Computational biophysics articles within Nature Physics

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  • Article |

    Cytoplasmic flows in the fruit fly oocyte can reorganize cellular components. These structured vortical flows arise through self-organizing dynamics of microtubules, molecular motors and cytoplasm.

    • Sayantan Dutta
    • , Reza Farhadifar
    •  & Michael J. Shelley

  • Article |

    The strengths of connections in networks of neurons are heavy-tailed, with some neurons connected much more strongly than most. Now a simple network model can explain how this heavy-tailed connectivity emerges across four different species.

    • Christopher W. Lynn
    • , Caroline M. Holmes
    •  & Stephanie E. Palmer

  • Article |

    Although using low-rank matrices is the go-to approach to model the dynamics of complex systems, its validity remains formally unconfirmed. An analysis of random networks and real-world data now sheds light on this low-rank hypothesis and its implications.

    • Vincent Thibeault
    • , Antoine Allard
    •  & Patrick Desrosiers

  • News & Views |

    Orderly or coherent multicellular flows are fundamental in biology, but their triggers are not understood. In epithelial tissues, the tug-of-war between cells is now shown to lead to intrinsic asymmetric distributions in cell polarities that drive such flows.

    • Guillermo A. Gomez

  • Article
    | Open Access

    Filaments of the FtsZ protein can form chiral assemblies. Now, active matter tools link the microscopic structure of active filaments to the large-scale collective phase of these assemblies.

    • Zuzana Dunajova
    • , Batirtze Prats Mateu
    •  & Martin Loose

  • News & Views |

    Regenerative animals accurately regrow lost appendages. Now, research suggests that mechanical waves propagating from the amputation edge have a key role in this process.

    • Yutaka Matsubayashi

  • News & Views |

    Developing tissues undergo collective cell movement and changes to their material properties, such as flow characteristics. Now tissue fluidity is linked to tissue growth.

    • Asako Shindo

  • News & Views |

    Embryonic development is characterized by large cellular flows. The cells retain their positional information despite these flows thanks to an unjamming of cells that pull along jammed cells in a way that preserves initial tissue patterning.

    • Sham Tlili

  • Article |

    Cervix and breast carcinomas are highly heterogeneous in their mechanical properties across scales. This heterogeneity provides the tumour with stability and room for cell motility.

    • Thomas Fuhs
    • , Franziska Wetzel
    •  & Josef A. Käs

  • News & Views |

    Plasmodium sporozoites can move in rotating vortices owing to their chiral shape and mechanical flexibility, revealing important physical aspects of collective motion.

    • Iva M. Tolić
    •  & Isabelle Tardieux

  • News & Views |

    Individual cilia are typically attached to cell surfaces, where they sweep back and forth. A new study charts the behavioural space of the beating patterns of cilia isolated from the cell.

    • Kirsty Y. Wan

  • Article
    | Open Access

    The beating of motile cilia arises from the collective action of hundreds of proteins. A study of the dynamics of cilia under different environmental and genetic conditions shows that the space of beating variations is low-dimensional.

    • Veikko F. Geyer
    • , Jonathon Howard
    •  & Pablo Sartori

  • Article |

    Macroscale patterns seen in biological systems such as animal coats or skin can be described by Turing’s reaction–diffusion theory. Now Turing patterns are shown to also exist in bismuth monolayers, an exemplary nanoscale atomic system.

    • Yuki Fuseya
    • , Hiroyasu Katsuno
    •  & Aharon Kapitulnik

  • Article |

    A computational framework draws analogy with foams to offer a comprehensive picture of how cell behaviours influence fluidization in embryonic tissues, highlighting the role of tension fluctuations in regulating tissue rigidity.

    • Sangwoo Kim
    • , Marie Pochitaloff
    •  & Otger Campàs

  • News & Views |

    SARS, MERS and now SARS-CoV-2 are unlikely to be the last emerging infections we face during our lifetimes. Tracing contacts both forward and backward through our heterogeneous populations will prove essential to future response strategies.

    • Johannes Müller
    •  & Mirjam Kretzschmar

  • Article |

    Certain bacteria cells respond to the stress of long-term exposure to antibiotics by changing their shape. Single-cell experiments and modelling cast this as a mechanical feedback strategy that makes bacteria more adaptive to surviving antibiotics.

    • Shiladitya Banerjee
    • , Klevin Lo
    •  & Aaron R. Dinner

  • Article |

    The authors investigate the relationship between the volume of malignant tumours and their metabolic processes using a large dataset of patients with cancer. They find that cancers follow a superlinear metabolic scaling law, which implies that the proliferation of cancer cells accelerates with increasing volume.

    • Víctor M. Pérez-García
    • , Gabriel F. Calvo
    •  & Ana M. García Vicente

  • News & Views |

    Whether a cell divides symmetrically or asymmetrically during early development determines the fate of its progeny. Now cell size has emerged as a key player in making this decision.

    • Alexandra Jilkine

  • Article |

    An observation that cells at the edge of a healing wound readily undergo intercalation leads to the finding that tissue fluidity is crucial for effective wound closure.

    • Robert J. Tetley
    • , Michael F. Staddon
    •  & Yanlan Mao

  • Article |

    Modelling and microscopy of thousands of cells together reveal the coupling through which the cell cycle influences the circadian clock. This coupling may explain why mammalian tissues growing at different rates have shifted circadian rhythms.

    • Colas Droin
    • , Eric R. Paquet
    •  & Felix Naef

  • Article |

    Biofilms of rod-shaped bacteria can grow from a two-dimensional layer of founder cells into a three-dimensional structure with a vertically aligned core. Here, the physics underlying this transition is traced down to the properties of individual cells.

    • Farzan Beroz
    • , Jing Yan
    •  & Ned S. Wingreen

  • Article |

    Interactions between cells can affect the way they migrate, impacting processes like cancer invasion and wound healing. Experiments on cell colonies of moderate density show that these interactions can enhance motility by increasing persistence.

    • Joseph d’Alessandro
    • , Alexandre P. Solon
    •  & Charlotte Rivière

  • Article |

    Cells rely on their proteins being positioned correctly for processes such as cell division and migration. A model based on Turing patterns provides an active mechanism for establishing this precise control in bacteria.

    • Seán M. Murray
    •  & Victor Sourjik

  • News & Views |

    Early forms of life could have started by molecular compounds coming together under conditions dense enough to promote reactions. But how might these droplets have undergone what we now know as cell division? The answer may be simpler than we think.

    • Ramin Golestanian

  • Article |

    Certain proteins are capable of self-replicating, including those associated with Alzheimer’s disease. Simulations now pinpoint the adsorption of monomeric proteins onto protein fibril surfaces as the mechanism responsible for self-replication.

    • Anđela Šarić
    • , Alexander K. Buell
    •  & Daan Frenkel

  • News & Views |

    The folded surface of the human brain, although striking, continues to evade understanding. Experiments with swelling gels now fuel the notion that brain folding is modulated by physical forces, and not by genetic, biological or chemical events alone.

    • Ellen Kuhl

  • Letter |

    A 3D-printed fetal brain undergoes constrained expansion to reproduce the shape of the human cerebral cortex. The soft gels of the model swell in solvent, mimicking cortical growth and revealing the mechanical origin of the brain’s folded geometry.

    • Tuomas Tallinen
    • , Jun Young Chung
    •  & L. Mahadevan

  • News & Views |

    Single-molecule techniques have long given us insight into the motion and interactions of individual molecules. But simulations now show that the dynamics inside single proteins is not as simple as we thought — and that proteins are forever changing.

    • Ralf Metzler

  • Article |

    Cells moving in a tissue undergo a rigidity transition resembling that of active particles jamming at a critical density—but the tissue density stays constant. A new type of rigidity transition implicates the physical properties of the cells.

    • Dapeng Bi
    • , J. H. Lopez
    •  & M. Lisa Manning

  • Article |

    Cells rely on coherent oscillatory processes, despite being subject to large fluctuations from their environment. Simple motifs found in all oscillatory systems are studied to determine the thermodynamic cost of maintaining this coherence.

    • Yuansheng Cao
    • , Hongli Wang
    •  & Yuhai Tu

  • News & Views |

    The myriad creatures that inhabit the waters of our planet all swim using different mechanisms. Now, a simple relation links key physical observables of underwater locomotion, on scales ranging from millimetres to tens of metres.

    • Johannes Baumgart
    •  & Benjamin M. Friedrich

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