Featured
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Article
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Spontaneous persistent activity and inactivity in vivo reveals differential cortico-entorhinal functional connectivity
Cortico-entorhinal interactions remain poorly understood. Here, the authors demonstrate that a model of interacting networks predicts spontaneous persistent activity and inactivity in the medial, but not lateral, entorhinal cortex in vivo.
- Krishna Choudhary
- , Sven Berberich
- & Mayank R. Mehta
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Article
| Open Access
Anomalous dynamics of a passive droplet in active turbulence
The fluctuating dynamics of a passive object suspended in an active fluid can provide fundamental insight into the fundamental non-equilibrium behavior of the fluid. Singh and Chaudhuri theoretically investigate the dynamics of a passive deformable droplet in active nematic turbulence and show how the motion of the droplet is influenced by the interplay of spatial correlations of the flow and the size of the droplet.
- Chamkor Singh
- & Abhishek Chaudhuri
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Matters Arising
| Open Access
On the statistical foundation of a recent single molecule FRET benchmark
- Ayush Saurabh
- , Lance W. Q. Xu
- & Steve Pressé
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Article
| Open Access
Stress-shape misalignment in confluent cell layers
When studying nematic ordering of cells in a monolayer, it is commonly assumed that the principal stress and cell shape axes are tightly coupled. Here, the authors measure cell shape and cell-generated contractile stresses and show that cells in monolayers form correlated, dynamic domains in which the stresses are systematically misaligned with the cell bodies.
- Mehrana R. Nejad
- , Liam J. Ruske
- & Julia M. Yeomans
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Article
| Open Access
F-actin architecture determines the conversion of chemical energy into mechanical work
F-actin architecture modulates transmission and generation of stresses in cells, yet its impact on myosin ATP hydrolysis remains unknown. The authors perform experiments measuring myosin ATP hydrolysis rates, showing that F-actin architecture can control myosin energy consumption.
- Ryota Sakamoto
- & Michael P. Murrell
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Article
| Open Access
Scalable computation of anisotropic vibrations for large macromolecular assemblies
Normal mode analysis is a crucial step in structural biology, but is based on an expensive diagonalisation of the system’s Hessian. Here the authors present INCHING, a GPU-based approach to accelerate this task up to >250 times over current methods for macromolecular assemblies.
- Jordy Homing Lam
- , Aiichiro Nakano
- & Vsevolod Katritch
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Article
| Open Access
Flow interactions lead to self-organized flight formations disrupted by self-amplifying waves
Schools, flocks and related forms of collective behavior and collective locomotion involve complicated fluid dynamical interactions. Here, using a “mock flock" of robotic flappers, authors report that the interaction between leaders and followers is similar to one-way springs, leading to lattice-like self-organization but also a new type of traveling-wave disturbance.
- Joel W. Newbolt
- , Nickolas Lewis
- & Leif Ristroph
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Article
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Spiral packing and chiral selectivity in model membranes probed by phase-resolved sum-frequency generation microscopy
The properties of lipid membranes are intimately controlled by their complex heterogeneous structure. Here, the authors use phase-resolved sum-frequency generation microscopy to fully determine the hierarchical lipid packing from the molecular to the mesoscopic scale.
- Alexander P. Fellows
- , Ben John
- & Martin Thämer
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Article
| Open Access
Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA
It is hard to correlate force, torque and localization information. The authors report Combined Optical and Magnetic BIomolecule TWEEZers, COMBI-Tweez, that integrates optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy: they demonstrate visualisation of higher order structural motifs in DNA.
- Jack W. Shepherd
- , Sebastien Guilbaud
- & Mark C. Leake
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Article
| Open Access
Triggered contraction of self-assembled micron-scale DNA nanotube rings
Contractile rings are formed from cytoskeletal filaments, specific crosslinkers and motor proteins during cell division. Here, authors form micron-scale contractile DNA rings from DNA nanotubes and synthetic crosslinkers, with both simulations and experiments showing ring contraction without motor proteins, offering a potential first step towards synthetic cell division machinery.
- Maja Illig
- , Kevin Jahnke
- & Kerstin Göpfrich
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Article
| Open Access
Dynamic similarity and the peculiar allometry of maximum running speed
How fast can animals run? Here, the authors show that maximum running speed is limited by different musculoskeletal constraints across animal size: kinetic energy capacity in small animals, and work capacity in large animals.
- David Labonte
- , Peter J. Bishop
- & Christofer J. Clemente
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Article
| Open Access
Monitoring the mass, eigenfrequency, and quality factor of mammalian cells
There is increasing interest in measuring the mechanical properties of living cells. Here, the authors develop a method to simultaneously measure the cell mass and two parameters related to its natural oscillation or resonance frequencies.
- Sophie Herzog
- , Gotthold Fläschner
- & Daniel J. Müller
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Article
| Open Access
The structure of tyrosine-10 favors ionic conductance of Alzheimer’s disease-associated full-length amyloid-β channels
The structural basis of membrane permeabilization by Alzheimer’s disease-related amyloid β (Aβ) peptides is elucidated. Membrane insertion of tyrosine-10 supports the most effective ionic conductance of the full-length Aβ1-42 compared to other isoforms.
- Abhijith G. Karkisaval
- , Rowan Hassan
- & Suren A. Tatulian
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Article
| Open Access
Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex
Prion-like domains are intrinsically disordered regions found in many RNA- and DNA-binding proteins. Here, the authors show that these domains can drive sequence-specific co-phase separation of chromatin remodeling complex with FET oncofusion proteins.
- Richoo B. Davis
- , Anushka Supakar
- & Priya R. Banerjee
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Article
| Open Access
Overlay databank unlocks data-driven analyses of biomolecules for all
In this work, the authors report NMR lipids Databank to promote decentralised sharing of biomolecular molecular dynamics (MD) simulation data with an overlay design. Programmatic access enables analyses of rare phenomena and advances the training of machine learning models.
- Anne M. Kiirikki
- , Hanne S. Antila
- & O. H. Samuli Ollila
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Article
| Open Access
Nominally identical microplastic models differ greatly in their particle-cell interactions
Microplastics research is often based on commercial model particles. Here, the authors show that nominally identical particles may differ significantly in their properties and thus in their interactions with cells.
- Simon Wieland
- , Anja F. R. M. Ramsperger
- & Holger Kress
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Article
| Open Access
Second quantization of many-body dispersion interactions for chemical and biological systems
The many-body dispersion (MBD) framework models long-range electronic correlation and optical response of molecular systems. Here, the authors present a second-quantized MBD method that opens an efficient path to treating collective quantum fluctuations in molecular complexes with large number of atoms.
- Matteo Gori
- , Philip Kurian
- & Alexandre Tkatchenko
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Article
| Open Access
Nonuniversal impact of cholesterol on membranes mobility, curvature sensing and elasticity
Cholesterol both thickens and condenses membranes, yet it also softens them under certain conditions. Here, authors uncover cholesterol’s dual role in the delicate balance of rigidity and flexibility in membranes, crucial for diverse biological functions.
- Matthias Pöhnl
- , Marius F. W. Trollmann
- & Rainer A. Böckmann
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Article
| Open Access
Intracellular tension sensor reveals mechanical anisotropy of the actin cytoskeleton
Biosensors so far have mostly reported external traction forces exerted against the extracellular matrix or within adhesion receptors. Here, the authors present a sensor that reports molecular tension within the F-actin cytoskeleton.
- Sorosh Amiri
- , Camelia Muresan
- & Michael Murrell
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Article
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Patterning and dynamics of membrane adhesion under hydraulic stress
Hydraulic fracturing remodels cell-cell adhesions in physiology and during development. Here, authors combine vesicle experiments and computational modeling to identify the physical principles behind biological fracking.
- Céline Dinet
- , Alejandro Torres-Sánchez
- & Margarita Staykova
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Article
| Open Access
In situ quantification of osmotic pressure within living embryonic tissues
Osmotic pressure is thought to play a key role in many cellular and developmental processes, but remains challenging to measure it in cells and tissues. Here, the authors present a sensor based on double emulsion droplets that allows quantification of osmotic pressure in situ and in vivo.
- Antoine Vian
- , Marie Pochitaloff
- & Otger Campàs
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Article
| Open Access
Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models
Predicting how proteins fold into specific native structures remains challenging. Here, the authors develop a simple physical model that accurately predicts protein folding mechanisms, paving the way for solving the folding process component of the protein folding problem.
- Koji Ooka
- & Munehito Arai
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Article
| Open Access
Deep-LASI: deep-learning assisted, single-molecule imaging analysis of multi-color DNA origami structures
Analysis of single-molecule experiments remains time-consuming and prone to human bias. Here, the authors propose Deep-Learning Assisted Single-molecule Imaging analysis, a tool to rapidly analyse single-, two- and three-color single-molecule FRET data.
- Simon Wanninger
- , Pooyeh Asadiatouei
- & Don C. Lamb
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Article
| Open Access
Liquid spherical shells are a non-equilibrium steady state of active droplets
Dissipative structures are governed by non-equilibrium thermodynamics. Here, the authors describe a size-dependent transition from active droplets to active spherical shells—a dissipative structure that arises from reaction diffusion gradients.
- Alexander M. Bergmann
- , Jonathan Bauermann
- & Job Boekhoven
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Article
| Open Access
Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast
Cell polarization of budding yeast recovers reliably and reproducibly from loss of one of its key components. Here, the authors show how this robustness emerges from redundant self-organization mechanisms coexisting within the underlying protein network.
- Fridtjof Brauns
- , Leila Iñigo de la Cruz
- & Erwin Frey
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Article
| Open Access
Macroscopic waves, biological clocks and morphogenesis driven by light in a giant unicellular green alga
Self-organised waves propagate throughout the alga Caulerpa. Light temporal patterns control the waves and algal morphology, potentially tying light-synchronized self-oscillations to one of the mysteries of single-cell development, morphogenesis.
- Eldad Afik
- , Toni J. B. Liu
- & Elliot M. Meyerowitz
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Article
| Open Access
The reaction-diffusion basis of animated patterns in eukaryotic flagella
In 1952, Turing unlocked the reaction-diffusion basis of natural patterns, such as zebra stripes. The authors propose a reaction-diffusion model that recreates characteristics of the flagellar waveform for bull sperm and Chlamydomonas flagella.
- James F. Cass
- & Hermes Bloomfield-Gadêlha
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Article
| Open Access
Mechanically enhanced biogenesis of gut spheroids with instability-driven morphomechanics
Understanding and controlling morphogenesis is vital for biology and organoid technology. Here, the authors report an efficient biomechanical system to generate gut spheroids, and reveal instability-driven morphogenetic transitions with computational models.
- Feng Lin
- , Xia Li
- & Yue Shao
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Article
| Open Access
Bacterial cell-size changes resulting from altering the relative expression of Min proteins
In bacteria such as E. coli, Min proteins ensure proper localization of the septum at the mid-zone of the cell before cell division. Here, the authors study the effects of changes in relative expression of Min proteins on cell size, providing evidence that Min proteins contribute to the regulation of cell size and the timing of septum formation.
- Harsh Vashistha
- , Joanna Jammal-Touma
- & Hanna Salman
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Article
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Synchronization in collectively moving inanimate and living active matter
Collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. Yet, how individuals achieve this coordination is often not understood. For migrating cells and motorized agents, Riedl et al. show that the synchronization of the intrinsic oscillator through nearest neighbour coupling establishes the necessary feedback leading to a uniform speed within the collective.
- Michael Riedl
- , Isabelle Mayer
- & Björn Hof
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Article
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Exploring non-equilibrium processes and spatio-temporal scaling laws in heated egg yolk using coherent X-rays
The soft-grainy microstructure of cooked egg yolk is the result of a series of out of equilibrium processes of its protein-lipid contents. Here, the authors develop a time-temperature phase diagram that shows the coupling of the nanoscale processes that result in the grainy-gel microstructure of cooked egg yolk.
- Nimmi Das Anthuparambil
- , Anita Girelli
- & Christian Gutt
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Article
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Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding
Protein synthesis is dependent on the ribosome’s ability to accurately select tRNA. Molecular simulations reveal divergent pathways for correct and incorrect tRNA during selection, indicating that tRNA alignment is key to protein production.
- Dylan Girodat
- , Hans-Joachim Wieden
- & Karissa Y. Sanbonmatsu
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Article
| Open Access
Scaling the tail beat frequency and swimming speed in underwater undulatory swimming
Mechanisms by which aquatic animals optimize their tailbeat frequency for swimming have not been fully explained. Here, the authors propose scaling laws for undulatory swimmers, relating beat frequency to length considering muscle biology and fluid interaction.
- Jesús Sánchez-Rodríguez
- , Christophe Raufaste
- & Médéric Argentina
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Article
| Open Access
Phase separation of protein mixtures is driven by the interplay of homotypic and heterotypic interactions
Mixtures of prion-like low complexity domains (PLCDs) are found in condensates such as stress granules. In this work, the authors report how the interplay between homotypic and heterotypic interactions contributes to condensate formation by mixtures of PLCDs.
- Mina Farag
- , Wade M. Borcherds
- & Rohit V. Pappu
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Article
| Open Access
Partition complex structure can arise from sliding and bridging of ParB dimers
In many bacteria and plasmids, DNA segregation is controlled by the ParABS system, an essential component of which is the formation of a nucleoprotein complex. Here, making use of recent discoveries, the authors develop a sliding and bridging model to predict the fine structure of this complex.
- Lara Connolley
- , Lucas Schnabel
- & Seán M. Murray
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Article
| Open Access
A model for organization and regulation of nuclear condensates by gene activity
Through a physics-based model framework, the authors propose a central role for the nonequilibrium processes underling gene activity in shaping morphology, dynamics, and regulation of diverse nuclear condensates.
- Halima H. Schede
- , Pradeep Natarajan
- & Krishna Shrinivas
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Article
| Open Access
Mapping mechanical stress in curved epithelia of designed size and shape
Marin-Llaurado and colleagues engineer curved epithelial monolayers of controlled geometry and develop a new technique to map their state of stress. They show that pronounced stress anisotropies influence cell alignment.
- Ariadna Marín-Llauradó
- , Sohan Kale
- & Xavier Trepat
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Article
| Open Access
Single cohesin molecules generate force by two distinct mechanisms
Cohesin protein complex is a molecular machine that extrudes DNA loops. Here, authors show that bending of the molecule’s long coiled coils is driven by thermal fluctuations and engagement of ATPase domains uses ATP energy to generate strong force.
- Georgii Pobegalov
- , Lee-Ya Chu
- & Maxim I. Molodtsov
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Article
| Open Access
Mutagenesis and structural studies reveal the basis for the specific binding of SARS-CoV-2 SL3 RNA element with human TIA1 protein
Here the authors reveal the binding interface for the SARS-CoV-2 SL3 RNA element to human TIA1 protein and find that disruptions of the identified viral RNA-host protein interactions with designed ASOs reduce SARS-CoV-2 infection in cells.
- Dong Zhang
- , Lulu Qiao
- & Ruhong Zhou
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Article
| Open Access
Nonthermal acceleration of protein hydration by sub-terahertz irradiation
The collective intermolecular dynamics of protein and water molecules, which overlap in subterahertz frequencies, are relevant for protein function expressions. Here the authors develop highly sensitive dielectric measurements, revealing that protein hydration is nonthermally accelerated by sub-terahertz irradiation.
- Jun-ichi Sugiyama
- , Yuji Tokunaga
- & Masahiko Imashimizu
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Article
| Open Access
Chemo-mechanical diffusion waves explain collective dynamics of immune cell podosomes
Dendritic cells can utilize the dynamics of podosomes to probe their microenvironment. Here, the authors propose a chemo-mechanical model for the height oscillations of individual podosomes and the collective wave dynamics in a podosome cluster.
- Ze Gong
- , Koen van den Dries
- & Vivek B. Shenoy
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Article
| Open Access
MoS2 nanopore identifies single amino acids with sub-1 Dalton resolution
Protein sequencing is one of the key aims of the nanopore field. Working toward this goal, here the authors report the direct identification of single amino acids in MoS2 nanopores with sub-1 Dalton resolution, as well as the discrimination of the amino acid isomers and amino acid phosphorylation.
- Fushi Wang
- , Chunxiao Zhao
- & Jiandong Feng
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Article
| Open Access
Antibody binding reports spatial heterogeneities in cell membrane organization
The organization of proteins and sugars on the cell membrane is crucial for cell signaling and function. Here, authors develop molecular probes and simulations to characterize the spatial organization of macromoleucles on live cell membranes.
- Daniel P. Arnold
- , Yaxin Xu
- & Sho C. Takatori
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Article
| Open Access
Curvature induces active velocity waves in rotating spherical tissues
The existence of multicellular systems relies on coordinated cell motion in three dimensions. Here, cell migration in rotating spherical tissues is shown to exhibit a collective mode with a single-wavelength velocity wave, which arises from the effect of curvature on the flocking behavior of cells on a spherical surface.
- Tom Brandstätter
- , David B. Brückner
- & Chase P. Broedersz
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Article
| Open Access
Size limits the sensitivity of kinetic schemes
Living things rely on extremely sensitive molecular circuits. Here, authors uncover a universal structural limit on kinetic scheme sensitivity, with implications for gene regulation & the functions of condensates.
- Jeremy A. Owen
- & Jordan M. Horowitz
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Article
| Open Access
A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants
Here the authors develop a computational method based on the maximum entropy principle to construct the structural ensemble of genomes using imaging data. The work reveals three-way contacts between loci and extensive conformational heterogeneity.
- Guang Shi
- & D. Thirumalai
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Article
| Open Access
Droplet superpropulsion in an energetically constrained insect
Sharpshooters can catapult their droplet excreta with a speed faster than their own movement speed. Challita et al. find that superpropulsion is achieved by the temporal tuning between the droplet and the stylus.
- Elio J. Challita
- , Prateek Sehgal
- & M. Saad Bhamla
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Article
| Open Access
Microphase separation of living cells
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
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Article
| Open Access
Light-driven biological actuators to probe the rheology of 3D microtissues
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
Technical challenges of studying the impact of plasma components on the efficacy of lipid nanoparticles for vaccine and therapeutic applications