Biological physics articles within Nature Communications

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  • Article
    | Open Access

    Bacteria can swim upstream by reorienting with respect to fluid flows. Here, the authors observe an oscillatory motion and describe the mechanisms behind these reorientation dynamics, which could help designing strategies for bacterial contamination prevention.

    • Arnold J. T. M. Mathijssen
    • , Nuris Figueroa-Morales
    •  & Andreas Zöttl

  • Article
    | Open Access

    The intrinsic inhomogeneity of polymer networks is masked by the usual ensemble-averaged measurements. Here the authors construct direct maps of crosslinks in an actin network by selective labeling the crosslinks with fluorescent markers and characterize the local elasticity and cross-correlation between crosslinks.

    • Lingxiang Jiang
    • , Qingqiao Xie
    •  & Steve Granick

  • Article
    | Open Access

    Chromatin is folded into Topologically Associating domains (TADs), with the organization and folding hierarchy of the TADs being highly dynamic. Here the authors develop a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency encounters present in Hi-C data within and between TADs and reconstruct TADs across cell differentiation, revealing local chromatin re-organization.

    • O. Shukron
    • , V. Piras
    •  & D. Holcman

  • Article
    | Open Access

    It has been previously shown theoretically that the average path length of random walks inside a closed domain is invariant. Here the authors demonstrate that this invariance property can be used to predict the mean residence time of swimming bacteria exploring structured micro-environments.

    • Giacomo Frangipane
    • , Gaszton Vizsnyiczai
    •  & Roberto Di Leonardo

  • Article
    | Open Access

    Active nematics consist of elongated self-driven units and can emerge in bacterial systems. Here the authors investigate such emergence in a growing bacterial biofilm and demonstrate that localized stress and mechanical instabilities drive the formation of large-scale order.

    • Yusuf Ilker Yaman
    • , Esin Demir
    •  & Askin Kocabas

  • Article
    | Open Access

    The membrane attack complex (MAC) is a hetero-oligomeric protein assembly that kills pathogens by perforating their cell envelopes. Here, the authors use atomic force microscopy to show that MAC proteins oligomerize within the membrane, allowing them to identify the kinetic bottleneck of MAC formation.

    • Edward S. Parsons
    • , George J. Stanley
    •  & Bart W. Hoogenboom

  • Article
    | Open Access

    Many bacteria swim with run-and-tumble motion in unconfined fluid. Here the authors report that confinement of these bacteria in a 3D porous medium changes this motion into hopping and trapping, in which the cells are intermittently and transiently trapped as they navigate the pore space.

    • Tapomoy Bhattacharjee
    •  & Sujit S. Datta

  • Article
    | Open Access

    Methodological advances have increased our understanding of chromatin structure through chromosome conformation capture techniques and high resolution imaging, but integration of these datasets is challenging. Here the authors propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model.

    • Ahmed Abbas
    • , Xuan He
    •  & Jianyang Zeng

  • Article
    | Open Access

    Motile and non-motile subpopulations often coexist in bacterial communities. Here, Xu et al. show that motile cells in colonies of common flagellated bacteria can self-organize into two adjacent motile rings, driving stable flows of fluid and materials around the colony.

    • Haoran Xu
    • , Justas Dauparas
    •  & Yilin Wu

  • Article
    | Open Access

    Personalized approaches to diagnosis and treatment monitoring could improve the management of cystic fibrosis patients. Here the authors show that multiscale differential dynamic microscopy can assess changes in cilia beating dynamics and coordination in patient-derived airway epithelial cells, in response to different CFTR-modulating drugs, in a patient-specific manner.

    • M. Chioccioli
    • , L. Feriani
    •  & P. Cicuta

  • Article
    | Open Access

    Cation-proton antiporters mediate selective ion exchange across cellular membranes to control pH, salt concentration and cell volume. Here the authors present a transition-path sampling method that overcomes the timescale gap between simulations (µs) and transport processes (s), which allows them to resolve the Na+ and H+ transport cycle of the Na+/H+ antiporter NhaP from Pyrococcus abyssi.

    • Kei-ichi Okazaki
    • , David Wöhlert
    •  & Gerhard Hummer

  • Article
    | Open Access

    The determination of entropy production from experimental data is a challenge but a recently introduced theoretical tool, the thermodynamic uncertainty relation, allows one to infer a lower bound on entropy production. Here the authors provide a critical assessment of the practical implementation of this tool.

    • Junang Li
    • , Jordan M. Horowitz
    •  & Nikta Fakhri

  • Article
    | Open Access

    Active fluids consist of self-driven particles which consume energy to drive spontaneous flow. Here the authors present a general theory of two-dimensional chiral active particles which spontaneously rotate and show that they can form a stable, coherently-rotating phase.

    • Ananyo Maitra
    •  & Martin Lenz

  • Article
    | Open Access

    How cellular noise impacts metabolic trade-offs remains unknown. Here, the authors use a quantitative single-cell mass imaging strategy to reveal that cellular noise impacts cellular biomass and triacylglycerol accumulation, as well as protein and fatty-acid recycling under starvation, differently.

    • A. E. Vasdekis
    • , H. Alanazi
    •  & G. Stephanopoulos

  • Article
    | Open Access

    Understanding collective motions in a group of interacting animal is a challenge owing to the lack of control over, for example, real fish schools. Here, the authors study the aggregation of C. elegans at controllable conditions and reproduce the experimental observations using a minimal model.

    • Takuma Sugi
    • , Hiroshi Ito
    •  & Ken H. Nagai

  • Article
    | Open Access

    Some retroviruses, including HIV, insert their DNA in a non-random manner in the host genome through a poorly understood selection mechanism. Here the authors develop a biophysical model of retroviral integration, identifying previously unnoticed universal principles that regulate this phenomenon.

    • D. Michieletto
    • , M. Lusic
    •  & E. Orlandini

  • Article
    | Open Access

    Septins are cytoskeletal filaments that localize at constriction sites and impact membrane remodeling. Here authors examine the curvature sensitivity of septins using bilayers on wavy patterns and derive a theoretical model that quantitatively describe the results.

    • Alexandre Beber
    • , Cyntia Taveneau
    •  & Aurélie Bertin

  • Article
    | Open Access

    The Membrane-Proximal External Region (MPER) of the HIV Env gp41 subunit is a target for broadly neutralizing antibodies. Here, the authors apply super-resolution stimulated emission depletion (STED) microscopy on single virions and provide insights into how the MPER epitope is recognized.

    • Pablo Carravilla
    • , Jakub Chojnacki
    •  & José L. Nieva

  • Article
    | Open Access

    Microscopic transition mechanisms impact many biophysical systems. In this work, the authors explore transition path times between thermodynamic states experimentally, and show symmetry breaking in the transition times under an external force that drives the system out of equilibrium.

    • J. Gladrow
    • , M. Ribezzi-Crivellari
    •  & U. F. Keyser

  • Article
    | Open Access

    The study of interfaces in bacterial systems is of relevance to the spreading of bacterial colonies and pathological infections. Here the authors investigate the dynamics of active/passive interfaces in bacterial swarms and find that the boundary can be described as a propagating, diffuse elastic interface.

    • Alison E. Patteson
    • , Arvind Gopinath
    •  & Paulo E. Arratia

  • Article
    | Open Access

    The dynamics of biomolecules can occur over a wide range of time and length scales. Here the authors develop a high-speed AFM height spectroscopy method to directly detect the motion of unlabeled molecules at Angstrom spatial and microsecond temporal resolution.

    • George R. Heath
    •  & Simon Scheuring

  • Article
    | Open Access

    Myosin motors drive the actin cytoskeleton out-of-equilibrium, but the role of myosin-driven active stresses in the accumulation and dissipation of mechanical work is unclear. Here, the authors synthesize an actomyosin material and find that the rate of entropy production increases non-monotonically with increasing accumulation of active stresses.

    • Daniel S. Seara
    • , Vikrant Yadav
    •  & Michael P. Murrell

  • Article
    | Open Access

    The detailed folding mechanisms of membrane proteins in their natural bilayer-like environments remains poorly understood due to the lack of tools for measuring stabilities and kinetics. Here, by simulating the folding of GlpG in a bilayer, the authors provide support for the helical-hairpin hypothesis and prompt a re-evaluation of a long-standing paradigm, the two-stage hypothesis.

    • Wei Lu
    • , Nicholas P. Schafer
    •  & Peter G. Wolynes

  • Article
    | Open Access

    Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.

    • Lukas F. Milles
    • , Eduard M. Unterauer
    •  & Hermann E. Gaub

  • Article
    | Open Access

    Despite their importance in plant development and defence the properties of (1,3)-β-glucan remain largely unknown. Here, the authors find that addition of (1,3)-β-glucans increases the flexibility of cellulose and its resilience to high strain, an effect originating in molecular level interactions.

    • Radwa H. Abou-Saleh
    • , Mercedes C. Hernandez-Gomez
    •  & Yoselin Benitez-Alfonso

  • Article
    | Open Access

    For various organisms, mRNA and protein copy numbers scale with cell volume. Here, the authors show that this result emerges naturally when ribosomes and RNAPs limit expression. Furthermore, the authors show that within their model this result breaks down for a sufficiently high volume/DNA ratio.

    • Jie Lin
    •  & Ariel Amir

  • Article
    | Open Access

    “Diffusing diffusivity” concept has been recently put forward to account for rapid structural rearrangements in soft matter and biological systems. Here the authors propose a general mathematical framework to compute the distribution of first-passage times in a dynamically heterogeneous medium.

    • Yann Lanoiselée
    • , Nicolas Moutal
    •  & Denis S. Grebenkov

  • Article
    | Open Access

    Gels filtering particles by interactions are a goal of nanotechnology; this is difficult when particles are larger than the mesh of the gel. Here, the authors present an equilibrium mechanism where binding dynamics of crosslinks are affected by interacting particles so that particles experience enhanced diffusion.

    • Carl P. Goodrich
    • , Michael P. Brenner
    •  & Katharina Ribbeck

  • Article
    | Open Access

    Rod-shaped bacteria are an example of active matter. Here the authors find that a growing bacterial colony harbours internal cellular flows affecting orientational ordering in its interior and at the boundary. Results suggest this system may belong to a new active matter universality class.

    • D. Dell’Arciprete
    • , M. L. Blow
    •  & W. C. K. Poon

  • Article
    | Open Access

    The skin of the African bush elephant features micrometer-wide channels whose function is water and mud retention for thermal regulation and protection from parasites. Here authors use microscopy and modelling to show that the channels are fractures of the animal thick and brittle skin outermost layer.

    • António F. Martins
    • , Nigel C. Bennett
    •  & Michel C. Milinkovitch

  • Article
    | Open Access

    Lipid-based membranes coupled to biochemical reaction networks can be difficult to implement in vitro. Here the authors use elastin-like peptides to create self-assembled vesicle structures containing transcription-translation systems for autonomous growth.

    • Kilian Vogele
    • , Thomas Frank
    •  & Tobias Pirzer

  • Article
    | Open Access

    Neutrophilic granulocytes release their own DNA (NETosis) as neutrophil extracellular traps to capture pathogens. Here, the authors use time-resolved fluorescence and atomic force microscopy and reveal that NETosis is highly organized into three distinct phases with a clear point of no return defined by chromatin status.

    • Elsa Neubert
    • , Daniel Meyer
    •  & Sebastian Kruss

  • Article
    | Open Access

    Vaccine adjuvants ensure sufficient engagement of the immune system in vaccination, however safety issues can be associated with novel chemical adjuvants. Here, Cao et al. report a physical radiofrequency adjuvant to simultaneously augment vaccine-induced humoral and cellular immune responses without potentially harmful adverse reactions.

    • Yan Cao
    • , Xiaoyue Zhu
    •  & Xinyuan Chen

  • Article
    | Open Access

    Tools from statistical physics can be used to investigate a large variety of fields ranging from economics to biology. Here the authors first adapt density-functional theory to predict the distributions of crowds in new environments and then validate their approach using groups of fruit flies.

    • J. Felipe Méndez-Valderrama
    • , Yunus A. Kinkhabwala
    •  & T. A. Arias

  • Review Article
    | Open Access

    Active matter systems are made up of self-driven components which extract energy from their surroundings to generate mechanical work. Here the authors review the subfield of active nematics and provide a comparison between theoretical findings and the corresponding experimental realisations.

    • Amin Doostmohammadi
    • , Jordi Ignés-Mullol
    •  & Francesc Sagués

  • Article
    | Open Access

    Bacteria communicate and organize via quorum sensing which is determined by biochemical processes. Here the authors aim to reproduce this behaviour in a system of synthetic active particles whose motion is induced by an external beam which is in turn controlled by a feedback-loop which mimics quorum sensing.

    • Tobias Bäuerle
    • , Andreas Fischer
    •  & Clemens Bechinger

  • Article
    | Open Access

    Single cell growth rate variability has been difficult to understand. Here, the authors apply a generalization of flux balance analysis to single cells based on maximum entropy modeling, and find that growth rate fluctuations of E. coli reflect metabolic flux variability and growth sub-optimality, in turn highlighting information costs for growth optimization.

    • Daniele De Martino
    • , Anna MC Andersson
    •  & Gašper Tkačik

  • Article
    | Open Access

    Active matter composed of filaments and molecular motors can contract. Here, the authors report the spontaneous out-of-plane buckling of reconstituted contracting poroelastic actomyosin sheets in the absence of external cues.

    • Y. Ideses
    • , V. Erukhimovitch
    •  & A. Bernheim-Groswasser

  • Article
    | Open Access

    Existing methods to extract structural information from single-molecule scattering measurements require large number of photons per image. Here the authors discuss a method to reconstruct the structure of a molecule from X-ray scattering data by using only three photons per image.

    • Benjamin von Ardenne
    • , Martin Mechelke
    •  & Helmut Grubmüller

  • Article
    | Open Access

    Spider aggregate glue avoids failure in humid environments but the fundamental mechanism behind it is still unknown. Here, the authors demonstrate that humidity-dependent structural changes of glycoproteins and sequestering of liquid water by low molecular mass compounds prevents adhesion failure of the glue in humid environments.

    • Saranshu Singla
    • , Gaurav Amarpuri
    •  & Ali Dhinojwala

  • Article
    | Open Access

    The structures of amyloid fibres are currently primarily studied through solid state NMR and cryo-EM. Here the authors present a free-standing graphene support device that allows diffraction imaging of non-crystalline amyloid fibrils with single X-ray pulses from an X-ray free-electron laser.

    • Carolin Seuring
    • , Kartik Ayyer
    •  & Henry N. Chapman

  • Article
    | Open Access

    How transcription factors find their targets in vivo is still poorly understood. Here the authors use molecular dynamics simulations to investigate how transcription factors diffuse on chromatin, providing a theoretical framework for understanding the key role of genome conformation in this process.

    • Ruggero Cortini
    •  & Guillaume J. Filion

  • Article
    | Open Access

    Cell membrane protrusions and invaginations are both driven by actin assembly but the mechanism leading to different membrane shapes is unknown. Using a minimal system and modelling the authors reconstitute the deformation modes and identify capping protein as a regulator of both deformation types.

    • Katharina Dürre
    • , Felix C. Keber
    •  & Andreas R. Bausch

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