# Biological physics

• Article
| Open Access

### Aging power spectrum of membrane protein transport and other subordinated random walks

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

### Friction modulation in limbless, three-dimensional gaits and heterogeneous terrains

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

### A hierarchical cellular structural model to unravel the universal power-law rheological behavior of living cells

Different types of cells exhibit a universal power-law rheological behavior which to this date has not been captured by a single theoretical model. Here, the authors propose a self-similar hierarchical cellular model that can naturally reproduce the universal power-law characteristics of cell rheology.

• Jiu-Tao Hang
• , Yu Kang
•  & Huajian Gao
• Article
| Open Access

### Learning non-stationary Langevin dynamics from stochastic observations of latent trajectories

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
• Article
| Open Access

### Fluidic bacterial diodes rectify magnetotactic cell motility in porous environments

Microswimmers can navigate porous environments, however the impact of their directed motility on their movement in fluid flow remains an open issue. The authors show that the motility of magnetotactic bacteria in flow through a porous constriction gives rise to nonlinear flow conductivity similar to electrical diodes.

• Nicolas Waisbord
• , Amin Dehkharghani
•  & Jeffrey S. Guasto
• Article
| Open Access

### Theory and simulations of condensin mediated loop extrusion in DNA

How chromosomes, which are polymers with nearly billion base pairs, are packaged in the restricted nuclear volume is not well understood. Here, the authors combine polymer physics, nonequilibrium fluctuation theorem, and simulations to quantitatively predict the force-dependent velocity and step-size distribution of condensin, which facilitates the folding of chromosomes by loop extrusion.

• Ryota Takaki
• , Atreya Dey
•  & D. Thirumalai
• Article
| Open Access

### Efficient generative modeling of protein sequences using simple autoregressive models

Deep learning is a powerful tool for the design of novel protein sequences, yet can be computationally very inefficient. Here the authors propose using simple forecasting models to efficiently generate a large number of novel protein structures.

• Jeanne Trinquier
• , Guido Uguzzoni
•  & Martin Weigt
• Article
| Open Access

### Emergence and melting of active vortex crystals

Whereas transitions from solid- to fluid-like states in systems of active particles have received much attention, the characterization of phase transitions in active fluids with self-organized vortices so far has remained elusive. James et al. take us on a numerical tour de force from active turbulence to active vortex crystals.

• Martin James
• , Dominik Anton Suchla
•  & Michael Wilczek
• Article
| Open Access

### Cell migration guided by long-lived spatial memory

Cells can modify their environment by depositing biochemical signals or mechanically remodelling the extracellular matrix; the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here authors show that motile cells leave long-lived physicochemical footprints along their way, which determine their future path.

• Joseph d’Alessandro
• , Alex Barbier--Chebbah
• Article
| Open Access

### Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells

Controlled actuation is an important aspect of synthetic cellular systems. Here, the authors combine pH responsive DNA origami structures with light triggered proton pump engineered E. coli to trigger a change in pH and control the deformation of giant unilamellar vesicles by simple illumination.

• Kevin Jahnke
• , Noah Ritzmann
•  & Kerstin Göpfrich
• Article
| Open Access

### Vimentin intermediate filaments stabilize dynamic microtubules by direct interactions

The tasks of the cytoskeleton depend on the fine-tuned interplay between the three filamentous components: actin filaments, microtubules, and intermediate filaments. Here, the authors show in a reconstituted in vitro system that vimentin intermediate filaments stabilize microtubules against depolymerization and support microtubule rescue by direct interactions.

• Laura Schaedel
• , Charlotta Lorenz
•  & Sarah Köster
• Article
| Open Access

### Curvature in the reproductive tract alters sperm–surface interactions

The effect of fallopian tube’s curvature on sperm motion has not been studied in detail. Here, the authors use droplet microfluidics to create soft curved interfaces, revealing a dynamic switch in sperm motility from a progressive surface-aligned mode at low curvatures, to an aggressive surface-attacking mode at high curvatures.

• , Melati S. Abdul Halim
•  & Reza Nosrati
• Article
| Open Access

### Bulk-surface coupling identifies the mechanistic connection between Min-protein patterns in vivo and in vitro

Self-organisation of Min protein patterns observed in vivo and in vitro differ qualitatively and quantitatively. Here the authors reconstituted Min proteins in laterally wide microchambers with a well-controlled height and show that the Min protein dynamics on the membrane crucially depend on the micro chamber height.

• Fridtjof Brauns
• , Grzegorz Pawlik
•  & Cees Dekker
• Article
| Open Access

### Cooperative stator assembly of bacterial flagellar motor mediated by rotation

Ito and co-workers unravel how bacteria such as Salmonella switch gears with their flagellar driving machinery. External load triggers the dynamic remodeling of the molecular complex sustaining the torque, and the number of stator units is adapted in a non-trivial, cooperative manner.

• Kenta I. Ito
• , Shuichi Nakamura
•  & Shoichi Toyabe
• Article
| Open Access

### Excitonic structure and charge separation in the heliobacterial reaction center probed by multispectral multidimensional spectroscopy

The primary energy conversion step in photosynthesis, charge separation, takes place in the reaction center. Here the authors investigate the heliobacterial reaction center using multispectral two-dimensional electronic spectroscopy, identifying the primary electron acceptor and revealing the charge separation mechanism.

• Yin Song
• , Riley Sechrist
•  & Jennifer P. Ogilvie
• Article
| Open Access

### Mechanical plasticity of collagen directs branch elongation in human mammary gland organoids

Mammary organoid growth from single primary human cells rely on distinct morphogenetic processes. Here, the authors observe by live cell imaging the importance of the plastic mechanical response of the extracellular matrix and cell migration for the underlying arborized structure formation process.

• B. Buchmann
• , L. K. Engelbrecht
•  & A. R. Bausch
• Article
| Open Access

### FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division

Bacterial cell division by cell wall synthesis proteins is guided by treadmilling filaments of the cytoskeleton protein FtsZ. Here authors use nanofabrication, advanced microscopy, and microfluidics to resolve the function of FtsZ treadmilling in the Gram-positive model organism Bacillus subtilis.

• Kevin D. Whitley
• , Calum Jukes
•  & Séamus Holden
• Article
| Open Access

### Statistics of pathogenic bacteria in the search of host cells

Chemotaxis may generally be thought to determine bacterial virulence and identification of appropriate host cells. Here, Otte, Ipiña et al. show that if this process is studied in vitro, purely mechanistic random search strategies must be included to explain the experimental results.

• Stefan Otte
• , Emiliano Perez Ipiña
•  & Fernando Peruani
• Article
| Open Access

### Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales

The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, the authors develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus.

• , Muriel C. F. van Teeseling
•  & Chase P. Broedersz
• Article
| Open Access

### Active carpets drive non-equilibrium diffusion and enhanced molecular fluxes

Fick’s laws describe the essential physics of diffusion, but it is challenging to extend them to systems out of equilibrium. The authors derive the diffusivity of particles near active carpets - a surface covered with hydrodynamic actuators, which provides a framework for transport in living matter.

• Francisca Guzmán-Lastra
• , Hartmut Löwen
•  & Arnold J. T. M. Mathijssen
• Article
| Open Access

### Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity

TEM-1 β-lactamase evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency and degrades β-lactam antibiotics with a strong preference for penicillins. Here authors developed a computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism and show a putative Precambrian β-lactamase that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements.

• Tushar Modi
• , Valeria A. Risso
•  & S. Banu Ozkan
• Article
| Open Access

### Markerless tracking of an entire honey bee colony

Honey bee colonies are hard to automatically monitor due to the high number of visually similar members which move rapidly and whose numbers change over time. Here, the authors report a method for markerless tracking of a bee colony by adapting convolutional neural networks for detection and tracking.

• Katarzyna Bozek
• , Laetitia Hebert
•  & Greg J. Stephens
• Article
| Open Access

### Quantifying information accumulation encoded in the dynamics of biochemical signaling

Understanding how cells discriminate between stimuli is an ongoing challenge. Here, the authors propose a mathematical framework for inferring the mutual information encoded in temporal signaling dynamics and use it to study how information is transmitted over time in response to different stimuli in NFκB, MAPK and p53 signaling pathways.

• Ying Tang
•  & Alexander Hoffmann
• Article
| Open Access

### Sniffing speeds up chemical detection by controlling air-flows near sensors

Sniff frequency naturally varies with animal type due to allometric scaling. Using data from live animals and a machine olfactory system, Spencer et al. reveal a deeper reason for sniffing with implications for designing gas detectors: the sniff is adapted to efficient odor detection.

• Thomas L. Spencer
•  & David L. Hu
• Article
| Open Access

### Harnessing peak transmission around symptom onset for non-pharmaceutical intervention and containment of the COVID-19 pandemic

Transmission by pre-symptomatic and asymptomatic viral carriers makes intervention and containment of the COVID-19 extremely challenging. Here, the authors construct an epidemiological model that focuses on transmission around the symptom onset, exploring specific transmission control measures.

• Liang Tian
• , Xuefei Li
•  & Lei-Han Tang
• Article
| Open Access

### Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Elucidating the molecular driving forces underlying liquid–liquid phase separation is a key objective for understanding biological function and malfunction. Here the authors show that a wide range of cellular proteins, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, which form condensates at low salt concentrations, can reenter a phase-separated regime at high salt concentrations.

• Georg Krainer
• , Timothy J. Welsh
•  & Tuomas P. J. Knowles
• Article
| Open Access

### Irreversibility in dynamical phases and transitions

The degree of irreversibility of a dynamical system is commonly characterized by the total rate of entropy production. Seara et al. introduce a measure that quantifies irreversibility from data in broad classes of spatiotemporal non-equilibrium systems.

• Daniel S. Seara
• , Benjamin B. Machta
•  & Michael P. Murrell
• Article
| Open Access

### From deterministic to fuzzy decision-making in artificial cells

Building regulatory networks often requires trade-offs between accuracy and speed. Here the authors show in a bistable network the transition from a slow decision making system to a rapid one dominated by small number fluctuations.

• Ferdinand Greiss
• , Shirley S. Daube
•  & Roy Bar-Ziv
• Article
| Open Access

### Vortex phase matching as a strategy for schooling in robots and in fish

Whether and how fish might benefit from swimming in schools is an ongoing intriguing debate. Li et al. conduct experiments with biomimetic robots and also with real fish to reveal a new behavioural strategy by which followers can exploit the vortices shed by a near neighbour.

• Liang Li
• , Máté Nagy
•  & Iain D. Couzin
• Article
| Open Access

### Learning the non-equilibrium dynamics of Brownian movies

A tracking-free approach by Gnesotto et al. is developed to distinguish active and thermal fluctuations in microscopy data of non-equilibrium systems such as cell membranes. The method relies on a dimensional reduction scheme revealing a hierarchy of the most dissipative dynamical components.

• Federico S. Gnesotto
•  & Chase P. Broedersz
• Article
| Open Access

### A particle-field approach bridges phase separation and collective motion in active matter

Interacting self-propelled particles exhibit phase separation or collective motion depending on particle shape. A unified theory connecting these paradigms represents a major challenge in active matter, which the authors address here by modeling active particles as continuum fields.

• Robert Großmann
• , Igor S. Aranson
•  & Fernando Peruani
• Article
| Open Access

### Mechanical forces drive ordered patterning of hair cells in the mammalian inner ear

The periodic organization of cells is typically associated with mechanisms based on intercellular signaling such as lateral inhibition and Turing patterning. Here the authors show that hair cells in the inner ear rearrange gradually into a checkerboard-like pattern through a tissue-wide shear motion that coordinates intercalation and delamination events.

• Roie Cohen
• , Liat Amir-Zilberstein
•  & David Sprinzak
• Article
| Open Access

### Learning molecular dynamics with simple language model built upon long short-term memory neural network

Artificial neural networks have been successfully used for language recognition. Tsai et al. use the same techniques to link between language processing and prediction of molecular trajectories and show capability to predict complex thermodynamics and kinetics arising in chemical or biological physics.

• Sun-Ting Tsai
• , En-Jui Kuo
•  & Pratyush Tiwary
• Article
| Open Access

### In primary airway epithelial cells, the unjamming transition is distinct from the epithelial-to-mesenchymal transition

During repair, development, or cancer metastasis, epithelial cells can become migratory through partial or full epithelial to mesenchymal transition (EMT). Here, the authors report that differentiated epithelial collectives may undergo cooperative and collective migration without evidence of partial EMT through an unjamming transition (UJT).

• Jennifer A. Mitchel
• , Amit Das
•  & Jin-Ah Park
• Article
| Open Access

### Human running performance from real-world big data

Laboratory performance tests provide the gold standard for running performance but do not reflect real running conditions. Here the authors use a large, real world dataset obtained from wearable exercise trackers to extract parameters that accurately predict race times and correlate with training.

• Thorsten Emig
•  & Jussi Peltonen
• Article
| Open Access

### Haloarchaea swim slowly for optimal chemotactic efficiency in low nutrient environments

Brownian motion places the ultimate limit on microorganisms’ ability to navigate. Thornton et al. show that Haloarchaea have a strategy of slow swimming and infrequent reorientation that exploits the randomising nature of Brownian motion to achieve optimal chemotaxis at the thermodynamic limit.

• Katie L. Thornton
• , Jaimi K. Butler
•  & Laurence G. Wilson
• Article
| Open Access

### Geometric pinning and antimixing in scaffolded lipid vesicles

Lipid bilayers feature an intricate interplay between membrane geometry and its chemical composition but lack of a model system with simultaneous control over membrane shape and composition prevented a fundamental understanding of curvature-induced effects. Here the authors demonstrate that the local substrate geometry and global chemical composition of the bilayer determine both the spatial arrangement and the sorting of lipid domains.

• Melissa Rinaldin
• , Piermarco Fonda
•  & Daniela J. Kraft
• Article
| Open Access

### Spatially selective manipulation of cells with single-beam acoustical tweezers

Acoustical tweezers can exert forces several orders of magnitude greater than optical tweezers but the absence of spatial selectivity and their limited resolution has prevented their use for many applications in microbiology. Here the authors perform spatially selective contactless manipulation and positioning of human cells.

• Michael Baudoin
• , Jean-Louis Thomas
•  & Alexis Vlandas
• Article
| Open Access

### Triacylglycerols sequester monotopic membrane proteins to lipid droplets

Triacylglycerols (TG) are synthesized at the endoplasmic reticulum (ER) bilayer and packaged into monolayer lipid droplets (LDs), but how proteins partition between ER and LDs is poorly understood. Here authors use synthetic model systems and find that proteins containing hydrophobic membrane association domains strongly prefer monolayers and that returning to the bilayer is unfavorable.

• Lucie Caillon
• , Vincent Nieto
•  & Abdou Rachid Thiam
• Article
| Open Access

### Collective cell mechanics of epithelial shells with organoid-like morphologies

The physical origins of man-made tissue morphologies with organ-like microscopic anatomy and functionality remain poorly understood. Here, authors propose a mechanistic theory of these structures, employing a 3D vertex model to reproduce the characteristic morphologies such as branched shapes.

• Jan Rozman
• , Matej Krajnc
•  & Primož Ziherl
• Article
| Open Access

### Directional translocation resistance of Zika xrRNA

Zika xrRNAs survive in host cells because they can be unwound and copied by replicases, but resist degradation by exonucleases. Here authors use atomistic models and simulations and uncover that pulling into a pore the xrRNA $${3}^{\prime}$$ ${3}^{\prime }$ end, as done by replicases, causes progressive unfolding; pulling the $${5}^{\prime}$$ ${5}^{\prime }$ end, as done by exonucleases, triggers molecular tightening.

• Antonio Suma
• , Lucia Coronel
•  & Cristian Micheletti
• Article
| Open Access

### Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

The molecular and physical mechanisms underlying chromatin folding at the single DNA molecule level remain poorly understood. Here, the authors use polymer modeling to investigate the conformations of two 2Mb-wide DNA loci in normal and cohesin depleted cells, and provide evidence that the architecture of the studied loci is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules.

• Mattia Conte
• , Luca Fiorillo
•  & Mario Nicodemi
• Article
| Open Access

### Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models

Explicit molecular modelling of biological membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Here authors present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics which facilitates efficient simulation of large biomembrane systems.

•  & Frank Noé
• Article
| Open Access

### Anisotropic ESCRT-III architecture governs helical membrane tube formation

ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here, the authors use cryo-ET, cryo-EM and mathematical modeling to reveal how the shape of the helical membrane tube arises from the assembly of two distinct bundles of helical filaments.

• Joachim Moser von Filseck
• , Luca Barberi
•  & Aurélien Roux
• Article
| Open Access

### Magnetic cilia carpets with programmable metachronal waves

Synthetic hair-like structures (cilia) controlled by an external field have been developed, especially for microfluidic applications. Here, Gu et al. make soft artificial cilia carpets with programmable magnetization patterns and utilize them to achieve pumping and locomotion in a soft robotic model.

• Hongri Gu
• , Quentin Boehler
• Article
| Open Access

### Extreme active matter at high densities

While active matter exhibits unusual dynamics at low density, high density behavior has not been explored. Mandal et al. show that extreme dense active matter, shows a rich spectrum of behaviour from intermittent plastic bursts and turbulence, to glassy states and jamming in the limit of infinite persistence time.

• Rituparno Mandal
• , Pranab Jyoti Bhuyan
• Article
| Open Access

### A transition to stable one-dimensional swimming enhances E. coli motility through narrow channels

Most biological and artificial self-propelled particles tend to be attracted by solid walls on their swimming pathways. Vizsnyiczai et al. show that, unexpectedly, confining E. coli cells inside a channel triggers stable locomotion along the channel axis once the channel is narrower than a critical value.

• Gaszton Vizsnyiczai
• , Giacomo Frangipane
•  & Roberto Di Leonardo
• Article
| Open Access

### High-throughput cell and spheroid mechanics in virtual fluidic channels

High-throughput rheological measurements of cells and cell clusters by microfluidics is limited by fixed channel dimensions. Here the authors create virtual fluidic channels inside the cuvette of commercial flow cytometers to dynamically tune channel cross section to enable rheological measurements from cells and cell clusters.

• Muzaffar H. Panhwar
• , Fabian Czerwinski
•  & Oliver Otto
• Article
| Open Access

### Dense active matter model of motion patterns in confluent cell monolayers

Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes. Here the authors show that cell motility coupled to the collective elastic modes of the cell sheet is sufficient to produce characteristic swirl-like correlations.

• Silke Henkes
• , Kaja Kostanjevec
•  & Eric Bertin
• Article
| Open Access

### Energy consumption and cooperation for optimal sensing

Cells exhibit exceptional chemical sensitivity, yet we haven’t fully understood how they achieve it. Here the authors consider the mutual information between signals and two coupled sensors as a proxy for sensing performance and show its optimisation depending on noise level and signal statistics.

• Vudtiwat Ngampruetikorn
• , David J. Schwab
•  & Greg J. Stephens