Physical biology最新文献_第10页

Nonparametric Bayesian inference for meta-stable conformational dynamics. 亚稳定构象动力学的非参数贝叶斯推理。

IF 2 4区生物学

Physical biology Pub Date : 2022-08-30 DOI: 10.1088/1478-3975/ac885e

Lukas Köhs, Kerri Kukovetz, Oliver Rauh, Heinz Koeppl

{"title":"Nonparametric Bayesian inference for meta-stable conformational dynamics.","authors":"Lukas Köhs, Kerri Kukovetz, Oliver Rauh, Heinz Koeppl","doi":"10.1088/1478-3975/ac885e","DOIUrl":"https://doi.org/10.1088/1478-3975/ac885e","url":null,"abstract":"Analyses of structural dynamics of biomolecules hold great promise to deepen the understanding of and ability to construct complex molecular systems. To this end, both experimental and computational means are available, such as fluorescence quenching experiments or molecular dynamics simulations, respectively. We argue that while seemingly disparate, both fields of study have to deal with the same type of data about the same underlying phenomenon of conformational switching. Two central challenges typically arise in both contexts: (i) the amount of obtained data is large, and (ii) it is often unknown how many distinct molecular states underlie these data. In this study, we build on the established idea of Markov state modeling and propose a generative, Bayesian nonparametric hidden Markov state model that addresses these challenges. Utilizing hierarchical Dirichlet processes, we treat different meta-stable molecule conformations as distinct Markov states, the number of which we then do not have to seta priori. In contrast to existing approaches to both experimental as well as simulation data that are based on the same idea, we leverage a mean-field variational inference approach, enabling scalable inference on large amounts of data. Furthermore, we specify the model also for the important case of angular data, which however proves to be computationally intractable. Addressing this issue, we propose a computationally tractable approximation to the angular model. We demonstrate the method on synthetic ground truth data and apply it to known benchmark problems as well as electrophysiological experimental data from a conformation-switching ion channel to highlight its practical utility.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40598172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Growth instabilities shape morphology and genetic diversity of microbial colonies. 生长不稳定性决定了微生物菌落的形态和遗传多样性。

IF 2 4区生物学

Physical biology Pub Date : 2022-08-19 DOI: 10.1088/1478-3975/ac8514

Alexander Golden, Ilija Dukovski, Daniel Segrè, Kirill S Korolev

{"title":"Growth instabilities shape morphology and genetic diversity of microbial colonies.","authors":"Alexander Golden, Ilija Dukovski, Daniel Segrè, Kirill S Korolev","doi":"10.1088/1478-3975/ac8514","DOIUrl":"10.1088/1478-3975/ac8514","url":null,"abstract":"Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11209841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40570732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The role of spatial structures of tissues in cancer initiation dynamics. 组织空间结构在癌变起始动力学中的作用。

IF 2 4区生物学

Physical biology Pub Date : 2022-08-18 DOI: 10.1088/1478-3975/ac8515

Cade Spaulding, Hamid Teimouri, Anatoly B Kolomeisky

{"title":"The role of spatial structures of tissues in cancer initiation dynamics.","authors":"Cade Spaulding, Hamid Teimouri, Anatoly B Kolomeisky","doi":"10.1088/1478-3975/ac8515","DOIUrl":"https://doi.org/10.1088/1478-3975/ac8515","url":null,"abstract":"It is widely believed that biological tissues evolved to lower the risks of cancer development. One of the specific ways to minimize the chances of tumor formation comes from proper spatial organization of tissues. However, the microscopic mechanisms of underlying processes remain not fully understood. We present a theoretical investigation on the role of spatial structures in cancer initiation dynamics. In our approach, the dynamics of single mutation fixations are analyzed using analytical calculations and computer simulations by mapping them to Moran processes on graphs with different connectivity that mimic various spatial structures. It is found that while the fixation probability is not affected by modifying the spatial structures of the tissues, the fixation times can change dramatically. The slowest dynamics is observed in 'quasi-one-dimensional' structures, while the fastest dynamics is observed in 'quasi-three-dimensional' structures. Theoretical calculations also suggest that there is a critical value of the degree of graph connectivity, which mimics the spatial dimension of the tissue structure, above which the spatial structure of the tissue has no effect on the mutation fixation dynamics. An effective discrete-state stochastic model of cancer initiation is utilized to explain our theoretical results and predictions. Our theoretical analysis clarifies some important aspects on the role of the tissue spatial structures in the cancer initiation processes.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40570734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Modeling the dynamics of innate immune response to Parkinson disease with therapeutic approach. 用治疗方法模拟先天免疫反应对帕金森病的动力学。

IF 2 4区生物学

Physical biology Pub Date : 2022-08-18 DOI: 10.1088/1478-3975/ac8516

Asma Badrah, Salma Al-Tuwairqi

引用次数: 1

Optimal policies for mitigating pandemic costs: a tutorial model. 减轻流行病成本的最佳政策:教程模型。

IF 2 4区生物学

Physical biology Pub Date : 2022-08-09 DOI: 10.1088/1478-3975/ac7e9e

M Serra, S Al-Mosleh, S Ganga Prasath, V Raju, S Mantena, J Chandra, S Iams, L Mahadevan

{"title":"Optimal policies for mitigating pandemic costs: a tutorial model.","authors":"M Serra, S Al-Mosleh, S Ganga Prasath, V Raju, S Mantena, J Chandra, S Iams, L Mahadevan","doi":"10.1088/1478-3975/ac7e9e","DOIUrl":"https://doi.org/10.1088/1478-3975/ac7e9e","url":null,"abstract":"There have been a number of pharmaceutical and non-pharmaceutical interventions associated with COVID-19 over the past two years. Various non-pharmaceutical interventions were proposed and implemented to control the spread of the COVID-19 pandemic. Most common of these were partial and complete lockdowns that were used in an attempt to minimize the costs associated with mortality, economic losses and social factors, while being subject to constraints such as finite hospital capacity. Here, we use a minimal model posed in terms of optimal control theory to understand the costs and benefits of such strategies. This allows us to determine top-down policies for how to restrict social contact rates given an age-structured model for the dynamics of the disease. Depending on the relative weights allocated to mortality and socioeconomic losses, we see that the optimal strategies range from long-term social-distancing only for the most vulnerable, partial lockdown to ensure not over-running hospitals, and alternating-shifts, all of which lead to significant reduction in mortality and/or socioeconomic losses. Crucially, commonly used strategies that involve long periods of broad lockdown are almost never optimal, as they are highly unstable to reopening and entail high socioeconomic costs. Using parameter estimates from data available for Germany and the USA early in the pandemic, we quantify these policies and use sensitivity analysis in the relevant model parameters and initial conditions to determine the range of robustness of our policies. Finally we also discuss how bottom-up behavioral changes affect the dynamics of the pandemic and show how they can work in tandem with top-down control policies to mitigate pandemic costs even more effectively.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40473285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Mechanical testing of particle streaming and intact extracellular mucilage nanofibers reveal a role of elastic force in diatom motility. 颗粒流和完整的细胞外黏液纳米纤维的力学测试揭示了弹性力在硅藻运动中的作用。

IF 2 4区生物学

Physical biology Pub Date : 2022-07-14 DOI: 10.1088/1478-3975/ac7d30

Braulio Gutiérrez-Medina, Ana Iris Peña Maldonado, Jessica Viridiana García-Meza

{"title":"Mechanical testing of particle streaming and intact extracellular mucilage nanofibers reveal a role of elastic force in diatom motility.","authors":"Braulio Gutiérrez-Medina, Ana Iris Peña Maldonado, Jessica Viridiana García-Meza","doi":"10.1088/1478-3975/ac7d30","DOIUrl":"https://doi.org/10.1088/1478-3975/ac7d30","url":null,"abstract":"Diatoms are unicellular microalgae with a rigid cell wall, able to glide on surfaces by releasing nanopolymeric fibers through central slits known as raphes. Here we consider the modelNitszchia communisto perform quantitative studies on two complementary aspects involved in diatom gliding. Using video microscopy and automated image analysis, we measure the motion of test beads as they are pulled by extracellular polymeric substances (EPS) fibers at the diatom raphe (particle streaming). A multimodal distribution of particle speed is found, evidencing the appearance of short-time events of high speed and acceleration (known as jerky motion) and suggesting that different mechanisms contribute to set diatom velocity during gliding. Furthermore, we use optical tweezers to obtain force-extension records for extracellular diatom nanofibers; records are well described by the worm-like chain model of polymer elasticity. In contrast to previous studies based on application of denaturing force (in the nN regime), application of low force (up to 6 pN) and using enable us to obtain the persistence length of intact fibers. From these measurements, mechanical parameters of EPS fibers such as radius and elastic constant are estimated. Furthermore, by modeling particle streaming as a spring in parallel with a dashpot, we show that the time involved in the release of mechanical energy after fiber detachment from beads (elastic snapping) agrees with our observations of jerky motion. We conclude that the smooth and jerky motions displayed by gliding diatoms correspond to molecular motors and elastic snapping, respectively, thus providing quantitative elements that incorporate to current models of the mechanics behind diatom locomotion.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40406099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Instabilities of complex fluids with partially structured and partially random interactions. 具有部分结构和部分随机相互作用的复杂流体的不稳定性。

IF 2 4区生物学

Physical biology Pub Date : 2022-07-13 DOI: 10.1088/1478-3975/ac55f9

Giorgio Carugno, Izaak Neri, Pierpaolo Vivo

引用次数: 13

Minimal sensor arrays for localizing objects using an electric sense 最小的传感器阵列，用于定位使用电感测对象

IF 2 4区生物学

Physical biology Pub Date : 2022-06-02 DOI: 10.1088/1478-3975/ac75a5

Babak Pourziaei, G. Lewis, John E. Lewis

{"title":"Minimal sensor arrays for localizing objects using an electric sense","authors":"Babak Pourziaei, G. Lewis, John E. Lewis","doi":"10.1088/1478-3975/ac75a5","DOIUrl":"https://doi.org/10.1088/1478-3975/ac75a5","url":null,"abstract":"Weakly electric fish encode perturbations in a self-generated electric field to sense their environment. Localizing objects using this electric sense requires that distance be decoded from a two-dimensional electric image of the field perturbations on their skin. Many studies of object localization by weakly electric fish, and by electric sensing in a generic context, have focused on extracting location information from different features of the electric image. Some of these studies have also considered the additional information gained from sampling the electric image at different times, and from different viewpoints. Here, we take a different perspective and instead consider the information available at a single point in space (i.e. a single sensor or receptor) at a single point in time (i.e. constant field). By combining the information from multiple receptors, we show that an object’s distance can be unambiguously encoded by as few as four receptors at specific locations on a sensing surface in a manner that is relatively robust to environmental noise. This provides a lower bound on the information (i.e. receptor array size) required to decode the three-dimensional location of an object using an electric sense.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46802746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spatiotemporal feedforward between PKM2 tetramers and mTORC1 prompts mTORC1 activation PKM2四聚体和mTORC1之间的时空前馈促使mTORC1激活

IF 2 4区生物学

Physical biology Pub Date : 2022-05-25 DOI: 10.1088/1478-3975/ac7372

Yu Xia, Shuming Wang, Chunbo Song, Ruo-yu Luo

引用次数: 0

One-dimensional acoustic potential landscapes guide the neurite outgrowth and affect the viability of B35 neuroblastoma cells 一维声电位景观引导神经突起生长并影响B35神经母细胞瘤细胞的生存能力

IF 2 4区生物学

Physical biology Pub Date : 2022-05-17 DOI: 10.1088/1478-3975/ac70a1

Kathrin Baumgartner, Sophie C. F. Mauritz, Sebastian Angermann, Manuel S. Brugger, C. Westerhausen

引用次数: 0