Feb 09 26
Featured Papers
Nonlinear diffusion and decay of a blob of turbulence spreading into a quiescent fluid
Takumi Matsuzawa, Minhui Zhu, Nigel Goldenfeld, William T. M. Irvine
Particle image velocimetry of a vortex-generated flow establishes the Kolmogorov–Barenblatt equation as a universal law for turbulent evolution and reveals that the turbulent cascade persists long after the removal of external forcing.
Morphodynamics of surface-attached active drops
Alejandro Martínez-Calvo, Sujit S. Datta
Boundary conditions and active stress strength dictate the emergence of complex steady-state shapes and internal flows, providing quantitative principles for the rational control of next-generation active materials.
Nonreciprocal many-body physics
Michel Fruchart, Vincenzo Vitelli
Diverse manifestations of broken action-reaction symmetry across classical and quantum systems yield universal collective behaviors, including novel phase transitions and non-normal noise amplification.
Diffusive and Enzymatic Modulation of the Dynamic Size Distribution of DNA Droplets
Michio Tateno and Omar A. Saleh
Phase separation ability dictates the growth and evolution of these condensed structures within a programmable nanoparticle model system.
Optogenetic control of transition to metamorphosis
Changyuan Wang, Denis F. Faerberg, Yuka Sekine, Takeaki Ozawa, John J. Tyson, Robert A. Marmion, Stanislav Y. Shvartsman
System identification based on time-dependent signaling perturbations enables the construction of a compact mathematical model that accurately predicts the timing of developmental commitment at the organismal scale.
Morphological instability of an invasive active-passive interface
Sumit Sinha, Haiqian Yang, L Mahadevan
Matrix viscoelasticity triggers long-wavelength undulations, while purely elastic environments provide a stabilizing mechanism against expansion.
Human mitotic spindles as active liquid crystals: From collective behaviors to discrete filaments
Suryanarayana Maddu, Colm P. Kelleher, Mustafa Basaran, Thomas Müller-Reichert, Michael J. Shelley, Daniel J. Needleman
Spindle microtubules exhibit collective behaviors described by continuum theory at scales exceeding 300 nanometers, whereas kinetochore-attached fibers and smaller-scale fluctuations reveal the limits of this active liquid-crystal framework.
More Papers
Deciphering Rapid Cell Signaling and Control of Cell Motility by Reverse Opto-Chemical Engineering
H. Hamzeh, A. Gong, M. Balbach, D. Fridman, H. G. Körschen, R. Pascal, F. Lavryk, A. Rennhack, R. Seifert, A. Hernandez-Clavijo, S. Pifferi, V. Dusend, B. K. Fleischmann, P. Sasse, A. Menini, B. M. Friedrich, L. Alvarez, and U. B. Kaupp
Virtual sensory landscapes generated by temporal light patterns and photo-triggers facilitate the remote navigation and real-time monitoring of cellular trajectories.
Dual recruitment of two CCM2 molecules to KRIT1 suppresses KLF4 expression
Huet-Calderwood, Clotilde, Fisher, Oriana S., Das, Sreya, Su, Valerie L., Boggon, Titus J., Calderwood, David A.
Specific PTB-NPxF interactions facilitate a novel PTB clustering mechanism essential for preventing harmful KLF4 overexpression in brain vasculature.
Ultrasound effectively destabilizes and disrupts the structural integrity of enveloped respiratory viruses
Veras, Flavio P., Nakamura, Gilberto, Pereira-da-Silva, Marcelo A., Ruiz, Gilia C. M., Constantino, Carlos J. L., Martins, Ronaldo, Arruda, Eurico, Cunha, Fernando Q., Bruno, Odemir M.
Resonance-driven mechanical destabilization at 3–20 MHz frequencies fragments viral envelopes and inhibits infectivity through a biophysical process distinct from classical cavitation or thermal effects.
Mechanical instabilities in drying protein droplets under substrate-free conditions
Ludovic Pauchard, Romain Bordes, Cécile Le Floch-Fouéré, Denis Renard
Acoustic levitation experiments reveal how the molecular origin of proteins dictates specific pathways of structural evolution and final particle morphology.
Impact of G-quadruplex RNA oxidation on its conformational dynamics and interaction with ALS-associated TDP-43
Ishiguro, Akira
Substitution of guanine with 8-oxoguanine triggers structural instability through altered hydrogen bonding and impairs TDP-43 recruitment, potentially compromising the intra-axonal mRNA transport necessary for motor neuron survival during aging.
Emergent hydrodynamic synchronization between microbeads labelingbacterial flagellar motors
Ishihara, T.; Uchida, N.; Nakamura, S.
Elastic deformation of the flagellar filaments facilitates intermittent in-phase locking, with stronger coupling between the motors leading to increased stability of the synchronized state.
Spatial relationships between vinculin tension and actin at cell adhesions define cell colony positioning and identity
Abigail Nagle, Cherry Leung, Elaheh Karbassi, Jessica Young, Michael Regnier, Jennifer Davis
Mechanical profiles derived from FRET-based force sensors distinguish cell types by their developmental origin and link specific tension distributions to distinct morphological characteristics.
Nanoscale Co-condensation and Stretch Resistance of FUS and DNA
Weiqian Dong, Wen-Ting Chu, Erkang Wang, Jin Wang
Coarse-grained molecular dynamics simulations reveal the microscopic structural evolution and dynamic stability of these liquid-like protein-DNA assemblies under mechanical tension.
A Frequency-Optimized Optogenetic Study of Network-Level Potentiation in Cortical Cultures on Microelectrode Arrays
Matteo Dominici, Ilya Auslender, Clara Zaccaria, Yasaman Heydari, Lorenzo Pavesi
Low-frequency test pulses (≤ 0.2 Hz) establish a stable baseline for quantifying localized, hours-long potentiation induced by targeted tetanic stimulation.
Early stages of collective cell invasion: Biomechanics
R. González-Albaladejo, M. Carretero, L. L. Bonilla
A fractional step cellular Potts model integrates durotaxis and active forces to simulate diverse mesenchymal, hybrid, and leader-cell-driven invasion patterns with enhanced realism prior to the onset of proliferation.
Cortical tension links curvature to tissue growth in the cellular Potts model
Kai Lennard Fastabend, Cécile M. Bidan, John W. C. Dunlop, and Philip Kollmannsberger
Spatial variations in mechanical pressure, generated by cell-level contractility, coordinate the frequency of division events to drive the macroscopic expansion of the tissue interface.
Reentrant Rigidity Transition in Planar Epithelia with Volume and Area Elasticity
Tanmoy Sarkar and Matej Krajnc
Compression-driven shifts between columnar and squamous cell shapes enable mechanical softening or stiffening, a behavior that differentiates three-dimensional tissue responses from those of traditional two-dimensional models.
High-speed atomic force microscopy reveals a surface-catalyzed elongation mechanism of the fungal functional amyloid hydrophobin RolA
Nao Takahashi, Tatsuya Kimura, Yuki Terauchi, Takumi Tanaka, Natsuki Abe, Akira Yoshimi, Takahiro Watanabe-Nakayama, Keietsu Abe
Lateral bundling of rodlets lowers the energy barriers for structural state switching and growth, doubling the elongation rate to facilitate the formation of oriented domain structures on the fungal surface.
Transition from traveling fronts to diffusion-limited growth in expanding populations
Louis Brezin, Kyle J. Shaffer, Kirill S. Korolev
Nutrient-driven slowing of biomass redistribution within nonmotile aggregates produces sublinear front speeds, explaining why many microbial colony areas increase linearly rather than quadratically with time.
Alternative probe chemistries for single-molecule analysis of long non-coding RNA
Pai, K. R.; Martin, A. M.; Kadrmas, M.; Widom, J. R.
Incorporating locked nucleic acid residues and morpholinos into probes stabilizes binding kinetics and enhances structural discrimination, allowing for precise mapping of sequence accessibility without the confounding effects of altered ionic concentrations.
Multilayered regulation of GluK3 kainate receptors is mediated by Neto subunits and zinc
Vinnakota, Rajesh, Dawath, Bhavya K., Assaiya, Anshul, Bhar, Suparna, Kumar, Janesh
Structural and functional analyses demonstrate how these modulators cooperatively stabilize distinct conformational states to precisely control receptor gating and desensitization kinetics.
Muscle Diffraction at the Life Science X-ray Scattering Beamline
Nguyen, K.; Hessel, A. L.; Sadler, R. L.; Engels, N. M.; Delligatti, C. E.; Harris, S. P.; Yang, L.
High-throughput methodological advances and semi-automated data processing facilitate rapid analysis of sarcomeric protein organization and myopathies across diverse human and animal models.
The redox driven Na+-pumping mechanism in Vibrio cholerae NADH-quinone oxidoreductase relies on dynamic conformational changes
Ishikawa-Fukuda, Moe, Seki, Takehito, Kishikawa, Jun-ichi, Masuya, Takahiro, Okazaki, Kei-ichi, Kato, Takayuki, Barquera, Blanca, Miyoshi, Hideto, Murai, Masatoshi
Internal protein movements synchronize the release of chemical energy with the directional transport of ions to facilitate cellular energy conservation.
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions
Langstein-Skora, Iris, Schmid, Andrea, Huth, Frauke, Shabani, Drin, Spechtenhauser, Lorenz, Likhodeeva, Mariia, Kunert, Franziska, Metzner, Felix J., Emenecker, Ryan J., Richardson, Mary O., Aftab, Wasim, Götz, Maximilian J., Payer, Sarah K., Pietrantoni, Niccoló, Valka, Valentina, Ravichandran, Sakthi K., Bartke, Till, Hopfner, Karl-Peter, Gerland, Ulrich, Korber, Philipp, Holehouse, Alex S.
Contextual chemical features such as charge and hydrophobicity modulate the activity of linear binding motifs to dictate biological functionality.
Seeing the chemistry of biomolecular condensates: in situ mapping of composition and water content
Sabri, E.; Mangiarotti, A.; Schmitt, C.; Dimova, R.
Raman-based spectral phasor analysis reveals that biomolecular condensates consist primarily of bulk-like water and that their internal hydrophobicity is driven by an interplay between macromolecular architecture and water partitioning.
Protein-free membrane fusion: a refined view of the delicate fusogenic properties of calcium
Accorsi, M.; Ni Earchai, R.; Yandrapalli, N.; Pramanik, S.; Dimova, R.
High DOPE concentrations and mechanical tension enable giant unilamellar vesicles to achieve full fusion by providing the instability necessary for pore opening while maintaining sufficient structural integrity to prevent bursting.
Surface concavity enhancing ultrasonic transmission from air to liquid
Xiuxing Tang, Liang Zhang, Zherui Hou, Minghao Zhou, Yajun Jiang, Duyang Zang
Geometrical wave focusing at the curved meniscus overcomes the extreme acoustic impedance mismatch between media to facilitate efficient energy coupling for sensing and communication applications.
Conformational dynamics at the pre-miR-377 Dicer site governs selective small-molecule recognition
Manigrasso, J.; mestdach, E.; quaia, R.; Dankova, D.; Bood, M.; Lemurell, M.; Geschwindner, S.; Frolov, A.; Disney, M.; Hogner, a.; Chi, c. N.; La Sala, G.
U25 shuffling between two positions generates interconverting triple structures that the ligand C1 selectively captures to stabilize intermediate conformations and shift the RNA population away from processing-competent states.
Mapping Bidirectional Allosteric Communication in Arf GTPases
Edgar V. Peters, Tejaswi Koduru, Scott A. McCallum, Estella F. Yee, Jacqueline Cherfils, Catherine A. Royer
Residues in the C-terminal half of the protein regulate the nucleotide-dependent conformational switch by modulating access to a functional molten globule ensemble through a “back-to-front” pathway.
Long-range genomic loci stochastically assemble into combinatorial forms of chromosome skeleton
Zhang, J.; Wang, S.; Watkins, S. C.; Xing, J.
Multivalent binding at distributed nucleation centers organizes these 100 Mb structures into a stable, redundant framework that guides large-scale chromosome compaction and smaller-scale folding across various cell types.
Chromatin boundary permeability is controlled by CTCF conformational ensembles
Rudnizky, S.; Murray, P. J.; Sorensen, E. W.; Koenig, T. J. R.; Pangeni, S.; Merino-Urteaga, R.; Chhabra, H.; Caccianini, L.; Davidson, I. F.; Osorio-Valeriano, M.; Hook, P. W.; Meneses, P.; Hao, J.; Zarb, J. S.; Hatzakis, N. S.; Timp, W.; Farnung, L.; Vos, S. M.; Peters, J.-M.; Aksimentiev, A.; Ha, T.
Spontaneous zinc finger rearrangements integrate DNA sequence and epigenetic marks to dictate the probabilistic stalling of cohesin, with PDS5A-mediated mechanical stabilization further reinforcing these directional boundaries.
When lipids embrace RNA: pH-driven dynamics and mechanisms of LNP-mediated siRNA delivery
Hossain, K. A.; Valerio, M.; Medina, P.; Souza, P. C. T.; Orozco, M.
Persistent electrostatic coupling between siRNA and locally protonated ionizable lipids within an inverted-hexagonal core stabilizes the cargo but restricts endosomal escape kinetics by hindering RNA release from the lipid scaffold.
A physics-informed data-driven framework for modeling hyperelastic materials with progressive damage and failure
Kshitiz Upadhyay
Gaussian Process Regression separately learns the intact material response and damage evolution while enforcing thermodynamic constraints and energetic consistency to ensure robust generalization across diverse loading modes from limited data.
Reentrance in a Hamiltonian flocking model
Letian Chen, Luke K. Davis
Kinetic frustration arising from strong spin-velocity coupling suppresses transverse diffusion to induce an arrested state, providing a conservative mechanism for the return to a homogeneous phase.
Spontaneous phase separation and pattern formation in a lyotropic nematic mixture
A. Bensabat, O. Skelton, J. Arlt, M. Bjelogrlic, D. Marenduzzo, G. Negro, T. N. Shendruk, T. A. Wood
Strong coupling between local density and orientational order triggers defect-mediated phase separation in chromonic mixtures, creating stable, self-assembled lamellar patterns where interfacial anchoring arrests the coalescence of isotropic droplets.
Fluctuation-Response Design Rules for Nonequilibrium Flows
Ying-Jen Yang, Ken A. Dill
A scalable path-entropy variational formalism enables the modulation of local transition rates to reach global dynamical objectives, distinguishing between timing- and branching-dominated fluctuations in complex biological networks.
Abnormal calcium release and delayed afterdepolarizations: A comparison of two mathematical models for human ventricular myocytes
Navneet Roshan, Rahul Pandit
SERCA pump activity, RyR leakage, and structural compartmentalization determine the morphological classification of these triggers and their transition into arrhythmogenic premature ventricular complexes across multiscale simulations.
Shear-Rate Dependent Surface Tension of Glass-Forming Fluids
Linnea Heitmeier and Thomas Voigtmann
Standard pressure anisotropy calculations fail to accurately quantify surface tension when non-Newtonian rheology is present within a shearing interface.
Improved diffusive approximation of Markov jump processes close to equilibrium
David Roberts, Trevor McCourt, Geremia Massarelli, Jeremy Rothschild, and Nahuel Freitas
A refined mathematical framework captures the large fluctuations and rare-event probabilities that standard methods typically fail to represent.
Entropy Production in Non-Gaussian Active Matter: A Unified Fluctuation Theorem and Deep Learning Framework
Yuanfei Huang, Chengyu Liu, Bing Miao, and Xiang Zhou
The probability-flow equivalence technique provides a rigorous basis for decomposition formulas that allow physics-informed neural networks to quantify dissipation directly from observed stochastic trajectories.
Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators
Panagiotis Antoniadis, Beatrice Pavesi, Simon Olsson, Ole Winther
PLaTITO achieves state-of-the-art performance on equilibrium sampling for out-of-distribution protein systems by leveraging coarse-grained representations and auxiliary conditioning signals like temperature and structural embeddings to enhance data efficiency.
Synaptic transmission: Munc13 assembles onto PI(4,5)P2-rich domains into trimers that cooperate to capture vesicles
Feng Li, Abhijith Radhakrishnan, Sudhanshu Gautam, Gabriel Diaz, Ramalingam Venkat Kalyana Sundaram, Jeff Coleman, Hong Zheng, Kirill Grushin, Matthieu Chavent, James E. Rothman, Frederic Pincet
Upright protein complexes transition into lateral hexameric structures through a diacylglycerol-stabilized conformational switch to finalize the priming process.
Defect structures and transitions in active nematic membranes
Yuki Hirota, Nariya Uchida
A continuous transition from curvature-mediated defect trapping to active turbulence occurs at a threshold scaling with the square of the coupling constant over bending stiffness, while director-field walls drive characteristic wave-like membrane deformations across both regimes.
Role of atomic force microscopy in characterization of heterotypic cancer spheroids and their interaction with microplastic particles
Kolesnik, Tatjana, Öhlinger, Kristin, Absenger-Novak, Markus, Meindl, Claudia, Fröhlich, Eleonore
Young’s modulus measurements reveal mechanical variations that correlate with cell doubling times and structural composition, providing a distinct characterization parameter that remains independent of observed microplastic internalization levels.
DNA binding drives phase separation of the Gcn4 bZIP domain and reveals its conformational ensemble in the diluted and condensate phases
Calio’, A.; Turbant, F.; Tully, M.; Sharma, S.; Schifino, G.; Parracino, M. A.; Peters, J.; Pastore, A.
A previously unrecognized kinked helical conformation within the bZIP domain persists across both coexisting phases, demonstrating that DNA-binding motifs can autonomously drive condensate formation without the need for activation domains.
Correlative scanning electron and super-resolution structured illumination microscopy
Hamilton, J. R.; Levis, S.; Hagen, G. M.
NanoSuit chemical treatment preserves mammalian testis samples to facilitate high-resolution validation of findings obtained through initial fluorescence-based imaging.
Investigation of Regulation and Binding Patterns of the Human Cathelicidin Peptide LL-37 in Complexation with Nucleic Acids, and its Impact on Neutrophil Extracellular Traps
Zielke, C.; Rad, B.; Nielsen, J.; Li, J.; Pimcharoen, S.; Sawant, M.; Lin, J.; Thiam, H. R.; Barron, A.
LL-37 expression levels dictate the clearance of neutrophil extracellular traps by governing the condensation of DNA into concentration-dependent architectures through interactions mediated by the peptide’s amphipathic \(\alpha\)-helical structure.
Intracellular TDP-43 amyloid nucleates from arrested nascent condensates
Wu, J.; Venkatesan, S.; Jensen, J.; Miller, T.; Lange, J. J.; McKinney, S. A.; Halldorsson, E.; Yu, Z.; Babu, V. M.; Sancho Salazar, L.; Haug, J.; Unruh, J.; Halfmann, R.
Templating by heterologous proteins triggers amyloid formation within these clusters, while molecular interactions or stress conditions that promote more mature condensation paradoxically prevent the pathological transition.
Probing and modeling cell-cell communication in 2D biomimetic tissues
Cécile Marie Vincent, Sapna Ravindran, Alexis M Prevost, Lea-Laetitia Pontani, Olivier Bénichou, Elie Wandersman
Gap junction-mediated transport across droplet interfaces reveals how the spatial connectivity of synthetic cell assemblies regulates the propagation of molecular signals.
Towards Understanding the Drivers of Antibody-Antigen Binding
Omeir Khan, Marcus Kankkunen, Michel Shaker, Henry Chow, Nikolas Moustakas, Siri Allegra-Berger, Maria Lazou, Sandor Vajda, Diane Joseph-McCarthy
FTMap characterization of binding hot spots across 50 complexes identifies specific protein surface regions that contribute disproportionately to molecular recognition, offering insights to improve rational paratope design and epitope prediction.
Molecular concentration field design using closed-form steady-state solutions
Dong Woo Kim, Alison Grinthal, Rebecca Schulman
Synthetic biological systems and programmable soft materials achieve complex functional organization through the application of precise spatial control.
Sub-Millivolt Voltage Imaging Reveals Gap Junction-Mediated Bioelectric Contact Inhibition
Ruehl, P.; Hussein, R.; Reuter, S.; Frahnert, K.; Nair, A. G.; Mrowka, R.; Schoenherr, R.; Heinemann, S. H.
A \(1/n\) scaling law of electrical volatility governs the transition from stochastic single-cell noise to collective stability, providing a biophysical mechanism for maintaining homeostasis that is disrupted when intercellular coupling is lost in cancer.
Planar arrangement of bacteriochlorophyll c aggregates in chlorosomes of Chloroflexus aurantiacus
Tomáš Bílý, David Kaftan, Rebecca F. Thompson, David Řeha, Jakub Pšenčík, Roman Tuma
Cryo-electron tomography reveals a long-range organization of self-assembling pigments that follows a planar lamellar model.
Soap Film Drainage Using a Centrifugal Thin Film Balance
Antoine Monier, Kévin Gutierrez, Cyrille Claudet, Franck Celestini, Christophe Brouzet, Christophe Raufaste
Effective gravity determines the stability and thinning dynamics of liquid layers to clarify the mechanisms of aerosol production from surface bubbles and their impact on climate processes.
Telomeric G-quadruplex intermediates unveiled by complex Markov network analysis
Sáinz-Agost, A., Falo, F., Fiasconaro, A.
All-atom simulations integrated with dimensionality reduction and Stochastic Steepest Descent characterize the hierarchical organization of structural basins and transition pathways that define the denaturation process.
FidlTrack: high-fidelity structure-aware single particle tracking resolves intracellular molecular motion in organelles sensing APP processing
Parutto, Pierre, Yuan, Yutong, Davì, Valentina, Pons-Lanau, Roger, Ebeling, Svenja, Gupta, Karnika, Bottanelli, Francesca, Garcia-Parajo, Maria F., Campelo, Felix, Kaminski, Clemens F., Chambers, Joseph E., Nixon-Abell, Jonathon, Avezov, Edward
Overcoming tracking errors caused by molecular crowding reveals the hidden kinetics of secretory sorting and nanobody binding within dense cellular environments.
Theory for enzymatic degradation of semi-crystalline polymer particles
Michael Schindler, Hernan Garate, Ludwik Leibler
A geometric model utilizing extended Voronoi/Delaunay tessellation predicts degradation kinetics by quantifying the competition between surface erosion and internal spherulite growth, revealing how impurities and nucleating agents hinder the depolymerization of plastic waste.
A dialog between cell adhesion and topology at the core of morphogenesis
Adrian Aguirre-Tamaral, Elisa Floris, Bernat Corominas-Murtra
Local, pair-wise cell-cell contact properties dictate the global geometric and material characteristics of embryonic tissues by shaping their overall topological organization.
Dynamic Bidirectional Coupling of Membrane Morphology and Rod Organization in Flexible Vesicles
Stijn van der Ham, André F. V. Matias, Marjolein Dijkstra, Hanumantha Rao Vutukuri
Packing-dependent transitions between nematic and smectic-like rod arrangements dictate the shift from elongated to plate-like vesicle geometries, allowing for reversible control of self-assembly through adjustments in membrane surface area and volume.
Inherent Leakage of Hydrophobic Gating in BK Channels
Zhiguang Jia and Jianhan Chen
A vapor barrier generated by hydrophobic dewetting of the inner pore in the deactivated state inherently facilitates the channel’s intrinsic opening.
Localization and frequency resolution in antennal hearing of insects
Justin Faber, Alexandros C. Alampounti, Marcos Georgiades, Joerg T. Albert, and Dolores Bozovic
Johnston’s organ utilizes active mechanical amplification and directional sensitivity to particle velocity to bypass the physical constraints of small interaural distances.
Information thermodynamics of cellular ion pumps
Julián D. Jiménez-Paz, Matthew P. Leighton, and David A. Sivak
Bipartite stochastic thermodynamics quantifies the energetic coupling between conformational changes and substrate translocation to determine the efficiency and entropy production of active transport proteins.
Anomalous Diffusion in Driven Electrolytes due to Hydrodynamic Fluctuations
Ramin Golestanian
A self-consistent field-theory framework reveals diverse scaling behaviors and transitions between two distinct regimes of tracer dynamics across all dimensions.
Determining the Chemical Potential via Universal Density Functional Learning
Florian Sammüller and Matthias Schmidt
Inhomogeneous classical fluid datasets facilitate the simultaneous extraction of equilibrium values across multiple simulation environments.
Modeling bacterial flow field with regularized singularities
Yaochen Yang, Daiki Matsunaga, Da Wei, Fanlong Meng
An anisotropically regularized stresslet combined with an isotropically regularized source dipole accurately captures both near-field and far-field fluid dynamics around swimming bacteria in free space and confined environments.
Allosteric coupling between PIP2 and Ca2+ binding sites gates TMEM16A channels
Jie Xu, Ana Santa-Cruz, Aishwarya Chandrashekar, Takeharu Kawano, R. Charles Kissell, Mehreen Zaka, Zhe Zhang, Meng Cui, Diomedes E. Logothetis, Leigh D. Plant
The α4 helix coordinates an electrostatic network where headgroup phosphates communicate ion occupancy to the pore while acyl chains stabilize the resulting open conformation through hydrophobic interactions.
Confinement and shear effects on the rotational diffusion of a minimal virus-inspired colloidal particle
Karen Gonzales-Flores, Ramón Castañeda-Priego, Francisco Alarcón
Increased peplomer density suppresses rotational motion primarily at high shear amplitudes, while the complex interplay between hydrodynamic forcing and thermal fluctuations at intermediate regimes dictates how these particles align with potential targets.
Strong Viscoelastic Glycerol Solutions Formed from Phenylalanine-Based Amine Oxide Surfactants
Zutian Bi, Ying Ge, Zhao Chen, Xiaomei Pei, Zhenggang Cui, Binglei Song
Alkyl phenylalanine amide oxides overcome typically weak solvophobic interactions in nonaqueous media to facilitate the assembly of giant aggregates and robust rheological networks.
Oxygen depletion in biomolecular condensates is dominated by macromolecular density
Garg, Ankush, Brasnett, Christopher, Marrink, Siewert J., Koren, Klaus, Kjaergaard, Magnus
High local concentrations of macromolecules physically displace oxygen from the droplet interior, allowing condensates to function as regulatory hubs for oxygen-sensitive biochemistry.
Developing a fluorescent derivative of GagPol as a tool for live-cell imaging of HIV-1 assembly
Gialdini, I.; Rat, V.; Anders-Oesswein, M.; Mueller, B.; Lamb, D. C.
Single- and double-labeled functional variants enable the quantification of relative polyprotein concentrations and intermolecular interactions at the single-cell level when paired with raster image cross-correlation spectroscopy.
Mass-specific single molecule pull-down from complex mixtures with bilayer-assisted mass photometry
Kushwah, M. S.; van Wee, R.; Thiele, J. C.; Foley, E. D. B.; Benesch, J. L.; Kukura, P.
PEG-passivated surfaces enable the quantification of protein oligomeric states and binding affinities at sub-nanomolar concentrations while maintaining high mass resolution and accuracy.
Positive cooperativity between RAS-binding and cysteine-rich domains regulates RAF membrane binding kinetics via lateral rebinding
Jimenez Salinas, Andres, Tevdorashvili, Kesaria, Grim, Julian, Morales, Alexia, Chakhrakia, Ani, Kwang Lee, Young
Quantitative bottom-up reconstitution reveals that synergistic interactions between lipids and protein domains provide the mechanistic foundation for RAF activation at the membrane.
Zoology of collective patterns modulated by non-reciprocal, long-range interactions
Edgardo Brigatti, Fernando Peruani
Vision-based angular constraints determine the specific spatial organization and transitions between different collective phases in active particle ensembles.
Mid-infrared light produces anti-ageing effects through resonant absorption by living organisms
Shao, C.; Peng, D.; Zhao, Y.; Shu, Y.; Zhuang, S.; Huang, Q.; Song, B.
Low-intensity 34-THz radiation extends Caenorhabditis elegans lifespan by 60% by targeting the vibrational modes of molecular phosphate groups to enhance mitochondrial bioenergetics and transcriptional efficiency.
Retina Microrheology via Oscillatory Atomic Force Microscopy
Connor D Amelung, Colter E Oroke, Lucas Ramirez, Sharon Gerecht
Layer-specific storage and loss moduli characterize a complex mechanical landscape essential for understanding tissue development and disease progression.
Modular DNA nanosensors enable state-aware multiplexed single-molecule mass photometry in complex media
Helmi, S.; Asor, R.; Miller, M.; Thiele, J. C.; Wu, D.; van Wee, R.; Song, S.; Zouboulis, K. C.; Benesch, J. L.; Robinson, C. V.; Kukura, P.
Supported lipid bilayer-anchored DNA scaffolds resolve protein oligomers and proteoforms by utilizing mobility as an orthogonal identifier to eliminate the need for labeling, washing, or sample enrichment.
Single-cell analysis of sterol-induced Ca2+ signaling in human astrocytes by dynamic mode decomposition
Larsen, M. P. W.; Lauritsen, L.; Jensen, R.; Zimmermann, R.; Wuestner, D.
Active oscillatory states driven by cholesterol are suppressed by oxysterol pretreatment or acute depletion, demonstrating a generalizable framework for decomposing and classifying complex spatiotemporal cellular signals.
Critical fluctuations of elastic moduli in jammed solids
Kumpei Shiraishi, Hideyuki Mizuno
Sample-to-sample variations in shear stiffness exhibit universal scaling regardless of the interparticle potential, contrasting with the potential-dependent scaling observed in the average response.
From Lipid Dynamics to Precision Predictions: A New Approach Method for Precision Modeling of Phosphoinositide Signaling
Hernandez-Hernandez, G.; Tieu, M.; Yang, P.-C.; Vivas, O.; Lewis, T. J.; Santana, L. F.; Clancy, C. E.
Sensitivity-guided inverse modeling and neural networks translate cell-specific lipid measurements into mechanistic simulations that predict signaling resilience or failure based on basal phosphoinositide composition.
Nonstop nanometric resolution of randomly moving point scatterers with focused light
Hensel, T. A.; Schwarz, O. L.; Karrasch, T.; Goepfrich, K.; Hell, S. W.
Simultaneous monitoring of multiple fluorophores via MINFLUX captures sub-10 nanometer biomolecular conformational transitions with millisecond temporal resolution.
Scaling of poroelastic coarsening and elastic arrest in crosslinked gels
Samuel A. Safran
Interfacial tension drives solvent domains to coarsen until long-ranged elastic stresses halt the process at a length scale determined by the shear modulus, following \(G^{-1/2}\) scaling for melt-like gels and \(G^{-1/3}\) for mesh-limited networks.
Denoise Stepwise Signals by Diffusion Model Based Approach
Xingdi Tong, Chenyu Wen
SSDM integrates a multi-scale convolutional network and attention mechanism within a diffusion framework to accurately reconstruct signal levels and transition points across diverse signal-to-noise ratios.
Cell strain-stiffening drives cell breakout from embedded spheroids
Shabeeb Ameen, Kyungeun Kim, Ligesh Theeyancheri, Minh Thanh, Mingming Wu, Alison E. Patteson, J. M. Schwarz, Tao Zhang
Localized stress amplification in elongated boundary cells, integrated with specific adhesion configurations, dictates the mechanical transition between individual escape and multi-cell collective streaming into the fibrous matrix.
Coarse grained modeling of self assembled DNA 3D structure using pragmatic soft ellipsoid contact potential
Abhirup Das, Jayashree Saha
Base-pairing, bending, and solvent effects are integrated into the framework to accurately reproduce experimental melting curves and hybridization phase transitions.
Electrochemical response of biological membranes to localized currents and external electric fields
Joshua B. Fernandes, Hyeongjoo Row, Kranthi K. Mandadapu, and Karthik Shekhar
Interplay between nanometer-scale interfacial layers and macroscopic domain geometries governs the spatial distribution of ions and potentials during transmembrane transport.
Predicting statistics of gene translocation events: Role of chromatin compaction and double-strand DNA break
Anirudh Jairam, Shuvadip Dutta, Sangram Kadam, Kiran Kumari, and Ranjith Padinhateeri
Spatial proximity and localized damage frequencies dictate the statistical distribution of structural rearrangements across the genome.
Spatiotemporal Patterns of Active Epigenetic Turnover
Fabrizio Olmeda, Misha Gupta, Onurcan Bektas, and Steffen Rulands
Chromatin-mediated coupling between methylation and demethylation cycles drives the formation of phase-locked domains of synchronized activity that are stabilized by genomic heterogeneity.
Interplay of generation time and spatial structure in epidemic dynamics and the reliability of reproduction ratio estimates
Claudio Ascione and Eugenio Valdano
Population-level estimates of \(R\) often miscalculate transmission potential by neglecting the dampening effects of local network saturation and the specific timing of secondary cases.
Shear-Induced Collective Shape Oscillations in Dense Soft Suspensions
Ioannis Hadjifrangiskou, Rahil N. Valani, Diogo E. P. Pinto
Repeated T1 neighbor exchanges within a shear-ordered lattice drive cyclic particle deformations through a feedback loop between topology and shape, establishing a generic mechanism for self-sustained oscillations that can be modeled by the evolution of the lattice angle.
Exact Stationary State of a \(d\)-dimensional Run-and-Tumble Particle in a Harmonic Potential
Mathis Guéneau, Satya N. Majumdar, Grégory Schehr
Stick-breaking processes provide closed-form solutions for the steady-state distributions across multiple dimensions, identifying a persistence-driven shape transition at the turning surface and its regularization by thermal noise.
Mixing properties of bi-disperse ellipsoid assemblies: Mean-field behaviour in a granular matter experiment
F. M. Schaller, H. Punzmann, G. E. Schröder-Turk, M. Saadatfar
Local packing fraction distributions within these jammed assemblies behave as an uncorrelated mixture of two mono-disperse systems, regardless of the compaction protocol employed.
Binding Paths: Describing Small Molecule Interactions with Disordered Proteins via a Markov State Model
Louet, A. A. B.; Hummer, G.; Vendruscolo, M.
Stochastic trajectories of ligand diffusion reveal targetable hotspots and quantify binding affinities for protein surfaces that lack traditional, well-defined pockets.
Combining experiments and simulations to study the impact of multiple phosphorylations at the AT8 epitope of the Tau protein
Lohberger, C.; Marien, J.; Bridot, C.; Prevost, C.; Allegro, D.; Tatoni, M.; Smet-Nocca, C.; Sacquin-Mora, S.; Barbier, P.; Cantrelle, F. X.; Martinho, M.; Belle, V.; Boll, E.
Local stiffening and long-range contact losses scale with the degree of phosphorylation, despite the protein’s global size and dynamics remaining largely unaffected.
Molecular mechanisms of flotillin complexes in organizing membrane microdomains
Lu, Ming-Ao, Qian, Yunwen, Ma, Liangwen, Hong, Jinzhi, Li, Xiaopeng, Yu, Li, Guo, Qiang, Gao, Ning
Human flotillin complexes assemble into dome-shaped oligomers that function as structural scaffolds for membrane organization.
Optically detected and radio wave-controlled spin chemistry in flavoproteins
Meng, K.; Nie, L.; Berger, J.; von Grafenstein, N. R.; Einholz, C.; Weber, S.; Essen, L.-O.; Rizzato, R.; Schleicher, E.; Bucher, D. B.
Genetically encodable proteins like iLOV and cryptochrome provide a high-contrast platform for widefield magnetic field sensing and radiofrequency-driven spatial modulation of photoluminescence.
Wash-Free Multi-Target Super-Resolution Microscopy with Photocaged DNA Labels
Kaltenschnee, N.; Dietz, M. S.; Kessler, L. F.; Li, Y.; Kaufmann, J.; Heckel, A.; Heilemann, M.
Light-modulated DNA hybridization via photocaging groups enables sequential imaging of multiple cellular features without the physical disruptions of manual label exchange, preserving structural accuracy at the nanometer scale.
Mouse sensorimotor cortex reflects complex kinematic details during reaching and grasping
mattkaufman@uchicago.edu (Harrison A Grier), mattkaufman@uchicago.edu (Matthew T Kaufman), mattkaufman@uchicago.edu (Sohrab Salimian)
M1 and S1 regions represent low-level joint kinematics with equivalent fidelity but diverge in the temporal modulation of high-level target-specific signals.
Quantifying optical sectioning in reflection microscopy with patterned illumination
Ventalon, C.; Nidriche, A.; Debarre, D.
Analytical models and experimental validations for line confocal and structured illumination techniques establish the relationship between system parameters and image quality, providing a framework for selecting the most effective sectioning strategy in reflection interference contrast microscopy.
In vivo autofluorescence lifetime imaging of spatial metabolic heterogeneities and learning-induced changes in the Drosophila mushroom body
pierre-yves.placais@espci.fr (Auguste Genovesio), pierre-yves.placais@espci.fr (Chiara Stringari), pierre-yves.placais@espci.fr (Mingyi Zhou), pierre-yves.placais@espci.fr (Philémon Roussel), pierre-yves.placais@espci.fr (Pierre-Yves Plaçais), pierre-yves.placais@espci.fr (Thomas Preat)
Neuropil and cortex areas exhibit distinct metabolic signatures that vary among specific neuron subtypes and undergo subtle, physiology-driven shifts during the formation of associative memories.
Single-Molecule Fluorescence and Crosslinking Reveal Ligand-Gated Toc34 Oligomerization Dynamics
Sree Kavya Penneru, Sriram Tiruvadi-Krishnan, Rajan Lamichhane, Barry D. Bruce
Preprotein recognition and translocation are coordinated by specific nucleotide and substrate interactions that modulate the reversible assembly of the translocon receptor.
Topological Investigation of Protein Folding and Intrinsic Disorder
Hammond, M. E.; Akulov, V.; van Noort, J.; Zwep, L. B.; Mashaghi, A.
Circuit topology quantifies intra-chain contact arrangements to differentiate between ordered and disordered states while predicting chain compaction, kinetics, and thermodynamics.
Accessibility of the unstructured α-tubulin C-terminal tail is controlled by microtubule lattice conformation
oryoma@umich.edu (David Sept), oryoma@umich.edu (Ezekiel C Thomas), oryoma@umich.edu (Kristen J Verhey), oryoma@umich.edu (Lynne Blasius), oryoma@umich.edu (Michael A Cianfrocco), oryoma@umich.edu (Morgan E DeSantis), oryoma@umich.edu (Morgan L Pimm), oryoma@umich.edu (Patrick DeLear), oryoma@umich.edu (Ryoma Ohi), oryoma@umich.edu (Ryota Horiuchi), oryoma@umich.edu (Takashi Hotta), oryoma@umich.edu (Takumi Higaki), oryoma@umich.edu (Yang Yue)
Transient interactions with the tubulin dimer body sequester the α-tubulin C-terminal tail until specific nucleotide states, drugs, or microtubule-associated proteins induce an expanded lattice conformation that promotes its exposure.
Coordinated control of both microtubule ends regulates mitotic spindle length
Fiorenza, S. A.; Cheeran, S.; Doria, E.; Tolic, I. M.; Meraldi, P.; Pavin, N.
Synchronized regulation of microtubule ends enables independent control of spindle length and poleward flux, reconciling previously contradictory findings regarding their mechanical relationship.
A kinetic proofreading argument to understand the role of H3K9-trimethylation in phase-separated chromatin states
Ralf Blossey, Helmut Schiessel
Inheritance of epigenetic heterochromatin marks across cell cycles is driven by polymer-assisted condensation creating a specialized environment for the high-fidelity restoration of histone methylation.
DEER of Singly Labelled Proteins to Evaluate Supramolecular Packing of Amyloid Fibrils
Tsay, K.; Equbal, A.; Li, Y.; Tsui, T.; Han, S.; Fichou, Y.
Background signal dimensionality distinguishes between mispacked heparin-induced tau fibrils and highly ordered seeded assemblies while tracking the evolution of aggregation intermediates.
A polymer physics model of the interphase cell nucleus for radiobiological simulations
Zhao, Man, Huang, Guomin, Xu, Zi, Huang, Xiaoyan, Liang, Ying
Multi-stage relaxation and distance-dependent DNA rejoining algorithms replicate complex chromatin architectures to predict radiation-induced chromosome aberrations with significantly improved accuracy across varying linear energy transfer levels.
Channel gating in bacteriorhodopsin-like channelrhodopsins with contrasting K+ and Na+ selectivity
Oleg A. Sineshchekov, Elena G. Govorunova, Hai Li, Yumei Wang, John L. Spudich
HcKCR1 and HcCCR utilize a specific gating mechanism previously proposed for cryptophyte bacteriorhodopsin-like cation channelrhodopsins.
The protocadherin 15 – LHFPL5 tip link complex is a heterotetrameric assembly in hair cell stereocilia
Sarah Clark, Jaba Mitra, Johannes Elferich, April Goehring, Jingpeng Ge, Taekjip Ha, Eric Gouaux
The molecular organization of this mechanosensory transduction complex is established despite its extremely low abundance in hair cells, providing a definitive model for the protein machinery of hearing and balance.
Antibody Fc receptor CD16a mediates natural killer cell activation via mechanotransduction of piconewton forces
Ma, R.; Garcia, K. C.; Cui, B.; Covert, M. W.
Actin foci formation and the phosphorylation of adaptors Cas-L and LAT integrate biochemical and biophysical signals to reshape cytoskeletal dynamics and downstream signaling pathways.
Photoinduced proton transfer in differently structured water: an EPR approach to solving a classic problem
Barbon, Antonio, Savitsky, Anton, Grigoriev, Igor A., Reznikov, Vladimir A., Kirilyuk, Igor A., Lushchekina, Sofya, Moroz, Ilia B., Eliash, Tamar, Friedman, Noga, Sheves, Mordehai, Carmieli, Raanan, Weiner, Lev
Chaotropic solutes such as guanidine hydrochloride and urea significantly inhibit hydrogen ion migration, enabling a sub-nanosecond detection method for quantifying kinetics in complex environments like ice and proteins.
From Connectivity to Rupture: A Coarse-Grained Stochastic Network Dynamics Approach to Polymer Network Mechanics
Shaswat Mohanty, Wei Cai
Network-level evolution rules efficiently model the transition from force localization to catastrophic failure while showing that bond rupture kinetics are independent of polymer chain length.
Bidirectional allosteric ligand regulation in a central glycolytic enzyme
Sundberg, B.; Lu, C.; Wells, M. L.; Weber, K. C.; Gong, Z.; Glasgow, A.
Activator and inhibitor binding to a shared allosteric pocket regulates Escherichia coli phosphofructokinase-1 by differentially reweighting its conformational ensemble toward either catalytically preorganized or inactive, apo-like substates.
Results of a large scale study of the binding of 50 type IIinhibitors to 348 kinases: The role of protein reorganization
Vardanyan, V. H.; Haldane, A.; Hwang, H.; Coskun, D.; Lihan, M.; Miller, E. B.; Friesner, R. A.; Levy, R. M.
Protein reorganization free energies estimated through Potts statistical models function as primary determinants of binding selectivity and yield more accurate predictions for novel inhibitors than current sequence-based machine learning approaches.
Electrostatic properties of disordered regions control transcription factor search and pioneer activity
Sakong, Sim, Fierz, Beat, Suter, David M.
Positive charges in the segments flanking the DNA-binding domain accelerate search kinetics on both free and chromatinized DNA, accounting for the varying strengths of pioneer factors.
Learning millisecond protein dynamics from what is missing in NMR spectra
Wayment-Steele, H. K.; El Nesr, G.; Hettiarachchi, R.; Ojoawo, A. M.; Kariyawasam, H.; Ovchinnikov, S.; Kern, D.
Dyna-1 employs the ESM-3 language model to identify evolutionarily conserved motions essential for catalysis and ligand binding by interpreting missing chemical shift assignments as signatures of conformational exchange.
Dynamical buffering of reconfiguration dynamics in intrinsically disordered proteins
Ivanovic, M. T.; Holla, A.; Nüesch, M. F.; von Roten, V.; Schuler, B.; Best, R. B.
Opposing changes in end-to-end distance distributions and intrachain diffusion coefficients cancel each other out to maintain nearly constant reconfiguration times across sequences of varying compactness.
The kinetics of ribonucleoprotein granules
Li, Y.; Li, X.; Xu, M.; Qi, Z.
SMART, a novel single-molecule assay, and a two-state mathematical model reveal that this assembly is a pathway-dependent, non-equilibrium process governed by multivalent interaction timescales and quantifiable free-energy landscapes.
Single-nanoparticle electrophoretic mobility determination and trapping using active-feedback 3D tracking
Johnson, A.; Welsher, K.
Sub-30 electron charge precision and simultaneous size determination facilitate the characterization of heterogeneous populations in complex biological environments without the need for microfluidic devices.
A proton transfer mechanism in the malaria parasite lactate/H+ symporter reveals a channel-like transporter without conformational changes
Wallis, C.; Gregory, K. P.; Fairweather, S. J.; van Dooren, G. G.; Lehane, A. M.; Corry, B.
Histidine 230 functions as a chemical gate that converts anionic substrates into neutral molecules for release, enabling the protein to switch between transporter and channel modes within a static pathway.