PRX Life最新文献_第2页

Speed Inversion in a Potts Glass Model of Cortical Dynamics 皮质动力学的Potts Glass模型中的速度反演

PRX Life Pub Date : 2023-07-27 DOI: 10.1103/prxlife.1.013005

K. Ryom, A. Treves

引用次数: 2

Tissue Flows Are Tuned by Actomyosin-Dependent Mechanics in Developing Embryos 胚胎发育中肌动球蛋白依赖机制调节组织流动

PRX Life Pub Date : 2023-07-25 DOI: 10.1103/prxlife.1.013004

R. Herrera-Perez, Christian Cupo, Cole Allan, A. Dagle, K. Kasza

引用次数: 1

Editorial: PRX Life, Where Physics and Life Sciences Converge 社论:PRX生命，物理学和生命科学交汇的地方

PRX Life Pub Date : 2023-07-20 DOI: 10.1103/prxlife.1.010001

S. Bradde, M. Gardel

引用次数: 0

Conflicting Roles of Flagella in Planktonic Protists: Propulsion, Resource Acquisition, and Stealth 鞭毛在浮游原生生物中的冲突作用:推进力、资源获取和隐身

PRX Life Pub Date : 2023-07-20 DOI: 10.1103/prxlife.1.013002

S. S. Asadzadeh, J. Walther, T. Kiørboe

引用次数: 0

Cell Lineage Statistics with Incomplete Population Trees 不完全种群树的细胞谱系统计

PRX Life Pub Date : 2023-05-09 DOI: 10.1103/PRXLife.1.013014

Arthur Genthon, Takashi Nozoe, L. Peliti, D. Lacoste

{"title":"Cell Lineage Statistics with Incomplete Population Trees","authors":"Arthur Genthon, Takashi Nozoe, L. Peliti, D. Lacoste","doi":"10.1103/PRXLife.1.013014","DOIUrl":"https://doi.org/10.1103/PRXLife.1.013014","url":null,"abstract":"Cell lineage statistics is a powerful tool for inferring cellular parameters, such as division rate, death rate or the population growth rate. Yet, in practice such an analysis suffers from a basic problem: how should we treat incomplete lineages that do not survive until the end of the experiment? Here, we develop a model-independent theoretical framework to address this issue. We show how to quantify fitness landscape, survivor bias and selection for arbitrary cell traits from cell lineage statistics in the presence of death, and we test this method using an experimental data set in which a cell population is exposed to a drug that kills a large fraction of the population. This analysis reveals that failing to properly account for dead lineages can lead to misleading fitness estimations. For simple trait dynamics, we prove and illustrate numerically that the fitness landscape and the survivor bias can in addition be used for the non-parametric estimation of the division and death rates, using only lineage histories. Our framework provides universal bounds on the population growth rate, and a fluctuation-response relation which quantifies the reduction of population growth rate due to the variability in death rate. Further, in the context of cell size control, we obtain generalizations of Powell's relation that link the distributions of generation times with the population growth rate, and show that the survivor bias can sometimes conceal the adder property, namely the constant increment of volume between birth and division.","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"2007 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125622524","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

From Effective Interactions Extracted Using Hi-C Data to Chromosome Structures in Conventional and Inverted Nuclei 从利用Hi-C数据提取的有效相互作用到常规核和倒核的染色体结构

PRX Life Pub Date : 2023-04-05 DOI: 10.1103/prxlife.1.013010

Sucheol Shin, Guang Shi, D. Thirumalai

{"title":"From Effective Interactions Extracted Using Hi-C Data to Chromosome Structures in Conventional and Inverted Nuclei","authors":"Sucheol Shin, Guang Shi, D. Thirumalai","doi":"10.1103/prxlife.1.013010","DOIUrl":"https://doi.org/10.1103/prxlife.1.013010","url":null,"abstract":"Contact probabilities between loci, separated by arbitrary genomic distance, for a number of cell types have been reported using genome-wide chromosome conformation capture (Hi-C) experiments. How to extract the effective interaction energies between active euchromatin (A) and inactive heterochromatin (B) directly from the experimental data, without an underlying polymer model, is unsolved. Here, we first calculate the pairwise effective interaction energies (A-A, B-B, or A-B) for interphase chromosomes based on Hi-C data by using the concept of Statistical Potential (SP), which assumes that the interaction energy between two loci is proportional to the logarithm of the frequency with which they interact. Polymer simulations, using the extracted interaction energy values $textit{without any parameter}$, reproduce the segregation between A and B type loci (compartments), and the emergence of topologically associating domains (TADs), features that are prominent in the Hi-C data for interphase chromosomes. Remarkably, the values of the SP automatically satisfy the Flory-Huggins phase separation criterion for all the chromosomes, which explains the mechanism of compartment formation in interphase chromosomes. Strikingly, simulations using the SP that accounts for pericentromeric constitutive heterochromatin (C-type), show hierarchical structuring with the high density of C-type loci in the nuclear center, followed by localization of the B type loci, with euchromatin being confined to the nuclear periphery, which differs from the expected nuclear organization of interphase chromosomes, but is in accord with the imaging data of the inverted nuclei found in photoreceptor rods in nocturnal mammals. The proposed parameter free method and applications show that compartment formation in conventional and inverted nuclei is best explained by the inequality between the effective interaction energies.","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"54 6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128003866","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: 1

Synchronous Replication Initiation of Multiple Origins 启动多源同步复制

PRX Life Pub Date : 2023-04-03 DOI: 10.1103/prxlife.1.013007

M. Berger, P. R. ten Wolde

{"title":"Synchronous Replication Initiation of Multiple Origins","authors":"M. Berger, P. R. ten Wolde","doi":"10.1103/prxlife.1.013007","DOIUrl":"https://doi.org/10.1103/prxlife.1.013007","url":null,"abstract":"Initiating replication synchronously at multiple origins of replication allows the bacterium Escherichia coli to divide even faster than the time it takes to replicate the entire chromosome in nutrient-rich environments. What mechanisms give rise to synchronous replication initiation remains however poorly understood. Via mathematical modelling, we identify four distinct synchronization regimes depending on two quantities: the duration of the so-called licensing period during which the initiation potential in the cell remains high after the first origin has fired and the duration of the blocking period during which already initiated origins remain blocked. For synchronous replication initiation, the licensing period must be long enough such that all origins can be initiated, but shorter than the blocking period to prevent reinitiation of origins that have already fired. We find an analytical expression for the degree of synchrony as a function of the duration of the licensing period, which we confirm by simulations. Our model reveals that the delay between the firing of the first and the last origin scales with the coefficient of variation (CV) of the initiation volume. Matching these to the values measured experimentally shows that the firing rate must rise with the cell volume with an effective Hill coefficient that is at least 20; the probability that all origins fire before the blocking period is over is then at least 92%. Our analysis thus reveals that the low CV of the initiation volume is a consequence of synchronous replication initiation. Finally, we show that the previously presented molecular model for the regulation of replication initiation in E. coli can give rise to synchronous replication initiation for biologically realistic parameters.","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128667521","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: 2

Theory of Rheology and Aging of Protein Condensates 蛋白质凝析物的流变与老化理论

PRX Life Pub Date : 2023-03-31 DOI: 10.1103/prxlife.1.013006

Ryota Takaki, L. Jawerth, Marko Popovi'c, F. Jülicher

{"title":"Theory of Rheology and Aging of Protein Condensates","authors":"Ryota Takaki, L. Jawerth, Marko Popovi'c, F. Jülicher","doi":"10.1103/prxlife.1.013006","DOIUrl":"https://doi.org/10.1103/prxlife.1.013006","url":null,"abstract":"Biological condensates are assemblies of proteins and nucleic acids that form membraneless compartments in cells and play essential roles in cellular functions. In many cases they exhibit the physical properties of liquid droplets that coexist in a surrounding fluid. Recently, quantitative studies on the material properties of biological condensates have become available, revealing complex material properties. In vitro experiments have shown that protein condensates exhibit time dependent material properties, similar to aging in glasses. To understand this phenomenon from a theoretical perspective, we develop a rheological model based on the physical picture of protein diffusion and stochastic binding inside condensates. The complex nature of protein interactions is captured by a distribution of binding energies, incorporated in a trap model originally developed to study glass transitions. Our model can describe diffusion of constituent particles, as well as the material response to time-dependent forces, and it recapitulates the age dependent relaxation time of Maxwell glass observed experimentally both in active and passive rheology. We derive a generalized fluctuation-response relations of our model in which the relaxation function does not obey time translation invariance. Our study sheds light on the complex material properties of biological condensates and provides a theoretical framework for understanding their aging behavior.","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134266487","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

Data-Driven Model Construction for Anisotropic Dynamics of Active Matter 活性物质各向异性动力学的数据驱动模型构建

PRX Life Pub Date : 2023-03-07 DOI: 10.1103/PRXLife.1.013009

Mengyang Gu, X. Fang, Yimin Luo

{"title":"Data-Driven Model Construction for Anisotropic Dynamics of Active Matter","authors":"Mengyang Gu, X. Fang, Yimin Luo","doi":"10.1103/PRXLife.1.013009","DOIUrl":"https://doi.org/10.1103/PRXLife.1.013009","url":null,"abstract":"The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in orientational alignment over time, accompanied by cell proliferation, under the influence of the weak guidance of a molecularly aligned substrate. However, a comprehensive understanding of how this order arises remains largely unknown. This knowledge gap may be attributed, in part, to a scarcity of mechanistic models that can capture the temporal progression of the complex nonequilibrium dynamics during the cellular alignment process. The orientational alignment occurs primarily when cells reach a high density near confluence. Therefore, for accurate modeling, it is crucial to take into account both the cell-cell interaction term and the influence from the substrate, acting as a one-body external potential term. To fill in this gap, we develop a hybrid procedure that utilizes statistical learning approaches to extend the state-of-the-art physics models for quantifying both effects. We develop a more efficient way to perform feature selection that avoids testing all feature combinations through simulation. The maximum likelihood estimator of the model was derived and implemented in computationally scalable algorithms for model calibration and simulation. By including these features, such as the non-Gaussian, anisotropic fluctuations, and limiting alignment interaction only to neighboring cells with the same velocity direction, this model quantitatively reproduce the key system-level parameters--the temporal progression of the velocity orientational order parameters and the variability of velocity vectors, whereas models missing any of the features fail to capture these temporally dependent parameters.","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131594932","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: 3

Normative Framework for Deriving Neural Networks with Multicompartmental Neurons and Non-Hebbian Plasticity 具有多室神经元和非边缘可塑性的神经网络的规范框架

PRX Life Pub Date : 2023-02-20 DOI: 10.1103/prxlife.1.013008

David Lipshutz, Yanis Bahroun, Siavash Golkar, Anirvan M. Sengupta, D. Chklovskii

{"title":"Normative Framework for Deriving Neural Networks with Multicompartmental Neurons and Non-Hebbian Plasticity","authors":"David Lipshutz, Yanis Bahroun, Siavash Golkar, Anirvan M. Sengupta, D. Chklovskii","doi":"10.1103/prxlife.1.013008","DOIUrl":"https://doi.org/10.1103/prxlife.1.013008","url":null,"abstract":"An established normative approach for understanding the algorithmic basis of neural computation is to derive online algorithms from principled computational objectives and evaluate their compatibility with anatomical and physiological observations. Similarity matching objectives have served as successful starting points for deriving online algorithms that map onto neural networks (NNs) with point neurons and Hebbian/anti-Hebbian plasticity. These NN models account for many anatomical and physiological observations; however, the objectives have limited computational power and the derived NNs do not explain multi-compartmental neuronal structures and non-Hebbian forms of plasticity that are prevalent throughout the brain. In this article, we unify and generalize recent extensions of the similarity matching approach to address more complex objectives, including a large class of unsupervised and self-supervised learning tasks that can be formulated as symmetric generalized eigenvalue problems or nonnegative matrix factorization problems. Interestingly, the online algorithms derived from these objectives naturally map onto NNs with multi-compartmental neurons and local, non-Hebbian learning rules. Therefore, this unified extension of the similarity matching approach provides a normative framework that facilitates understanding multi-compartmental neuronal structures and non-Hebbian plasticity found throughout the brain.","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128668545","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: 3