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Modeling cancer progression: an integrated workflow extending data-driven kinetic models to bio-mechanical PDE models Phys. Biol. (IF 2.0) Pub Date : 2024-02-19 Navid Mohammad Mirzaei, Leili Shahriyari
Computational modeling of cancer can help unveil dynamics and interactions that are hard to replicate experimentally. Thanks to the advancement in cancer databases and data analysis technologies, these models have become more robust than ever. There are many mathematical models which investigate cancer through different approaches, from sub-cellular to tissue scale, and from treatment to diagnostic
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An effective hydrodynamic description of marching locusts Phys. Biol. (IF 2.0) Pub Date : 2024-02-14 Dan Gorbonos, Felix B Oberhauser, Luke L Costello, Yannick Günzel, Einat Couzin-Fuchs, Benjamin Koger, Iain D Couzin
A fundamental question in complex systems is how to relate interactions between individual components (‘microscopic description’) to the global properties of the system (‘macroscopic description’). Furthermore, it is unclear whether such a macroscopic description exists and if such a description can capture large-scale properties. Here, we address the validity of a macroscopic description of a complex
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An individual-based model to explore the impact of psychological stress on immune infiltration into tumour spheroids Phys. Biol. (IF 2.0) Pub Date : 2024-02-05 Emma Leschiera, Gheed Al-Hity, Melanie S Flint, Chandrasekhar Venkataraman, Tommaso Lorenzi, Luis Almeida, Chloe Audebert
In recent in vitro experiments on co-culture between breast tumour spheroids and activated immune cells, it was observed that the introduction of the stress hormone cortisol resulted in a decreased immune cell infiltration into the spheroids. Moreover, the presence of cortisol deregulated the normal levels of the pro- and anti-inflammatory cytokines IFN-γ and IL-10. We present an individual-based model
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Structure of the space of folding protein sequences defined by large language models Phys. Biol. (IF 2.0) Pub Date : 2024-01-31 A Zambon, R Zecchina, G Tiana
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the protein sequence landscape as defined by an effective energy that is a proxy of sequence foldability. This landscape shares characteristics with optimization challenges
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Fitness effects of a demography-dispersal trade-off in expanding Saccharomyces cerevisiae mats Phys. Biol. (IF 2.0) Pub Date : 2024-01-22 Rebekah Hall, Akila Bandara, Daniel A Charlebois
Fungi expand in space and time to form complex multicellular communities. The mechanisms by which they do so can vary dramatically and determine the life-history and dispersal traits of expanding populations. These traits influence deterministic and stochastic components of evolution, resulting in complex eco-evolutionary dynamics during colony expansion. We perform experiments on budding yeast strains
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A thermodynamical model of non-deterministic computation in cortical neural networks Phys. Biol. (IF 2.0) Pub Date : 2023-12-11 Elizabeth A Stoll
Neuronal populations in the cerebral cortex engage in probabilistic coding, effectively encoding the state of the surrounding environment with high accuracy and extraordinary energy efficiency. A new approach models the inherently probabilistic nature of cortical neuron signaling outcomes as a thermodynamic process of non-deterministic computation. A mean field approach is used, with the trial Hamiltonian
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An exploration of the binding prediction of anatoxin-a and atropine to acetylcholinesterase enzyme using multi-level computer simulations Phys. Biol. (IF 2.0) Pub Date : 2023-11-23 Showkat Ahmad Mir, Jamoliddin Razzokov, Vishwajeet Mukherjee, Iswar Baitharu, Binata Nayak
Acetylcholinesterase (AChE) is crucial for the breakdown of acetylcholine to acetate and choline, while the inhibition of AChE by anatoxin-a (ATX-a) results in severe health complications. This study explores the structural characteristics of ATX-a and its interactions with AChE, comparing to the reference molecule atropine for binding mechanisms. Molecular docking simulations reveal strong binding
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Calcium regulates cortex contraction in Physarum polycephalum Phys. Biol. (IF 2.0) Pub Date : 2023-11-17 Bjoern Kscheschinski, Mirna Kramar, Karen Alim
The tubular network-forming slime mold Physarum polycephalum is able to maintain long-scale contraction patterns driven by an actomyosin cortex. The resulting shuttle streaming in the network is crucial for the organism to respond to external stimuli and reorganize its body mass giving rise to complex behaviors. However, the chemical basis of the self-organized flow pattern is not fully understood
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High-throughput design of cultured tissue moulds using a biophysical model: optimising cell alignment Phys. Biol. (IF 2.0) Pub Date : 2023-10-30 James P Hague, Allison E Andrews, Hugh Dickinson
The technique presented here identifies tethered mould designs, optimised for growing cultured tissue with very highly-aligned cells. It is based on a microscopic biophysical model for polarised cellular hydrogels. There is an unmet need for tools to assist mould and scaffold designs for the growth of cultured tissues with bespoke cell organisations, that can be used in applications such as regenerative
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Rapid prediction of lab-grown tissue properties using deep learning Phys. Biol. (IF 2.0) Pub Date : 2023-10-19 Allison E Andrews, Hugh Dickinson, James P Hague
The interactions between cells and the extracellular matrix are vital for the self-organisation of tissues. In this paper we present proof-of-concept to use machine learning tools to predict the role of this mechanobiology in the self-organisation of cell-laden hydrogels grown in tethered moulds. We develop a process for the automated generation of mould designs with and without key symmetries. We
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Calcium storage in multivesicular endo-lysosome Phys. Biol. (IF 2.0) Pub Date : 2023-10-17 Cameron C Scott, Vaibhav Wasnik, Paula Nunes-Hassler, Nicolas Demaurex, Karsten Kruse, Jean Gruenberg
It is now established that endo-lysosomes, also referred to as late endosomes, serve as intracellular calcium store, in addition to the endoplasmic reticulum. While abundant calcium-binding proteins provide the latter compartment with its calcium storage capacity, essentially nothing is known about the mechanism responsible for calcium storage in endo-lysosomes. In this paper, we propose that the structural
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Facilitating cell segmentation with the projection-enhancement network Phys. Biol. (IF 2.0) Pub Date : 2023-10-09 Christopher Z Eddy, Austin Naylor, Christian T Cunningham, Bo Sun
Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly require recording sub-optimally sampled data that greatly reduces the utility of such 3D data, especially in crowded sample space with significant axial overlap between
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Seeking and sharing information in collective olfactory search Phys. Biol. (IF 2.0) Pub Date : 2023-10-09 Emanuele Panizon, Antonio Celani
Searching for a target is a task of fundamental importance for many living organisms. Long-distance search guided by olfactory cues is a prototypical example of such a process. The searcher receives signals that are sparse and very noisy, making the task extremely difficult. Information-seeking strategies have thus been proven to be effective for individual olfactory search and their extension to collective
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Quantitative insights in tissue growth and morphogenesis with optogenetics Phys. Biol. (IF 2.0) Pub Date : 2023-09-28 Mayesha Sahir Mim, Caroline Knight, Jeremiah J Zartman
Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis
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Universal calcium fluctuations in Hydra morphogenesis Phys. Biol. (IF 2.0) Pub Date : 2023-09-22 Oded Agam, Erez Braun
Understanding the collective physical processes that drive robust morphological transitions in animal development necessitates the characterization of the relevant fields involved in morphogenesis. Calcium (Ca2+) is recognized as one such field. In this study, we demonstrate that the spatial fluctuations of Ca2+ during Hydra regeneration exhibit universal characteristics. To investigate this phenomenon
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EMT induces characteristic changes of Rho GTPases and downstream effectors with a mitosis-specific twist Phys. Biol. (IF 2.0) Pub Date : 2023-09-12 Kamran Hosseini, Annika Frenzel, Elisabeth Fischer-Friedrich
Epithelial-mesenchymal transition (EMT) is a key cellular transformation for many physiological and pathological processes ranging from cancer over wound healing to embryogenesis. Changes in cell migration, cell morphology and cellular contractility were identified as hallmarks of EMT. These cellular properties are known to be tightly regulated by the actin cytoskeleton. EMT-induced changes of actin-cytoskeletal
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Phase transitions in insect swarms Phys. Biol. (IF 2.0) Pub Date : 2023-08-22 Andy M Reynolds
In contrast with laboratory insect swarms, wild insect swarms display significant coordinated behaviour. It has been hypothesised that the presence of a fluctuating environment drives the formation of transient, local order (synchronized subgroups), and that this local order pushes the swarm into a new state that is robust to environmental perturbations. The hypothesis is supported by observations
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Quantitative modeling of EGF receptor ligand discrimination via internalization proofreading Phys. Biol. (IF 2.0) Pub Date : 2023-08-22 Jaleesa A Leblanc, Michael G Sugiyama, Costin N Antonescu, Aidan I Brown
The epidermal growth factor receptor (EGFR) is a central regulator of cell physiology that is stimulated by multiple distinct ligands. Although ligands bind to EGFR while the receptor is exposed on the plasma membrane, EGFR incorporation into endosomes following receptor internalization is an important aspect of EGFR signaling, with EGFR internalization behavior dependent upon the type of ligand bound
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Out-of-equilibrium gene expression fluctuations in the presence of extrinsic noise Phys. Biol. (IF 2.0) Pub Date : 2023-08-10 Marta Biondo, Abhyudai Singh, Michele Caselle, Matteo Osella
Cell-to-cell variability in protein concentrations is strongly affected by extrinsic noise, especially for highly expressed genes. Extrinsic noise can be due to fluctuations of several possible cellular factors connected to cell physiology and to the level of key enzymes in the expression process. However, how to identify the predominant sources of extrinsic noise in a biological system is still an
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Fundamental insights into the correlation between chromosome configuration and transcription Phys. Biol. (IF 2.0) Pub Date : 2023-08-04 Swayamshree Senapati, Inayat Ullah Irshad, Ajeet K Sharma, Hemant Kumar
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have
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Emergent dynamics in an astrocyte-neuronal network coupled via nitric oxide Phys. Biol. (IF 2.0) Pub Date : 2023-08-03 Bhanu Sharma, Spandan Kumar, Subhendu Ghosh, Vikram Singh
In the brain, both neurons and glial cells work in conjunction with each other during information processing. Stimulation of neurons can induce calcium oscillations in astrocytes which in turn can affect neuronal calcium dynamics. The ‘glissandi’ effect is one such phenomenon, associated with a decrease in infraslow fluctuations, in which synchronized calcium oscillations propagate as a wave in hundreds
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Enhanced germination and electrotactic behaviour of Phytophthora palmivora zoospores in weak electric fields Phys. Biol. (IF 2.0) Pub Date : 2023-07-28 Eleonora Moratto, Stephen Rothery, Tolga O Bozkurt, Giovanni Sena
Soil-dwelling microorganisms use a variety of chemical and physical signals to navigate their environment. Plant roots produce endogenous electric fields which result in characteristic current profiles. Such electrical signatures are hypothesised to be used by pathogens and symbionts to track and colonise plant roots. The oomycete pathogen Phytophthora palmivora generates motile zoospores which swim
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Corrigendum: Correlation, response and entropy approaches to allosteric behaviors: a critical comparison on the ubiquitin case (2023Phys. Biol.20056002). Phys. Biol. (IF 2.0) Pub Date : 2023-07-28 Fabio Cecconi,Giulio Costantini,Carlo Guardiani,Marco Baldovin,Angelo Vulpiani
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Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization Phys. Biol. (IF 2.0) Pub Date : 2023-07-26 Jarosław Paturej, Aykut Erbaş
Interphase chromosomes are known to organize non-randomly in the micron-sized eukaryotic cell nucleus and occupy certain fraction of nuclear volume, often without mixing. Using extensive coarse-grained simulations, we model such chromosome structures as colloidal particles whose surfaces are grafted by cyclic polymers. This model system is known as Rosetta. The cyclic polymers, with varying polymerization
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Data-driven discovery of stochastic dynamical equations of collective motion Phys. Biol. (IF 2.0) Pub Date : 2023-07-17 Arshed Nabeel, Vivek Jadhav, Danny Raj M, Clément Sire, Guy Theraulaz, Ramón Escobedo, Srikanth K Iyer, Vishwesha Guttal
Coarse-grained descriptions of collective motion of flocking systems are often derived for the macroscopic or the thermodynamic limit. However, the size of many real flocks falls within ‘mesoscopic’ scales (10 to 100 individuals), where stochasticity arising from the finite flock sizes is important. Previous studies on mesoscopic models have typically focused on non-spatial models. Developing mesoscopic
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Mitochondrial networks through the lens of mathematics Phys. Biol. (IF 2.0) Pub Date : 2023-07-14 Greyson R Lewis, Wallace F Marshall
Mitochondria serve a wide range of functions within cells, most notably via their production of ATP. Although their morphology is commonly described as bean-like, mitochondria often form interconnected networks within cells that exhibit dynamic restructuring through a variety of physical changes. Further, though relationships between form and function in biology are well established, the extant toolkit
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Bayesian filtering for model predictive control of stochastic gene expression in single cells Phys. Biol. (IF 2.0) Pub Date : 2023-07-12 Zachary R Fox, Gregory Batt, Jakob Ruess
This study describes a method for controlling the production of protein in individual cells using stochastic models of gene expression. By combining modern microscopy platforms with optogenetic gene expression, experimentalists are able to accurately apply light to individual cells, which can induce protein production. Here we use a finite state projection based stochastic model of gene expression
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Correlation, response and entropy approaches to allosteric behaviors: a critical comparison on the ubiquitin case Phys. Biol. (IF 2.0) Pub Date : 2023-07-10 Fabio Cecconi, Giulio Costantini, Carlo Guardiani, Marco Baldovin, Angelo Vulpiani
Correlation analysis and its close variant principal component analysis are tools widely applied to predict the biological functions of macromolecules in terms of the relationship between fluctuation dynamics and structural properties. However, since this kind of analysis does not necessarily imply causation links among the elements of the system, its results run the risk of being biologically misinterpreted
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Approximate simulation of cortical microtubule models using dynamical graph grammars Phys. Biol. (IF 2.0) Pub Date : 2023-07-07 Eric Medwedeff, Eric Mjolsness
Dynamical graph grammars (DGGs) are capable of modeling and simulating the dynamics of the cortical microtubule array (CMA) in plant cells by using an exact simulation algorithm derived from a master equation; however, the exact method is slow for large systems. We present preliminary work on an approximate simulation algorithm that is compatible with the DGG formalism. The approximate simulation algorithm
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Infiltration of tumor spheroids by activated immune cells Phys. Biol. (IF 2.0) Pub Date : 2023-07-03 Mrinmoy Mukherjee, Oleksandr Chepizhko, Maria Chiara Lionetti, Stefano Zapperi, Caterina A M La Porta, Herbert Levine
Recent years have seen a tremendous growth of interest in understanding the role that the adaptive immune system could play in interdicting tumor progression. In this context, it has been shown that the density of adaptive immune cells inside a solid tumor serves as a favorable prognostic marker across different types of cancer. The exact mechanisms underlying the degree of immune cell infiltration
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The emergence of lines of hierarchy in collective motion of biological systems Phys. Biol. (IF 2.0) Pub Date : 2023-06-29 James M Greene, Eitan Tadmor, Ming Zhong
The emergence of large-scale structures in biological systems, and in particular the formation of lines of hierarchy, is observed at many scales, from collections of cells to groups of insects to herds of animals. Motivated by phenomena in chemotaxis and phototaxis, we present a new class of alignment models that exhibit alignment into lines. The spontaneous formation of such ‘fingers’ can be interpreted
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Allometry of Escherichia coli surface area with volume: effect of size variability, filamentation and division dynamics Phys. Biol. (IF 2.0) Pub Date : 2023-06-20 Tanvi Kale, Dhruv Khatri, Chaitanya A Athale
The cell surface area (SA) increase with volume (V) is determined by growth and regulation of size and shape. Most studies of the rod-shaped model bacterium Escherichia coli have focussed on the phenomenology or molecular mechanisms governing such scaling. Here, we proceed to examine the role of population statistics and cell division dynamics in such scaling by a combination of microscopy, image analysis
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Individual bias and fluctuations in collective decision making: from algorithms to Hamiltonians Phys. Biol. (IF 2.0) Pub Date : 2023-06-13 Petro Sarkanych, Mariana Krasnytska, Luis Gómez-Nava, Pawel Romanczuk, Yurij Holovatch
In this paper, we reconsider the spin model suggested recently to understand some features of collective decision making among higher organisms (Hartnett et al 2016 Phys. Rev. Lett. 116 038701). Within the model, the state of an agent i is described by the pair of variables corresponding to its opinion Si=±1 and a bias ω i toward any of the opposing values of S i . Collective decision making is interpreted
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PyEcoLib: a python library for simulating stochastic cell size dynamics Phys. Biol. (IF 2.0) Pub Date : 2023-06-13 César Nieto, Sergio Camilo Blanco, César Vargas-García, Abhyudai Singh, Pedraza Juan Manuel
Recently, there has been an increasing need for tools to simulate cell size regulation due to important applications in cell proliferation and gene expression. However, implementing the simulation usually presents some difficulties, as the division has a cycle-dependent occurrence rate. In this article, we gather a recent theoretical framework in PyEcoLib, a python-based library to simulate the stochastic
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Fractal dimension to characterize interactions between blood and lymphatic endothelial cells Phys. Biol. (IF 2.0) Pub Date : 2023-06-12 Donghyun Paul Jeong, Daniel Montes, Hsueh-Chia Chang, Donny Hanjaya-Putra
Spatial patterning of different cell types is crucial for tissue engineering and is characterized by the formation of sharp boundary between segregated groups of cells of different lineages. The cell−cell boundary layers, depending on the relative adhesion forces, can result in kinks in the border, similar to fingering patterns between two viscous partially miscible fluids which can be characterized
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Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens Phys. Biol. (IF 2.0) Pub Date : 2023-06-02 Sheryl L Chang, Carl J E Suster, Rebecca J Rockett, Adam J Svahn, Oliver M Cliff, Alicia Arnott, Qinning Wang, Rady Kim, Basel Suliman, Mailie Gall, Tania C Sorrell, Vitali Sintchenko, Mikhail Prokopenko
Modelling evolution of foodborne pathogens is crucial for mitigation and prevention of outbreaks. We apply network-theoretic and information-theoretic methods to trace evolutionary pathways of Salmonella Typhimurium in New South Wales, Australia, by studying whole genome sequencing surveillance data over a five-year period which included several outbreaks. The study derives both undirected and directed
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Evolutionary stability of social interaction rules in collective decision-making Phys. Biol. (IF 2.0) Pub Date : 2023-05-30 Anna Sigalou, Richard P Mann
Social animals can use the choices made by other members of their groups as cues in decision making. Individuals must balance the private information they receive from their own sensory cues with the social information provided by observing what others have chosen. These two cues can be integrated using decision making rules, which specify the probability to select one or other options based on the
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Towards a free energy-based elastic network model and its application to the SARS-COV2 binding to ACE2 Phys. Biol. (IF 2.0) Pub Date : 2023-05-30 Hyuntae Na, Guang Song
Classical normal mode analysis (cNMA) is a standard method for studying the equilibrium vibrations of macromolecules. A major limitation of cNMA is that it requires a cumbersome step of energy minimization that also alters the input structure significantly. Variants of normal mode analysis (NMA) exist that perform NMA directly on PDB structures without energy minimization, while maintaining most of
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What geometrically constrained models can tell us about real-world protein contact maps Phys. Biol. (IF 2.0) Pub Date : 2023-05-26 J Jasmin Güven, Nora Molkenthin, Steffen Mühle, Antonia S J S Mey
The mechanisms by which a protein’s 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture bulk real-world 3D protein-protein properties well. One approach is using protein contact maps (PCMs) to better understand proteins’ properties. In this study, we
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A simple cognitive model explains movement decisions in zebrafish while following leaders Phys. Biol. (IF 2.0) Pub Date : 2023-05-17 Lital Oscar, Liang Li, Dan Gorbonos, Iain D Couzin, Nir S Gov
While moving, animals must frequently make decisions about their future travel direction, whether they are alone or in a group. Here we investigate this process for zebrafish (Danio rerio), which naturally move in cohesive groups. Employing state-of-the-art virtual reality, we study how real fish (RF) follow one or several moving, virtual conspecifics (leaders). These data are used to inform, and test
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Network topology enables efficient response to environment in Physarum polycephalum Phys. Biol. (IF 2.0) Pub Date : 2023-05-16 Siyu Chen, Karen Alim
The network-shaped body plan distinguishes the unicellular slime mould Physarum polycephalum in body architecture from other unicellular organisms. Yet, network-shaped body plans dominate branches of multi-cellular life such as in fungi. What survival advantage does a network structure provide when facing a dynamic environment with adverse conditions? Here, we probe how network topology impacts P.
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Timescale separation in the coordinated switching of bacterial flagellar motors Phys. Biol. (IF 2.0) Pub Date : 2023-05-10 Guanhua Yue, Rongjing Zhang, Junhua Yuan
The output of the bacterial chemotaxis signaling pathway, the level of the intracellular regulator CheY-P, modulates the rotation direction of the flagellar motor, thereby regulating bacterial run-and-tumble behavior. The multiple flagellar motors on an E. coli cell are controlled by a common cytoplasmic pool of CheY-P. Fluctuation of the CheY-P level was thought to be able to coordinate the switching
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Comparison of thermal and athermal dynamics of the cell membrane slope fluctuations in the presence and absence of Latrunculin-B Phys. Biol. (IF 2.0) Pub Date : 2023-05-05 Srestha Roy, Rahul Vaippully, Muruga Lokesh, Gokul Nalupurackal, Vandana Yadav, Snigdhadev Chakraborty, Manoj Gopalakrishnan, Privita Edwina Rayappan George Edwin, Saumendra Kumar Bajpai, Basudev Roy
Conventionally, only the normal cell membrane fluctuations have been studied and used to ascertain membrane properties like the bending rigidity. A new concept, the membrane local slope fluctuations was introduced recently (Vaippully et al 2020 Soft Matter 16 7606), which can be modelled as a gradient of the normal fluctuations. It has been found that the power spectral density (PSD) of slope fluctuations
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Module representatives for refining gene co-expression modules Phys. Biol. (IF 2.0) Pub Date : 2023-05-04 Nathan Mankovich, Helene Andrews-Polymenis, David Threadgill, Michael Kirby
This paper concerns the identification of gene co-expression modules in transcriptomics data, i.e. collections of genes which are highly co-expressed and potentially linked to a biological mechanism. Weighted gene co-expression network analysis (WGCNA) is a widely used method for module detection based on the computation of eigengenes, the weights of the first principal component for the module gene
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Theoretical understanding of evolutionary dynamics on inhomogeneous networks Phys. Biol. (IF 2.0) Pub Date : 2023-04-21 Hamid Teimouri, Dorsa Sattari Khavas, Cade Spaulding, Christopher Li, Anatoly B Kolomeisky
Evolution is the main feature of all biological systems that allows populations to change their characteristics over successive generations. A powerful approach to understand evolutionary dynamics is to investigate fixation probabilities and fixation times of novel mutations on networks that mimic biological populations. It is now well established that the structure of such networks can have dramatic
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Collective response to local perturbations: how to evade threats without losing coherence Phys. Biol. (IF 2.0) Pub Date : 2023-04-11 Emanuele Loffredo, Davide Venturelli, Irene Giardina
Living groups move in complex environments and are constantly subject to external stimuli, predatory attacks and disturbances. An efficient response to such perturbations is vital to maintain the group’s coherence and cohesion. Perturbations are often local, i.e. they are initially perceived only by few individuals in the group, but can elicit a global response. This is the case of starling flocks
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Computer simulation reveals the effect of severing enzymes on dynamic and stabilized microtubules Phys. Biol. (IF 2.0) Pub Date : 2023-04-03 Aritra Sen, Ambarish Kunwar
Microtubule (MT) severing enzymes Katanin and Spastin cut the MT into smaller fragments and are being studied extensively using in-vitro experiments due to their crucial role in different cancers and neurodevelopmental disorders. It has been reported that the severing enzymes are either involved in increasing or decreasing the tubulin mass. Currently, there are a few analytical and computational models
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Transfer function approach to understanding periodic forcing of signal transduction networks Phys. Biol. (IF 2.0) Pub Date : 2023-03-29 Nguyen H N Tran, Andrew H A Clayton
Signal transduction networks are responsible for transferring biochemical signals from the extracellular to the intracellular environment. Understanding the dynamics of these networks helps understand their biological processes. Signals are often delivered in pulses and oscillations. Therefore, understanding the dynamics of these networks under pulsatile and periodic stimuli is useful. One tool to
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Sociogenesis in unbounded space: modelling self-organised cohesive collective motion Phys. Biol. (IF 2.0) Pub Date : 2023-03-28 Zohar Neu, Luca Giuggioli
Maintaining cohesion between randomly moving agents in unbounded space is an essential functionality for many real-world applications requiring distributed multi-agent systems. We develop a bio-inspired collective movement model in 1D unbounded space to ensure such functionality. Using an internal agent belief to estimate the mesoscopic state of the system, agent motion is coupled to a dynamically
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Optimal metabolic strategies for microbial growth in stationary random environments Phys. Biol. (IF 2.0) Pub Date : 2023-03-21 Anna Paola Muntoni, Andrea De Martino
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense, optimal strategy selection is achieved when bacteria grow at the fastest rate possible in that medium. While this view of optimality is well suited for cells that have
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Stochasticity may generate coherent motion in bird flocks Phys. Biol. (IF 2.0) Pub Date : 2023-02-24 Andy M Reynolds
Murmurations along with other forms of flocking have come to epitomize collective animal movements. Most studies into these stunning aerial displays have aimed to understand how coherent motion may emerge from simple behavioral rules and behavioral correlations. These studies may now need revision because recently it has been shown that flocking birds, like swarming insects, behave on the average as
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Swarm formation as backward diffusion Phys. Biol. (IF 2.0) Pub Date : 2023-02-17 Andy M Reynolds, Nicholas T Ouellette
Considerable progress has been made in understanding insect swarms—forms of collective animal behaviour that unlike bird flocks, fish schools and animal herds do not possess global order. Nonetheless, little is known about swarm formation. Here we posit a mechanism for the formation of insect swarms that is consistent with recent empirical observations reported by (Patel and Ouellette 2022). It correctly
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Correlation between speed and turning naturally arises for sparsely sampled cell movements Phys. Biol. (IF 2.0) Pub Date : 2023-01-26 Vitaly V Ganusov, Viktor S Zenkov, Barun Majumder
Mechanisms regulating cell movement are not fully understood. One feature of cell movement that determines how far cells displace from an initial position is persistence, the ability to perform movements in a direction similar to the previous movement direction. Persistence is thus determined by turning angles (TA) between two sequential displacements and can be characterized by an average TA or persistence
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Diffusive exit rates through pores in membrane-enclosed structures Phys. Biol. (IF 2.0) Pub Date : 2023-01-24 Zitao Yang, Elena F Koslover
The function of many membrane-enclosed intracellular structures relies on release of diffusing particles that exit through narrow pores or channels in the membrane. The rate of release varies with pore size, density, and length of the channel. We propose a simple approximate model, validated with stochastic simulations, for estimating the effective release rate from cylinders, and other simple-shaped
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The flagellar length control system: exploring the physical biology of organelle size Phys. Biol. (IF 2.0) Pub Date : 2023-01-24 Wallace F Marshall
How cells build and maintain dynamic structures of defined size is currently an important unsolved problem in quantitative cell biology. The flagella of the unicellular green alga Chlamydomonas provide a highly tractable model system to investigate this general question, but while the powerful genetics of this organism have revealed numerous genes required for proper flagellar length, in most cases
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On kinetics and extreme values in systems with random interactions Phys. Biol. (IF 2.0) Pub Date : 2022-12-20 Martin Girard
Biological environments such as the cytoplasm are comprised of many different molecules, which makes explicit modeling intractable. In the spirit of Wigner, one may be tempted to assume interactions to derive from a random distribution. Via this approximation, the system can be efficiently treated in the mean-field, and general statements about expected behavior of such systems can be made. Here, I
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Velocity correlations in jackdaw flocks in different ecological contexts Phys. Biol. (IF 2.0) Pub Date : 2022-12-15 Daniel O’Coin, Guillam E Mclvor, Alex Thornton, Nicholas T Ouellette, Hangjian Ling
Velocity correlation is an important feature for animal groups performing collective motions. Previous studies have mostly focused on the velocity correlation in a single ecological context. It is unclear whether correlation characteristics vary in a single species in different contexts. Here, we studied the velocity correlations in jackdaw flocks in two different contexts: transit flocks where birds
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History-dependent attachment of Pseudomonas aeruginosa to solid–liquid interfaces and the dependence of the bacterial surface density on the residence time distribution Phys. Biol. (IF 2.0) Pub Date : 2022-12-13 A L Ritter, Yow-Ren Chang, Zachary Benmamoun, William A Ducker
This study investigates how the recent history of bacteria affects their attachment to a solid–liquid interface. We compare the attachment from a flowing suspension of the bacterium, Pseudomonas aeruginosa PAO1, after one of two histories: (a) passage through a tube packed with glass beads or (b) passage through an empty tube. The glass beads were designed to increase the rate of bacterial interactions
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How to build an epithelial tree Phys. Biol. (IF 2.0) Pub Date : 2022-11-22 Sarah V Paramore, Katharine Goodwin, Celeste M Nelson
Nature has evolved a variety of mechanisms to build epithelial trees of diverse architectures within different organs and across species. Epithelial trees are elaborated through branch initiation and extension, and their morphogenesis ends with branch termination. Each of these steps of the branching process can be driven by the actions of epithelial cells themselves (epithelial-intrinsic mechanisms)
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Proteolytic and mechanical remodeling of the extracellular matrix by invadopodia in cancer Phys. Biol. (IF 2.0) Pub Date : 2022-11-21 L Perrin, B Gligorijevic
Cancer invasion and metastasis require remodeling of the adjacent extracellular matrix (ECM). In this mini review, we will cover the mechanisms of proteolytic degradation and the mechanical remodeling of the ECM by cancer cells, with a focus on invadopodia. Invadopodia are membrane protrusions unique to cancer cells, characterized by an actin core and by the focal degradation of ECM via matrix metalloproteases