Biological physics articles within Nature Communications

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  • Article
    | Open Access

    In this work the authors report a quasi two-dimensional population of living cells that can spontaneously self-assemble into finite-sized domains, an analogue of the microphase separation known in inert matter.

    • A. Carrère
    • , J. d’Alessandro
    •  & J.-P. Rieu

  • Article
    | Open Access

    The mechanical properties of biological tissues are key to their integrity and function. Here, the authors engineer 3D microtissues from optogenetically modified fibroblasts and use light to quantify tissue elasticity and strain propagation using their own constituent cells as internal actuators.

    • Adrien Méry
    • , Artur Ruppel
    •  & Thomas Boudou

  • Article
    | Open Access

    Meindlhumer et al. report a combined theoretical/experimental study of how the propagation direction of Min protein patterns can be altered by a bulk flow of solution.

    • Sabrina Meindlhumer
    • , Fridtjof Brauns
    •  & Erwin Frey

  • Article
    | Open Access

    It is unclear what constraints exist on cellular life in frigid environments. Here, the authors demonstrate that reactive oxygen species and gene-expression speed impose a barrier to replication at low temperatures in yeast, with lower levels enabling quicker replication, and develop a model to describe this phenomenon.

    • Diederik S. Laman Trip
    • , Théo Maire
    •  & Hyun Youk

  • Article
    | Open Access

    Here the authors introduce dual communities, characterized by strong connections at their boundaries, and show that they are formed as a trade-off between efficiency and resilience in supply networks.

    • Franz Kaiser
    • , Philipp C. Böttcher
    •  & Dirk Witthaut

  • Article
    | Open Access

    While the impact of F-actin architecture on stress transmission is well studied, the role of architecture on stress generation remains unclear. Here authors use in vitro model and show that distinct organizations constrain myosin motion.

    • Camelia G. Muresan
    • , Zachary Gao Sun
    •  & Michael P. Murrell

  • Article
    | Open Access

    The communication in active systems plays an important role in their self-organization, yet the detail is not fully understood. Here, Ziepke et al. show the formation of complex structures at multiple scales amongst interactive agents that locally process information transmitted by chemical signals.

    • Alexander Ziepke
    • , Ivan Maryshev
    •  & Erwin Frey

  • Article
    | Open Access

    Homeostasis of DNA density is a hallmark of living cells. The authors show via mathematical modelling how two cycles, a titration-based concentration cycle and a nucleotide activation cycle, together drive replication in E. coli at all growth rates.

    • Mareike Berger
    •  & Pieter Rein ten Wolde

  • Article
    | Open Access

    Surface modification of nanoparticles by cell membrane (CM) coating to improve their bio-interface properties often results in partial coating. Here the authors show that partial coating is an intermediate state due to the absorption of CM fragments or vesicles and can be resolved by increasing CM fluidity with external phospholipids.

    • Lizhi Liu
    • , Dingyi Pan
    •  & Vesa-Pekka Lehto

  • Article
    | Open Access

    Constructing a minimal protein machinery for self-division of membrane compartments is a major goal of bottom-up synthetic biology. Here, authors achieved the assembly, placement and onset of contraction of a minimal division ring in lipid vesicles.

    • Shunshi Kohyama
    • , Adrián Merino-Salomón
    •  & Petra Schwille

  • Article
    | Open Access

    Amyotrophic Lateral Sclerosis related TDP-43 protein translocates to stress granules with a concomitant reduction in mobility. Here, the authors use single molecule tracking and find a stress-induced reduction in TDP-43 mobility also in the cytoplasm potentially relevant for TDP-43 aggregation.

    • Lisa Streit
    • , Timo Kuhn
    •  & Karin M. Danzer

  • Article
    | Open Access

    Pancreatic ductal adenocarcinomas (PDAC) exhibit complex morphologies challenging to capture in organoid models. Here, the authors develop PDAC organoids that can recreate branched structures and, with the use of a minimal mathematical model, shed light to pathways and processes directing the dynamics of self-organization and branching morphogenesis.

    • S. Randriamanantsoa
    • , A. Papargyriou
    •  & A. R. Bausch

  • Article
    | Open Access

    Understanding how order emerges in active matter may facilitate macroscopic control of microscopic objects. Here, Williams et al. show how to control the transport of passive microscopic particles in presence of motile algae in conjunction with boundary-induced accumulation of microswimmers.

    • Stephen Williams
    • , Raphaël Jeanneret
    •  & Marco Polin

  • Article
    | Open Access

    Dynamic remodeling of the actin cytoskeleton underlies cell movement, but is challenging to characterize at the molecular level. Here, the authors present a method to extract actin filament velocities in living cells, and compare their results to current models of cytoskeletal dynamics.

    • Cayla M. Miller
    • , Elgin Korkmazhan
    •  & Alexander R. Dunn

  • Article
    | Open Access

    SAP97/hDLG is a ubiquitous, alternatively spliced, and conserved modular scaffolding protein involved in the organization cell junctions and excitatory synapses. Here, authors confirm that SAP97/hDLG condenses in to nanosized molecular domains in both heterologous cells and hippocampal pyramidal neurons. Authors demonstrate that in vivo and in vitro condensation, molecular signatures of nanoscale condensates and exchange kinetics of SAP97/hDLG is modulated by the local availability of alternatively spliced isoforms. Additionally, SAP97/hDLG isoforms exhibits a differential sensitivity to Ca2+ bound Calmodulin, resulting in altered properties of nanocondensates and their real-time regulation

    • Premchand Rajeev
    • , Nivedita Singh
    •  & Deepak Nair

  • Article
    | Open Access

    Two main mechanisms have been proposed to shape 3D genome architecture - loop extrusion and phase separation. Here the authors combine these mechanisms in polymer models in a manner that best fits 3D genome, based on both Hi-C and super-resolution locus imaging data, proposing that these two physical processes can indeed coexist simultaneously within cells to define loops and TADs.

    • Mattia Conte
    • , Ehsan Irani
    •  & Mario Nicodemi

  • Article
    | Open Access

    Tissue boundaries in our body separate organs and enable healing, but boundary mechanics are not well known. Here, the authors define mechanical rules for colliding cell monolayers and use these rules to make complex, predictable tessellations.

    • Matthew A. Heinrich
    • , Ricard Alert
    •  & Daniel J. Cohen

  • Article
    | Open Access

    Drosophila mesoderm invagination begins with the formation of a furrow. Here they show that a long-range mechanism, powered by actomyosin contraction between the embryo polar caps, works like a ‘cheese-cutter wire’ indenting the tissue surface and folding it into a propagating furrow.

    • Julien Fierling
    • , Alphy John
    •  & Matteo Rauzi

  • Article
    | Open Access

    Anti-cancer cytotoxic T cell responses largely vary among individuals. Here authors show, by stochastic modeling on high throughput T cell behavior and matched tumor spheroid fate data generated by a microfluidics system, that tumor killing is dependent on T cell cooperativity, which might contribute to the heterogeneity of T cell responses.

    • Gustave Ronteix
    • , Shreyansh Jain
    •  & Charles N. Baroud

  • Article
    | Open Access

    Defining the dimension in bounded, inhomogeneous or discrete physical systems may be challenging. The authors introduce here a dynamics-based notion of dimension by analysing diffusive processes in space, relevant for non-ideal physical systems and networks.

    • Robert Peach
    • , Alexis Arnaudon
    •  & Mauricio Barahona

  • Article
    | Open Access

    Bacterial motility relies on the mechanics of the “hook” the 60 nm biopolymer at the base of rotating flagella. Here, authors observe the hook stiffening as it is twisted by the rotation of the flagellum, a mechanical feat evolved for its function.

    • Ashley L. Nord
    • , Anaïs Biquet-Bisquert
    •  & Francesco Pedaci

  • Article
    | Open Access

    In theory, driven biological oscillators can display complex dynamic behaviors, but these are experimentally difficult to observe. Here the authors, using microfluidics, show that a synthetic cell-free gene oscillator displays period doubling and even quadrupling.

    • Lukas Aufinger
    • , Johann Brenner
    •  & Friedrich C. Simmel

  • Article
    | Open Access

    Active matter exhibits a range of collective behaviors offering insights into how complex patterns can emerge at different length scales. Here, Hsu et al. confine active filaments on the spherical surface of a lipid vesicle and observe the formation of off-equator polar vortices and jammed patterns.

    • Chiao-Peng Hsu
    • , Alfredo Sciortino
    •  & Andreas R. Bausch

  • Article
    | Open Access

    “A hallmark of living systems is their homochirality, the selection of specific mirror symmetry in their molecules. Here, the authors show that chiral symmetry can be spontaneously broken in complex, random chemical systems via exploitation of environmental energy sources – a possible mechanism for the emergence of homochirality in life.”

    • William D. Piñeros
    •  & Tsvi Tlusty

  • Article
    | Open Access

    Cellular adhesions have the remarkable property that they adapt their stability to the applied mechanical load. Here, authors describe a generic physical mechanism that explains self-stabilization of idealized adhesion systems under shear.

    • Andrea Braeutigam
    • , Ahmet Nihat Simsek
    •  & Benedikt Sabass

  • Article
    | Open Access

    The ability to predict epigenetic regulation is an important challenge in biology. Here the authors describe heterochromatin nanodomains (HNDs) and compare four different types of H3K9me2/3-marked HNDs in mouse embryonic stem cells. They further develop a computational framework to predict genome-wide HND maps from DNA sequence and protein concentrations, at single-nucleotide resolution.

    • Graeme J. Thorn
    • , Christopher T. Clarkson
    •  & Vladimir B. Teif

  • Article
    | Open Access

    The rapid temperature drop during plunge-freezing affects the structural ensembles obtained by cryo-EM. To quantify the extent of perturbation, Bock and Grubmüller combined continuum calculations, MD simulations, and kinetic models.

    • Lars V. Bock
    •  & Helmut Grubmüller

  • Article
    | Open Access

    Cas9 off-target sites can be predicted by many bioinformatics tools. Here the authors present low complexity mechanistic model that characterizes SpCas9 kinetics in free-energy terms, allowing quantitative prediction of off-target activity in bulk-biochemistry, single molecule, and whole-genome profiling experiments.

    • Behrouz Eslami-Mossallam
    • , Misha Klein
    •  & Martin Depken

  • Article
    | Open Access

    Blood microcirculation supplies neurons with oxygen and nutrients, and contributes to clearing their neurotoxic waste. Here, the authors analyse blood flow simulations to establish the physical laws linking the microvascular architecture to the macroscopic transport properties that control oxygen supply and waste clearance.

    • Florian Goirand
    • , Tanguy Le Borgne
    •  & Sylvie Lorthois

  • Article
    | Open Access

    Systems of confined active filaments within a deformable vesicle are of relevance for development of active materials constructed from anisotropic particles. The authors propose a framework to control the transformations of the vesicle shape and filament organization.

    • Matthew S. E. Peterson
    • , Aparna Baskaran
    •  & Michael F. Hagan

  • Article
    | Open Access

    Biological molecular motors convert chemical energy into mechanical motion by coupling catalytic reactions to large-scale structural transitions. Here, the authors report the design of a rotating DNA nanomechanism that comprises a camshaft whose rotary motion can be transformed into reciprocating large-scale transitions in the structure of the surrounding stator.

    • Eva Bertosin
    • , Christopher M. Maffeo
    •  & Hendrik Dietz

  • Article
    | Open Access

    The self-assembly of colloidal particles can be applied to create new structures and materials in the framework of systems chemistry. The authors demonstrate the realization of autonomous oscillating structure formation on the meso-scale, relevant for systems relying on DNA interactions.

    • H. Dehne
    • , A. Reitenbach
    •  & A. R. Bausch

  • Article
    | Open Access

    Bacterial biofilms exhibit complex spatiotemporal pattern formation. Here the authors report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure.

    • Japinder Nijjer
    • , Changhao Li
    •  & Jing Yan

  • Article
    | Open Access

    Deviations from Brownian motion leading to anomalous diffusion are ubiquitously found in transport dynamics but often difficult to characterize. Here the authors compare approaches for single trajectory analysis through an open competition, showing that machine learning methods outperform classical approaches.

    • Gorka Muñoz-Gil
    • , Giovanni Volpe
    •  & Carlo Manzo

  • Article
    | Open Access

    Experimental data obtained in single-particle tracking experiments are challenging to interpret. The authors propose an approach for determining the dynamics of the stochastic motion of molecules based on the power spectrum, relevant to various non-stationary scale-free random walks.

    • Zachary R. Fox
    • , Eli Barkai
    •  & Diego Krapf

  • Article
    | Open Access

    A long puzzle in snake’s locomotion, sidewinding allows them to travel at an angle and reorient in some environments without loss of speed. Here, authors provide a mathematical argument to the evolution of sidewinding gaits and reinforce an analogy between limbless terrestrial locomotion and optics.

    • Xiaotian Zhang
    • , Noel Naughton
    •  & Mattia Gazzola

  • Article
    | Open Access

    Langevin dynamics describe transient behavior of many complex systems, however, inferring Langevin equations from noisy data is challenging. The authors present an inference framework for non-stationary latent Langevin dynamics and test it on models of spiking neural activity during decision making.

    • Mikhail Genkin
    • , Owen Hughes
    •  & Tatiana A. Engel

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