Biological physics articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Polymer knots are important for a range of biological systems and engineering applications, yet the variables influencing knotting probability are not well understood. Here the authors develop a nanofluidic device that can detect knots and provide a free energy formalism that can quantify knotting probability in their system.

    • Susan Amin
    • , Ahmed Khorshid
    •  & Walter Reisner

  • Article
    | Open Access

    Investigating photosynthesis processes in biological samples is challenging due to their complex and disordered structure. Based on analog quantum simulations with superconducting quantum circuits, the authors show how the interplay of quantum coherence and environmental interactions affects energy transport.

    • Anton Potočnik
    • , Arno Bargerbos
    •  & Andreas Wallraff

  • Article
    | Open Access

    Single molecule approaches demonstrated that enzymatic catalysis is stochastic which could lead to deviations from classical predictions. Here authors rebuild the theory of enzymatic inhibition to show that stochastic fluctuations on the single enzyme level could make inhibitors act as activators.

    • Tal Robin
    • , Shlomi Reuveni
    •  & Michael Urbakh

  • Article
    | Open Access

    Mechanical properties of protein hydrogels are critical to mimic natural tissue but correlating bulk properties on the molecular level remains challenging. Here the authors show that the hierarchy of crosslinkers and load-bearing modules on a molecular level defines the mechanical properties of the hydrogel.

    • Junhua Wu
    • , Pengfei Li
    •  & Yi Cao

  • Article
    | Open Access

    Reptation theory has been widely adopted to describe the dynamics of entangled polymer solution, whereby a polymer follows the curvilinear Brownian motion along a tube. Here, the authors challenge this theory by showing long-time dynamics of semi-flexible polymers modulated by topological constraints.

    • Philipp Lang
    •  & Erwin Frey

  • Article
    | Open Access

    The transport dynamics of messenger ribonucleoproteins in neurons is crucial to our neuronal functions, but the detail remains elusive. Song et al. show that they are transported along the dendrites in alternating run and rest phases with their own random sojourn times, following an aging Lévy walk.

    • Minho S. Song
    • , Hyungseok C. Moon
    •  & Hye Yoon Park

  • Article
    | Open Access

    Misfolding of superoxide dismutase 1 (SOD1) is linked to amyotrophic lateral sclerosis. Here the authors characterize the unfolding/refolding of single SOD1 molecules using optical tweezers, identifying partially folded intermediates that lead to misfolding after the formation of a native-like core.

    • Supratik Sen Mojumdar
    • , Zackary N. Scholl
    •  & Michael T. Woodside

  • Article
    | Open Access

    The mechanism allowing sperm to steer is not fully understood. The authors find that superposition of two harmonic waves breaks the flagellar beat symmetry temporally rather than spatially, and that this mechanism is enhanced by the sexual hormone progesterone, which changes the motility pattern.

    • Guglielmo Saggiorato
    • , Luis Alvarez
    •  & Jens Elgeti

  • Article
    | Open Access

    Aggregation of amyloidogenic peptides into fibrils and crystals has incidence in several amyloid-related diseases. Here, the authors investigate the origins of the fibril-to-crystal conversion in amyloidogenic hexapeptides pointing to the amyloid crystals as the ground state in the protein folding energy landscape.

    • Nicholas P. Reynolds
    • , Jozef Adamcik
    •  & Raffaele Mezzenga

  • Article
    | Open Access

    During cell division animal cells generate intracellular pressure and round against their environment, but the genes responsible for this are largely unknown. Here the authors use a microcantilever- and RNAi-based assay to screen > 1000 genes and identify 49 genes involved in mitotic cell rounding; many are novel to this process.

    • Yusuke Toyoda
    • , Cedric J. Cattin
    •  & Daniel J. Müller

  • Article
    | Open Access

    Tissue remodeling involves substantial involvement of the contractile actomyosin cytoskeleton. Here the authors model the spatiotemporal evolution of actomyosin densities during Drosophila germband extension and find affine and nonaffine deformations that depend on the magnitude of local contractile stress.

    • Deb Sankar Banerjee
    • , Akankshi Munjal
    •  & Madan Rao

  • Article
    | Open Access

    Binding and unbinding kinetics are important determinants of protein-protein or small molecule protein functional interactions that can guide drug development. Here the authors exploit the multi-ensemble Markov model framework to develop a computational approach that allows the estimation of binding kinetics reaching into the seconds timescale.

    • Fabian Paul
    • , Christoph Wehmeyer
    •  & Frank Noé

  • Article
    | Open Access

    The structure and mechanics of tissues is constantly perturbed by endogenous forces originated from cells. Here the authors show that 3D collagen gels, major components of connective tissues and extracellular matrix, are significantly and irreversibly remodelled by cellular traction forces and by macroscopic strains.

    • Jihan Kim
    • , Jingchen Feng
    •  & Bo Sun

  • Article
    | Open Access

    The fission yeast cytokinetic ring assembles by Search-Capture-Pull-Release from precursor nodes that include formin Cdc12 and myosin Myo2. The authors reconstitute Search-Capture-Pull in vitro and find that Myo2 pulling on Cdc12-associated actin filaments mechano-inhibits Cdc12-mediated assembly, which enables proper ring assembly in vivo.

    • Dennis Zimmermann
    • , Kaitlin E. Homa
    •  & David R. Kovar

  • Article
    | Open Access

    Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.

    • Tamar Friedlander
    • , Roshan Prizak
    •  & Gašper Tkačik

  • Article
    | Open Access

    Self-organization is observed in cytoskeletal systems but emergence of order from disorder is poorly understood. Using a high density actomyosin system, the authors capture the transition from disorder to order, which is driven by enhanced alignment effects caused by increase in multi-filament collisions.

    • Ryo Suzuki
    •  & Andreas R. Bausch

  • Article
    | Open Access

    Holes in endothelial barriers, called transendothelial cell macroapertures (TEMs), are predicted to be limited by line tension of unknown origin. Here the authors identify an actomyosin cable encircling TEMs and establish a role for ezrin in stabilising F-actin bundles, allowing their crosslinking by non-muscle myosin IIa.

    • Caroline Stefani
    • , David Gonzalez-Rodriguez
    •  & Emmanuel Lemichez

  • Article
    | Open Access

    Membrane protein diffusion is affected by distinct mechanisms such as molecular crowding and medium elasticity. Here the authors present an analytical approach to analyse single particle trajectories and distinguish mixed subdiffusive processes affecting membrane protein mobility in living cells.

    • Yonatan Golan
    •  & Eilon Sherman

  • Article
    | Open Access

    Bacteria continuously inject energy into their surroundings and thus induce chaotic like flows, namely meso-scale turbulence. Here, the authors show that transition to meso-scale turbulence and inertial turbulence observed in pipes share the same scaling behavior that belongs to the directed percolation universality class.

    • Amin Doostmohammadi
    • , Tyler N. Shendruk
    •  & Julia M. Yeomans

  • Article
    | Open Access

    Active fluids consist of self-driven particles that can drive spontaneous flow without the intervention of external forces. Here Woodhouseet al. show how to design logic circuits using this phenomenon in active fluid networks, which could be further exploited for autonomous microfluidic computing.

    • Francis G. Woodhouse
    •  & Jörn Dunkel

  • Article
    | Open Access

    Glycolipids are commonly found in densely stacked biological membranes, which show unusually strong self-cohesion compared to phospholipid membranes. Here, the authors attribute this phenomenon to the lack of long-range repulsion between glycolipid membranes, a consequence of the headgroup architecture.

    • Matej Kanduč
    • , Alexander Schlaich
    •  & Emanuel Schneck

  • Article
    | Open Access

    Energy dissipation characterizes the states far from equilibrium, whilst how it affects the local organization remains elusive. Here, Muruganet al. show that the non-equilibrium systems exhibit topologically protected boundary modes that have been known in electronic and mechanical systems.

    • Arvind Murugan
    •  & Suriyanarayanan Vaikuntanathan

  • Article
    | Open Access

    The dynamics of actin cytoskeleton is essential to the function of living cells. Here, Foffanoet al. describe a nonequilibrium filament model to mimic the formation of cytoskeleton and pinpoint the key role played by the actin entanglement during the transition from homogeneous to bundled networks.

    • Giulia Foffano
    • , Nicolas Levernier
    •  & Martin Lenz

  • Article
    | Open Access

    Forming self-assembled soft materials with unconventional properties can be useful in many different applications. Here, Sciortino and co-workers have designed and experimentally realized a one-pot DNA hydrogel that melts both on heating and on cooling.

    • Francesca Bomboi
    • , Flavio Romano
    •  & Francesco Sciortino

  • Article
    | Open Access

    The actomyosin cytoskeleton consists of a contractile array but how it becomes organized is not clear. Here the authors reconstitute a controllable contractile system to show that force balances at boundaries determine contraction dynamics, and spatial anisotropy leads to self-organization or aligned contractile fibres.

    • Matthias Schuppler
    • , Felix C. Keber
    •  & Andreas R. Bausch

  • Article
    | Open Access

    Measuring the size distribution of nanomaterials in biological fluids is crucial to understand their properties in vivo. Here, the authors apply fluorescence recovery after photobleaching to measure protein aggregation in serum and to study permeability of biological membranes in mouse models.

    • Ranhua Xiong
    • , Roosmarijn E. Vandenbroucke
    •  & Kevin Braeckmans

  • Article
    | Open Access

    The interaction between myosin motors and F-actin is well described, but the impact of actin organization on contractility is not well described. Here the authors use a 2D biomimetic system and computational modelling to show that contractility of isotropic actomyosin is cooperative, and contraction velocity scales with myosin activation area.

    • Ian Linsmeier
    • , Shiladitya Banerjee
    •  & Michael P. Murrell

  • Article
    | Open Access

    Passive particles surrounded by swimming protists diffuse tens of times faster than their thermal motion, which might have an impact on microscopic predator-prey interaction in nature. Here, Jeanneret et al.investigate its physical origin and identify direct particle entrainment as the dominant feature.

    • Raphaël Jeanneret
    • , Dmitri O. Pushkin
    •  & Marco Polin

  • Article
    | Open Access

    The control of microswimmers such as bacteria is important for emerging applications of active bioinspired materials. Here, the authors demonstrate the use of vortical shear to expel suspended motile bacteria from the vicinity of a rotating microparticle.

    • Andrey Sokolov
    •  & Igor S. Aranson

  • Article
    | Open Access

    Active matter, such as swimming bacteria, show unique behaviors under confinement, but it is experimentally challenging to measure them. Takatoriet al. show the use of acoustic tweezers to trap self-propelled Janus particles as an enabling tool to investigate collective motions in living systems.

    • Sho C. Takatori
    • , Raf De Dier
    •  & John F. Brady

  • Article
    | Open Access

    The ability to discriminate objects along the optic axis is a benchmark for three-dimensional imaging techniques. Here, the authors combine metastable-state switching and opposing objective lenses to suppress out-of-focus background and record three-dimensional nanoscale images of living cells.

    • Ulrike Böhm
    • , Stefan W. Hell
    •  & Roman Schmidt

  • Article |

    The interaction between light and molecules can lead to hybrid quantum-physical states of light and matter. Here, the authors demonstrate one such effect, spatial modulation of light, with the protein photosystem I as a first demonstration of this quantum effect with such a biological molecule.

    • Itai Carmeli
    • , Moshik Cohen
    •  & Shachar Richter

  • Article |

    The shape of red blood cells is highly sensitive to surrounding liquid environment. Here, Miccio et al. make red blood cells into optofluidic lenses with fully controllable focal length at the microscale, which can be used for imaging and optical magnification in addition to blood diseases detection.

    • L. Miccio
    • , P. Memmolo
    •  & P. Ferraro

  • Article |

    Pulse oximetry is a non-invasive means for measuring blood oxygen saturation and pulse rate, with typical sensors based on rigid electronics. Here, the authors develop a pulse oximeter based solely on organic materials, allowing flexible devices and hence increasing the potential sensing locations on the body.

    • Claire M. Lochner
    • , Yasser Khan
    •  & Ana C. Arias

  • Article
    | Open Access

    Endothelial cell division is highly sensitive to fluid conditions and essential for blood vessel healing. Here Rossen et al.demonstrate how cell division triggers the emergence of long-range votex patterns in endothelial tissue under conditions that mimic blood vessel formation and blood clots.

    • Ninna S. Rossen
    • , Jens M. Tarp
    •  & Lene B. Oddershede

  • Article
    | Open Access

    Random walks on a network describe the dynamics of many natural and artificial systems. Here, Perkins et al.study the path distribution—characterizing how the walker moves—and find that it is either finite, stretched exponential or power law for any random walk on a finite network.

    • Theodore J. Perkins
    • , Eric Foxall
    •  & Roderick Edwards

  • Article |

    Gravitaxis describes the ability of microorganisms to adjust their swimming motion on the gravitational field, yet its mechanism remains unclear. Here, the authors show that an asymmetric shape of colloidal particles is alone sufficient to induce gravitactic motion in the absence of density inhomogeneity.

    • Borge ten Hagen
    • , Felix Kümmel
    •  & Clemens Bechinger

  • Article |

    Flocking emerges from communication within groups of animals. Here, Kumar et al. create a flock in inanimate matter, by showing that a vibrated layer of a small number of millimetre-sized tapered rods, amidst a background of spherical beads, spontaneously aligns into a state of coherent motion.

    • Nitin Kumar
    • , Harsh Soni
    •  & A. K. Sood

  • Article
    | Open Access

    Dynamic force spectroscopy is widely applied to probe molecular interactions by forcible bond breaking, but it currently lacks an analytical theory that spans the divide between experiment and simulation. Here, such a unified framework is developed and shown to be accurate for slow and fast loading.

    • Jakob T. Bullerjahn
    • , Sebastian Sturm
    •  & Klaus Kroy

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