been extensively explored, limited attention has been given to the hindwing base deployment and retraction, which are believed to be driven by thoracic muscles. Using high-speed cameras and robotic flapping-wing models, here we demonstrate that rhinoceros beetles can effortlessly elevate the hindwings to flight position without the need for muscular activity. We show that opening the elytra triggers a spring-like partial release of the hindwings from the body, allowing the clearance needed for subsequent flapping motion that brings the hindwings into flight position. The results also show that after flight, beetles can leverage the elytra to push the hindwings back into the resting position, further strengthening the hypothesis of a passive deployment mechanism. Finally, we validate the hypothesis with a flapping microrobot that passively deploys its wings for stable controlled flight and retracts them neatly upon landing, which offers a simple yet effective approach to the design of insect-like flying micromachines.
{"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":"22 1","pages":""},"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}
In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a gel-like state. In the present work, we formulate a thermodynamically consistent kinetic framework to study the interplay between phase separation, chemical reaction and aging in spatially inhomogeneous macromolecular mixtures. A numerical algorithm is also proposed to simulate domain growth from collisions of liquid and gel domains via passive Brownian motion in both two and three spatial dimensions. Our results show that the coarsening behavior is significantly influenced by the degree of gelation and Brownian motion. The presence of a gel phase inside condensates strongly limits the diffusive transport processes, and Brownian motion coalescence controls the coarsening process in systems with high area/volume fractions of gel-like condensates, leading to formation of interconnected domains with atypical domain growth rates controlled by size-dependent translational and rotational diffusivities.
{"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":"41 1","pages":""},"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}
Among living organisms, there are species that change their patterns on their body surface during their growth process and those that maintain their patterns. Theoretically, it has been shown that large-scale species do not form distinct patterns. However, exceptionally, even large-scale species like giraffes form and maintain patterns, and previous studies have shown that the growth plays a crucial role in pattern formation and transition. Here we show how the growth of the domain contributes to Turing bifurcation based on the reaction-diffusion system by applying the Gray-Scott model to the reaction terms, both analytically and numerically, focusing on the phenomenon of pattern formation and maintenance in large species like giraffes, where melanocytes are widely distributed. After analytically identifying the Turing bifurcation related to the growth rate, we numerically verify the pattern formation and maintenance in response to the finite-amplitude perturbations of the blue state specific to the Gray-Scott model near the bifurcation. Furthermore, among pairs of the parameters that form Turing patterns in a reaction-diffusion system on a fixed domain, we determine a pair of the parameters that maximizes the growth rate for the Turing bifurcation in a reaction-diffusion system on a time-dependently growing domain. Specifically, we conduct a numerical analysis to pursue the pair of the parameters in the Turing space that can be the most robust in maintaining the patterns formed on the fixed domain, even as the domain grows. This study may contribute to specifically reaffirming the importance of growth rate in pattern formation and understanding patterns that are easy to maintain even during growth.
{"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":"64 1","pages":""},"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}
Fei Zheng, Antonio Suma, Christopher Maffeo, Kaikai Chen, Mohammed Alawami, Jingjie Sha, Aleksei Aksimentiev, Cristian Micheletti, Ulrich F Keyser
The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies on the passage of a long biopolymer through a nanoscale aperture. Understanding the dynamics of polymer translocation through nanopores, especially the relation between ionic current signal and polymer conformations is thus essential for the successful identification of targets. Here, by analyzing ionic current traces of dsDNA translocation, we reveal that features up to now uniquely associated with knots are instead different structural motifs: plectonemes. By combining experiments and simulations, we demonstrate that such plectonemes form because of the solvent flow that induces rotation of the helical DNA fragment in the nanopore, causing torsion propagation outwards from the pore. Molecular dynamic simulations reveal that plectoneme initialization is dominated by the applied torque while the translocation time and size of the plectonemes depend on the coupling of torque and pulling force, a mechanism that might also be relevant for in vivo DNA organization. Experiments with nicked DNA constructs show that the number of plectonemes depends on the rotational constraints of the translocating molecules. Thus, our work introduces plectonemes as essential structural features that must be considered for accurate analysis of polymer transport in the nanopore.
从细菌基因交换到病毒感染，DNA 聚合物通过纳米级孔隙的传输是许多生物过程的核心。在单分子纳米孔传感中，核酸和蛋白质分析物的检测依赖于长生物聚合物通过纳米级孔隙。因此，了解聚合物通过纳米孔的转位动力学，特别是离子电流信号与聚合物构型之间的关系，对于成功识别目标至关重要。在这里，通过分析dsDNA转位的离子电流痕迹，我们揭示了迄今为止与结独特相关的特征是不同的结构模式："偏转膜"（plectonemes）。通过结合实验和模拟，我们证明了这种折线的形成是由于溶剂流引起了纳米孔中螺旋 DNA 片段的旋转，从而导致从孔中向外的扭转传播。分子动力学模拟显示，纠缠体的初始化受外加扭矩的支配，而纠缠体的转移时间和大小则取决于扭矩和拉力的耦合，这种机制可能也与体内 DNA 的组织有关。用缺口 DNA 构建物进行的实验表明，偏转子的数量取决于转位分子的旋转限制。因此，我们的工作将折线作为基本的结构特征引入了纳米孔，要准确分析聚合物在纳米孔内的传输，就必须考虑到这一点。
{"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":"31 1","pages":""},"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}
Mairembam Kelvin Singh, R. K. Brojen Singh, Moirangthem Shubhakanta Singh
Prions are proteinaceous infectious particles that cause neurodegenerative diseases in humans and animals. The complex nature of prions, with respect to their conformations and aggregations, has been an important area of research for quite some time. Here, we develop a model of prion dynamics prior to the formation of oligomers and subsequent development of prion diseases within a stochastic framework, based on the analytical Master Equation and Stochastic Simulation Algorithm by Gillespie. The results that we obtain shows that solvent water molecules act as driving agents in the dynamics of prion aggregation. Further, it is found that aggregated and non-aggregated proteins tend to co-exist in an equilibrium state, depending upon the reaction rate constants. These results may provide a theoretical and qualitative contexts of possible therapeutic strategies in the treatment of prion diseases.
{"title":"Pre-oligomerisation stochastic dynamics of prions driven by water molecules","authors":"Mairembam Kelvin Singh, R. K. Brojen Singh, Moirangthem Shubhakanta Singh","doi":"arxiv-2407.16250","DOIUrl":"https://doi.org/arxiv-2407.16250","url":null,"abstract":"Prions are proteinaceous infectious particles that cause neurodegenerative\u0000diseases in humans and animals. The complex nature of prions, with respect to\u0000their conformations and aggregations, has been an important area of research\u0000for quite some time. Here, we develop a model of prion dynamics prior to the\u0000formation of oligomers and subsequent development of prion diseases within a\u0000stochastic framework, based on the analytical Master Equation and Stochastic\u0000Simulation Algorithm by Gillespie. The results that we obtain shows that\u0000solvent water molecules act as driving agents in the dynamics of prion\u0000aggregation. Further, it is found that aggregated and non-aggregated proteins\u0000tend to co-exist in an equilibrium state, depending upon the reaction rate\u0000constants. These results may provide a theoretical and qualitative contexts of\u0000possible therapeutic strategies in the treatment of prion diseases.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141782914","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}
The change in the color pattern of the petals of Passiflora incarnata is studied using the chaos theory in the form of logistic maps and plotted using the corresponding bifurcation diagram. Based on a colorful inspection of the beginning of violet-colored dots along the filament of the flower's bud stage and the emergence of alternating bands of violet and white color in the matured bloom, it is possible to deduce that a two-degree model for polynomial mapping can be used to study color oscillations in the flower.
{"title":"New Theoretical Insights Unraveling Color Pattern in the Flowers of Passiflora incarnata","authors":"Ishaan Misra, V. Ramanathan","doi":"arxiv-2407.18979","DOIUrl":"https://doi.org/arxiv-2407.18979","url":null,"abstract":"The change in the color pattern of the petals of Passiflora incarnata is\u0000studied using the chaos theory in the form of logistic maps and plotted using\u0000the corresponding bifurcation diagram. Based on a colorful inspection of the\u0000beginning of violet-colored dots along the filament of the flower's bud stage\u0000and the emergence of alternating bands of violet and white color in the matured\u0000bloom, it is possible to deduce that a two-degree model for polynomial mapping\u0000can be used to study color oscillations in the flower.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141867146","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}
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