Feb 16 26
Featured Papers
A molecular and spatial resource defining tubulin isotype organization during corneal development
Raneesh Ramarapu, William R Stoehr, Mia Miesen, Sarah Border, Sara Thomasy, Crystal D. Rogers
Highly conserved tubulin isotypes display dynamic spatial redistribution across apico-basal and central-peripheral axes, with TUBA5/TUBA4A specifically localized to migratory stromal progenitors and the maturing endothelium.
Agouti integrates environmental cues to regulate paternal behaviour
Forrest Dylan Rogers, Sehee Kim, Sarah A. Mereby, Anna M. Kasper, Anastasios B. Callanan, Ricardo Mallarino, Catherine Jensen Peña
Hypothalamic expression of this signaling molecule modulates the melanocortin system to increase the duration of caregiving tasks such as huddling and grooming.
Evaporation-Induced Pattern Formation and Wetting in Active Microtubule-Kinesin Droplets
Vahid Nasirimarekani, Mehrana R. Nejad, Olinka Ramírez-Soto, Susan Ali, Stefan Karpitschka, L. Mahadevan, Isabella Guido
Extensile stresses and evaporation-driven flows cooperate to govern non-monotonic contact-line dynamics and radial biopolymer organization within the sessile network.
Optimal bioelectric control accelerates collective wound healing
Yodh, J. S.; Lin, Y.; Sinha, S.; Krishnan, V.; Mahadevan, L.; Cohen, D. J.
Spatiotemporally patterned electric fields leverage cell-cell mechanical adhesion and biophysics-informed timing to prevent cellular jamming and significantly enhance the speed of collective migration during the closure of circular wounds.
More Papers
Quantifying 3D Live-Cell Membrane Dynamics Using Dynamic Metal-Induced Energy Transfer Spectroscopy (dynaMIET)
Gallea, J. I.; Karedla, N.; Wang, D.; Enderlein, J.; Chen, T.
Integrating fluorescence correlation spectroscopy with nanometer-sensitive energy transfer enables the concurrent measurement of lateral molecular diffusion and vertical membrane undulations across various cellular organelles with microsecond temporal resolution.
Active loop extrusion modulates the mechanical response of chromatin under tension
Hossein Salari and Daniel Jost
Motor stalling kinetics determine the density and size of loops, thereby dictating the structural transitions and effective stiffness of the fiber.
Critical phase transition in bee movement dynamics can be modeled using a two-dimensional cellular automaton
Ivan Shpurov and Tom Froese
Simple local interaction rules within the simulation generate the emergent long-range spatial and temporal correlations observed in biological honeybee clusters near their critical point.
Intrinsic Plasticity Underlies the Malleability of Neural Network Heterogeneity
Daniel Trotter, Taufik Valiante, and Jeremie Lefebvre
Variations in synaptic input interact with neuronal excitability to determine the distribution of firing patterns across a recurrent population.
Mathematical Modeling of AA Amyloidosis: Coupling SAA-HDL Binding Dynamics with Path-Dependent Renal Aging
Kuznetsov, A. V.
Cumulative damage from cytotoxic oligomers and architectural disruption by fibrils creates an irreversible functional deficit determined by the unique duration and severity of a patient’s prior inflammatory episodes.
A predictive mechanochemical modeling framework for the deformation and remodeling of the nuclear lamina
Francis, E. A.; Sarikhani, E.; Naghsh-Nilchi, H.; Jahed, Z.; Rangamani, P.
Actin cap-mediated compression on nanopillar substrates regulates YAP/TAZ nuclear localization and demonstrates that reduced lamin A/C expression significantly increases the susceptibility of the nuclear envelope to rupture under specific topographical loads.
Heterogeneity in cilia patterning enables multiple flow functions within a single cell
Laan, D. M.; Kourkoulou, A. M.; Ramirez-San-Juan, G. R.
Paramecium tetraurelia partitions its continuous ciliary array into a dense, high-frequency anterior region for feeding and a sparser, slower-beating region for locomotion.
Chronotype asymmetry arises from stochastic sleep homeostasis under circadian entrainment
Nguyen, N. T.; Truong, V. H.; Myung, J.
Stochastic variance in sleep pressure build-up near the limits of physiological entrainment transforms left-skewed circadian period distributions into the right-skewed distributions observed in behavioral chronotypes.
Magnetic sensitivity of cryptochrome 4a in domesticated quail with migratory origins
Bartoelke, R.; Henbest, K. B.; Schmidt, J.; Kasahara, T.; Cubbin, D. R.; Gravell, J.; Bassetto, M.; Dautaj, G.; Pitcher, T. L.; Murton, P. D. F.; Saberamoli, G.; Forst, J. J.; Khazani, M.; Apte, S.; Olavesen, C.; Hayward, H.; Pare-Labrosse, O.; Antill, L. M.; Xu, J.; Hore, P. J.; Timmel, C. R.; Mackenzie, S. R.; Mouritsen, H.
Spectroscopic similarities to the European robin protein suggest the species could serve as a practical laboratory model for investigating the biophysical mechanisms of magnetoreception.
Fusion of lipid membranes: an alternative pathway
Jin, D.; Li, Z.; Roke, S.; Klein, J.
Biologically relevant transmembrane potentials drive protein-free membrane fusion by inducing electroporation that initiates the formation of intermembrane splayed lipids and peripore stalks.
Diurnal regulation of flagellar length and swimming speed in the red-tide raphidophyte Chattonella marina
Fujita, Y.; Kage, A.; Nishizaka, T.
Active modulation of beat frequency and intraflagellar transport-mediated flagellar length optimizes locomotive performance for vertical migration as a potential energy-saving strategy.
RNA Selectively Modulates Activity of Virulent Amyloid PSMα3 and Host Defense LL-37 via Phase Separation and Aggregation Dynamics
Rayan, B.; Barnea, E.; Indig, R.; Pantoja, C. F.; Gayk, J.; Lupu-Haber, Y.; Upcher, A.; Argoetti, A.; Aunstrup Larsen, J.; Buell, A. K.; Zweckstetter, M.; Landau, M.
RNA-driven phase transitions and aggregation pathways selectively diminish the human cytotoxicity of host-defense peptides while simultaneously stabilizing the functional potency and virulence of bacterial amyloid assemblies.
Protonation-dependent substrate release in a bacterial homolog of vesicular glutamate
Charles Plate, Natalia Dmitrieva, Samira Gholami, Mercedes Alfonso-Prieto, Sanket A. Deshmukh, Davide Mandelli, Paolo Carloni, Christoph Fahlke
DgoT co-transports two protons with galactonate, which binds in a deprotonated form but exits the transporter in either a protonated or deprotonated state.
Actomyosin active torques determine body plan handedness in C. elegans
Mallick, A.; Pfanzelter, J.; Pimpale, L. G.; Grill, S. W.
Inverting the direction of active cortical torques through Lifeact::mKate2 overexpression flips chiral flows and cell-contact patterns to produce situs inversus nematodes, establishing these torques as the instructive cue for organismal left-right symmetry breaking.
BEEP Learning: Multi-View Image Decomposition for Massively Multiplexed Biological Fluorescence Microscopy
Wang, R.; Hnin, T.; Feng, Y.; Valm, A. M.
A rank-one-tensor-based generalized linear model leverages emission, excitation, and bleaching signatures to accurately differentiate numerous fluorophores in high-noise imaging environments.
Synergistic Antibody Neutralization of SEB is Driven by Allosteric Transfer Entropy
Ganggang Bai, Yanhong Ge, Yuhong Su, Chuance Sun, Buyong Ma
Perturbations within the first and second solvation shells modulate global residue correlations between monoclonal antibodies 6D3 and 14G8 to facilitate toxin neutralization despite their distal binding sites.
A rapid, low-cost approach to solid immersion lens fabrication for enhanced resolution in optical microscopy
Rooney, L. M.; Christopher, J.; Foylan, S.; Butterworth, C.; Walker, L. D.; Copeland, L.; Coubrough, K.; The SOMC 2025 Consortium, ; Gould, G. W.; Cunningham, M. R.; Bauer, R.; McConnell, G.
UV-curable resin optics produced in a single step match the performance of traditional glass components while reducing material costs by five orders of magnitude and enabling successful implementation by non-expert users.
Dynamics of single cell-cell junctions as an indicator of cell state switch
Senthilazhagan, K.; Das, A.
Variations in the mechanosensitivity of E- and N-cadherin isoforms to cytoskeletal forces generate a mechanochemical landscape that determines the adhesive properties and emergence of aggressive hybrid epithelial-mesenchymal states.
Subdomains of Endophilin-NBAR Can Synergistically Drive Membrane Remodeling and Facilitate Controlled Membrane Scission
Beiter, J. R.; Tsai, F.-C.; Bassereau, P.; Voth, G. A.
Sensing and generating negative Gaussian curvature promotes the transition to hemifission during dynamic bud formation.
Light-Activated Self-thermophoretic Janus Nanopropellers
Henri Truong, Chiara Moretti, Lionel Buisson, Benjamin Abecassis, Eric Grelet
Gold-silica nanoparticles with a 33-nanometer radius overcome Brownian diffusion to enable directed, fuel-free transport in three-dimensional fluids through a reversible and tunable mechanism.
Tunable asymmetric swimming in biflagellate microswimmers
Benjamin J. Walker, Clément Moreau, Tommie L. Robinson, Zhaochen J. Xu, Daniel I. Goldman, Eamonn A. Gaffney, Kirsty Y. Wan
Constructive and destructive interactions between flagellar forces link beat frequency differences to path curvature, providing a general mechanism for steering in both biological organisms and bio-inspired robots.
Tracking the Brownian motion of DNA-functionalized magnetic nanoparticles for conformation analysis beyond the optical resolution limit
Christian Janzen, Fabian Schmid-Michels, Yahya Shubbak, Melanie Wegener, Karl-Josef Dietz, Inga Ennen, Rico Huhnstock, Arno Ehresmann, Andreas Hütten
Diffusion coefficient distributions resolve biomolecular contour lengths through an attenuated corona model that remains sensitive to structural scaling even in the presence of particle aggregation and polydispersity.
Spatio-temporal air flow properties in a 3D personalised model of the human lung
Jonathan Stéphano, Michaël Brunengo, Riccardo Di Dio, Thomas Laporte, Benjamin Mauroy
Coupled fluid-structure interaction simulations integrate nonlinear tissue mechanics with multi-scale airway geometry to quantify wall shear stress distributions and local ventilation variables.
Functional stability and recurrent spike-timing-dependent plasticity in rhythmogenesis
Gabi Socolovsky and Maoz Shamir
A compensatory feedback loop between activity and connectivity counteracts individual synaptic fluctuations to preserve the global temporal properties of the network.
Master equation approach to the \(n\)-coalescent problem
Bahram Houchmandzadeh
Exact analytical solutions for the time to the most recent common ancestor and tree topology are derived for finite-population models, such as Wright-Fisher and Moran, as an alternative to standard diffusion approximations.
How Molecular Motors’ Interaction Shapes Flagellar Beat and Its Fluctuations
F. Fanelli, A. Puglisi
Direct coupling between adjacent motors increases the oscillation period and induces bi-stable limit cycles characterized by abrupt activity avalanches and a non-monotonic response in the quality factor of stochastic fluctuations.
A hybrid compass mechanism combining radical pairs and magnetite crystals
P. J. Hore
Magnetic nanoparticles amplify the Earth’s magnetic field to provide nearby radical pairs with a significantly stronger signal, potentially increasing the sensitivity of the avian compass by 10 to 100 times.
Motor biases reflect a misalignment between visual and proprioceptive reference frames
shion07070017@gmail.com (Amber Jiang), shion07070017@gmail.com (Jonathan S Tsay), shion07070017@gmail.com (J Ryan Morehead), shion07070017@gmail.com (Richard B Ivry), shion07070017@gmail.com (Tianhe Wang)
Eye-centric and body-centric coordinate discrepancies drive systematic reaching errors across diverse motor tasks, surpassing traditional explanations based on biomechanical constraints or hand-sensing inaccuracies.
Asymmetry-induced distinct mechanisms and the transporting role of sodium in bacterial fluoride channel Fluc
Montalvillo Ortega, F.; Mills, K.; Torabifard, H.
Pore I and Pore II utilize distinct single-ion and multi-ion translocation mechanisms, respectively, while a central sodium ion functions as an oscillating cofactor to coordinate and accelerate ion movement.
Fuel-driven catalytic molecular templating
Mitra, M.; Mukherjee, R.; Jurinovic, K.; Ouldridge, T. E.
Active displacement of products from DNA templates overcomes product inhibition to enable enzyme-free turnover and sequence-specific information propagation.
Allosteric and energetic remodeling of a PDZ domain by protein domain extensions
Hidalgo-Carcedo, Cristina, Faure, Andre J., Martí-Aranda, Aina, Zarin, Taraneh, Lehner, Ben
Analysis of more than 7,000 mutations quantifies how small structural extensions reshape the energetic and allosteric landscape of the protein domain.
Single-Cell Parameter Inference Reveals Kinetic Heterogeneity in Synthetic Mammalian Gene Expression
Joshua Azukas, Rafał Krzysztoń, Christopher Helenek, Simon Carter, Stan Xiaogang Li, Gábor Balázsi, Helmut H. Strey
Transcriptional negative feedback mechanisms interact with natural mammalian gene expression processes to modulate both temporal and population-level noise.
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data
Daher, Ali, Trucu, Dumitru, Eftimie, Raluca
A computational pipeline integrating Approximate Bayesian Computation and gradient-based optimization with finite volume solvers quantifies TGF-beta signaling parameters and spatial concentration fields from human skin transcriptomics datasets.
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 structural states and predict essential physical properties such as chain compaction, folding kinetics, and thermodynamics.
Cumulative geomagnetic disturbances modulate global photosystem stoichiometry through temperature-dependent gating
Kitashov, A. V.
Terrestrial vegetation integrates these magnetic perturbations into redox-regulatory networks via radical pair spin dynamics, utilizing the fluctuations as an evolutionary signal that is most effectively processed under cold and moderate thermal regimes.
Molecular tension indicators reveal unexpectedly complex regulation of tension in live mouse organs
Fujiwara, Keita, Fujiki, Katsunori, Akama, Tomoya O., Shirahige, Katsuhiko, Shiojima, Ichiro, Nakamura, Tomoyuki, Hirai, Maretoshi
High-resolution, FRET-free imaging demonstrates that mechanical patterns are heterogeneous and vary significantly between individual molecules across distinct anatomical regions.
Molecular insights into fungal inositol phosphorylceramide synthesis and its inhibition by antifungal aureobasidin A
Chen, Jiehui, Ke, Yan, Zhang, Min, Lin, Xinyuan, Hua, Zhengkang, Zhang, Di, Hu, Xinlin, Ding, Xuyang, Li, Jiameng, Yang, Ping, Yu, Hongjun
Trapped ceramide-bound and drug-bound states reveal the enzyme’s precise catalytic and inhibitory mechanisms, establishing a structural foundation for the development of next-generation antifungal therapies.
A Non-Alchemical Absolute Binding Free Energy Framework for Small Molecule Drugs
Shi, Y.; Li, J.
Incorporating a regularization potential eliminates endpoint catastrophes and unphysical artifacts, yielding superior predictive accuracy and numerical stability across diverse charged and neutral protein-ligand systems.
The magnetic field-dependent fluorescence of MagLOV2 in live bacterial cells is consistent with the radical pair mechanism
Ross, B. L.; Lodesani, A.; Aiello, C. D.
Fluorescence intensity exhibits a non-monotonic response that peaks at 1 mT and reverses sign at 2 mT before plateauing above 70 mT.
Hook Stiffness as a Mechanical Switch for Torque Regulation in the Bacterial Flagellar Motor
Biswajit Das, Jianhua Xing, Ajeet K. Sharma, Hao Ge
Directional torque regulation relies on hook stiffness to manage the mechanical transitions between the motor’s mirror-reversed clockwise and counter-clockwise rotational states.
The biophysical properties of the bacterial nucleoid are dynamic, heterogeneous, and responsive to perturbations of cellular processes
Dai, X.; McCarthy, L.; Way, L.; Wiesler, E.; Liao, Q.; Wang, X.; Biteen, J. S.
The bacterial nucleoid maintains a viscosity 2.5-fold higher than the surrounding cytoplasm and undergoes metabolic-dependent mechanical shifts that regulate cellular processes independently of three-dimensional genome architecture.
Inferring bacterial cell size dynamics across media conditions
Nieto, César, Igler, Claudia, Singh, Abhyudai
Escherichia coli and Salmonella enterica exhibit transient, media-dependent fluctuations in cell dimensions that can be modeled using time-varying division rates derived from the ratio of optical density to cell counts.
Systematic mutational mapping reveals optimal amyloid formation for RIPK function
Martin, M.; Bolognesi, B.
Conserved aliphatic interfaces maintain the amyloid nucleation of RIPK1 and RIPK3 at an evolutionarily tuned “sweet-spot” where both excessive and insufficient assembly impair necroptotic signaling.
Membrane tubulation by adhesion of spherical nanoparticles
Weikl, T. R.
Cooperative wrapping into linear chains reduces bending costs through shared membrane necks, providing a significant energetic advantage over individual particle engulfment.
Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments
Acharya, B.; Lammichane, S.; Brown, T. P.; Chavant, M.; Im, W.
Validated MARTINI 3 models demonstrate that phthiocerol dimycocerosate (PDIM) translocation and aggregation are specifically driven by liquid-disordered environments, establishing a computational platform for large-scale mycobacterial membrane studies.
Membrane Environment Sets the Functional pKa of Ionizable Lipids
Trollmann, M. M. F.; Rossetti, P.; Böckmann, R. A.
Surface-to-core translocation and lateral domain segregation drive downward pKa shifts of up to 3.5 units in aminolipids, with saturated helper lipids further amplifying these transitions to enable pH-responsive cargo release.
Pre-yielding mechanical response near the jamming transition
Hidemasa Bessho, Takeshi Kawasaki, Kunimasa Miyazaki
Frictionless particle assemblies manifest non-linear rheological signatures at strain amplitudes traditionally assumed to be within the linear elastic regime.
Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models
Yu Xie, Ludwig Winkler, Lixin Sun, Sarah Lewis, Adam E. Foster, José Jiménez Luna, Tim Hempel, Michael Gastegger, Yaoyi Chen, Iryna Zaporozhets, Cecilia Clementi, Christopher M. Bishop, Frank Noé
Steering protocols and exact reweighting enable diffusion models to generate biased ensembles that rapidly recover precise equilibrium statistics and thermodynamic observables for rare molecular transitions.
Three dimensional contractile droplet under confinement
Adriano Tiribocchi, Marco Lauricella, Andrea Montessori, Sauro Succi
Interplay between spontaneous flows and elasticity drives distinct motile regimes, including unidirectional self-propulsion in bulk and a novel oscillating forward motion involving periodic wall collisions under microchannel confinement.
Uncovering Potential Effects of Spontaneous Waves on Synaptic Development: The Visual System as a Model
Jennifer Crodelle and Wei P. Dai
These endogenous activity patterns organize the initial framework of neural connections before the brain receives its first external sensory signals.
Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts
Juhyeong Jeon, Wonjin Yang, Sangmin Park, Jin Hae Kim, Young-Ho Lee, Wookyung Yu
Integrating structural libraries from coarse-grained simulations and machine learning models captures transient states and tracks conformational rearrangements caused by temperature variations, mutations, and environmental changes.
Asymptotic Effects of Incident Angle and Lateral Conduction in Electromagnetic Skin Heating
Ulises Jaime-Yepez, Hongyun Wang, Shannon E. Foley, Hong Zhou
Analytical expressions for the first- and second-order terms of the asymptotic expansion provide accurate temperature predictions at moderate length scale ratios where secondary physical factors become significant.
Self-Organized Bioelectricity via Collective Pump Alignment: Physical Origin of Chemiosmosis
Ryosuke Nishide, Kunihiko Kaneko
Reciprocal feedback between ion pump orientation and the intracellular electrochemical environment drives a spontaneous phase transition that transforms disordered fluctuations into the stable membrane gradients required for life.
Local Confinement within Plasma Membrane Nanodomains Drives Constitutive Activity of GPCRs
Zhou, X.; Shemeteva, M.; Picard, L.-P.; Simon, F.; Brown, A.; Dhillon, G.; Weiss, L. E.; Prosser, R. S.; Gradinaru, C. C.
Frequent stochastic encounters between receptors and G proteins within shared cholesterol-sensitive nanodomains, rather than the formation of stable pre-coupled complexes, underpin the high constitutive activity observed in receptors like A2AR.
Chemical interactions in polyethylene glycol-induced condensates lead to an anomalous FRET response from a flexible linker-fluorescent protein crowding sensor
Mohapatra, A.; Antarasen, J.; Latham, D. R.; Barilla, M. A.; Davis, C. M.; Kisley, L.
Biphasic systems formed by chemical interactions between PEG and the protein sensor’s flexible hinge region yield misleading average signals, establishing DNA-based sensors as more reliable alternatives that do not undergo phase separation.
ATPγS substantially defeats the biasing mechanism for kinesin steps
Karnawat, Vishakha, Toleikis, Algirdas, Carter, Nicholas J., Molloy, Justin E., Cross, Robert A.
A proposed kinetic state allows for unsteered movement and increased backstepping by disabling the motor’s forward-biased stepping and coupled hydrolysis cycle.
Traction force transmission via bioactive matrix hydrogel promotes epithelial collective migration mediated by integrin
Ouyang, Mingxing, Cao, Yu, Sheng, Hui, Liu, Hongjie, Liu, Lei, Li, Chunmei, Bu, Bing, Deng, Linhong
Cell-generated matrix traction forces promote directed collective migration by activating mechanosensitive calcium channels and ERK signaling through integrin-mediated mechanotransduction at the cell-matrix interface.
Real-time mass-resolved label-free single-molecule immunoassay
Brouwer, C.; Muratori, F.; Melo, L.; Anastasia, L.; Pappone, C.; Grant, E.
Interferometric scattering microscopy (iSCAT) quantifies protein-protein interactions in complex biological fluids by directly counting individual binding events, yielding concentrations comparable to standard ELISA measurements while capturing native association kinetics.
R5 and R7 positions on fluoroquinolone scaffolds drive F-actin filament disruption
Gupta, Rahul Jaiprakash, Nair, Hridhya, Sarhadi, Tanveera Rounaque, Nagotu, Shirisha, Gupta, Pramodkumar P., Mishra, Rahul Manojkumar, Dantu, Sarath Chandra, Kale, Avinash
Amino and bulky ring substitutions at the R5 and R7 positions facilitate the concentration-dependent dismantling of F-actin aggregates by later-generation fluoroquinolones, offering a chemical template for brain-penetrant neurodegenerative disease therapies.
Quantifying interleaflet coupling of phase behavior and observing anti-registered phases in asymmetric lipid bilayers
Kennison-Cook, K. B.; Cooper, A. M.; Heberle, F. A.
Greater acyl-chain length mismatch between leaflets increases the lipid exchange required to reach the miscibility boundary and promotes the formation of misaligned domains due to heightened hydrophobic energy penalties.
Myosin Filaments of Vertebrate Skeletal and Cardiac Muscle are Highly Similar, but not Identical
tilko, p. g.; Rastegarpouyani, H.; Esfahani, B. G.; Pinto, J. R.; Taylor, K.
Rabbit skeletal and mammalian cardiac thick filaments differ primarily in the positioning of myosin binding protein C and titin domains, representing a conserved vertebrate strategy for force control and endothermy that contrasts with the highly variable structures found in specialized insect flight muscles.
Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids
D’Asaro, D.; Arbona, J.-M.; Vaillant, C.; Jost, D.
Sparse distribution of cohesin complexes mediates a dual role of loop extrusion and inter-sister tethering, resulting in preferential alignment between non-homologous chromosomal regions.
Ratiometric signaling produces robust temporal integration for accurate cellular gradient sensing
Ghose, D.; Nolen, J.; Guan, K.; Elston, T.; Lew, D. J.
Biochemical memory of previous receptor encounters allows G protein collectives to perform unbiased temporal averaging, suppressing noise and enabling cells to surpass theoretical limits for directional accuracy in chemical gradients.
A Goldilocks zone of DNA flexibility defines stable yet plastic nucleosomes, tuned by histone chemistry
Perez-Lopez, J. I.; Maristany, M. J.; Farr, S. E.; Huertas, J.; Collepardo-Guevara, R.
Topologically protected intermediates formed within a specific range of DNA flexibility allow for controlled deformation, while core arginines and tail lysines provide the primary non-additive mechanism for modulating structural stability and DNA accessibility.
Effect of Charge Density on the Viscoelasticity and Underwater Adhesion of Entangled Complex Coacervates from Semi-Rigid Polysaccharides
Maxime Precheur, Ali Kanan, Alexei Dmitrievitsj Filippov, Kylian Virieux, Stéphane Trombotto, Fouzia Boulmedais, Mehdi Vahdati
Hyaluronic acid-based systems demonstrate that optimizing ionic interactions regulates the phase transitions and mechanical relaxation times required to maximize energy dissipation in aqueous environments.
Lipid gating of BK channels and mechanism of activation by negatively charged lipids
Mironenko, A.; de Groot, B. L.; Kopec, W.
Entry of lipid tails or molecules into the pore through lateral fenestrations regulates ion flow, while negatively charged lipids facilitate channel opening by preventing this obstruction, increasing potassium occupancy, and stabilizing the open-state structure.
Kinetic Model of E-P Condensates Dynamics Reveals Transcriptional Speed, Noise, Energy Trade-offs
Swayamshree Senapati, Ajeet K. Sharma, Hemant Kumar
Competition between regulatory factors establishes bistable promoter states at the cost of increased transcriptional noise, revealing a direct mechanical link between regulatory stability and expression variability.
Multimodal characterization of flow-induced thrombus initiation and growth in extracorporeal membrane oxygenation
Nilsson, Frida, Sochor, Benedikt, Henriksson, Sara, Roth, Stephan V., Broman, Lars Mikael, Prahl Wittberg, Lisa
Integrating computational fluid dynamics, ultra small angle X-ray scattering, and scanning electron microscopy correlates local hemodynamic environments with the internal fibrin architecture and cellular morphology of clots.
Engineering nanocondensate formation through sequence composition and patterning
Schneider, T. N.; Stoffel, F.; Buehler, M. A.; Mrzilkova, K.; Radiom, M.; Arosio, P.
Net charge and sequence blockiness stabilize metastable nanocondensates by minimizing interfacial tension and establishing an electrostatics-driven coalescence barrier that prevents coarsening.
H pilin cyclisation and pilus biogenesis are promiscuous but electrostatic perturbations impair conjugation efficiency
He, Shan, Ishimoto, Naito, Wong, Joshua L. C., David, Sophia, Sanchez-Garrido, Julia, Bogdanov, Mikhail, Beis, Konstantinos, Frankel, Gad
Phosphatidylethanolamine in the recipient cell membrane facilitates DNA transfer by mediating the electrostatic interaction with the pilus, a process disrupted when specific amino acid substitutions increase the positive charge of the donor apparatus.
Cellular Chemical Dynamics Governing Signal Transduction and Adaptive Gene Expression: Beyond Classical Kinetics
Kim, J.; Kim, S.; Jang, S.; Park, S. J.; Song, S.; Jeung, K.; Jung, G. Y.; Kim, J.-H.; Koh, H. R.; Sung, J.
Analytical expressions derived from reaction-time distributions quantify stochastic protein fluctuations in E. coli and reveal that gene activation and maturation processes uniquely govern the transient and steady-state variability of adaptive responses.
Ribosome demand links transcriptional bursts to protein expression noise
riddhiman.dhar@iitkgp.ac.in (Riddhiman Dhar), riddhiman.dhar@iitkgp.ac.in (Sampriti Pal), riddhiman.dhar@iitkgp.ac.in (Upasana Ray)
High translational efficiency amplifies phenotypic heterogeneity by scaling protein fluctuations exclusively in genes characterized by intermittent transcription.
Novel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria
María del Carmen Marín, Masae Konno, Andrey Rozenberg, Oded Béjà, Keiichi Inoue
Characterization of paSzR and psSzR establishes that schizorhodopsins function as light-driven inward proton pumps within the bacterial domain, expanding the known distribution of this protein family beyond its initial discovery in Asgard archaea.
Cell-Level Model to Predict the Spatiotemporal Dynamics of Neurodegenerative Disease
Shih-Huan Huang (黃士桓), Matthew W. Cotton, Tuomas P. J. Knowles, David Klenerman, and Georg Meisl
A critical switch fraction identifies the threshold at which disease progression shifts from slow, localized seeding to rapid, runaway propagation.
Emergent dynamics of active systems on curved environments
Euan D. Mackay, Giulia Janzen, D. A. Matoz-Fernandez, and Rastko Sknepnek
Geometric coupling governs the spatial organization and phase behavior of self-propelled agents by dictating the placement and movement of topological defects.
Tuning the gate and the gear: The LRRC26 (γ1) subunit modulates intrinsic gating and voltage-sensor coupling of the BK channel
Felipe Echeverría, Antonio Peña-Pichicoi, Miguel Fernandez, Willy Carrasquel-Ursulaez, Juan P. Castillo, Osvaldo Alvarez, Ramon Latorre
Destabilization of the closed state and strengthened energetic coupling to the voltage sensor increase the channel-opening equilibrium constant 106-fold without altering the activation of the voltage sensors themselves.
Spatial coin-tossing by kinesin-1 head and tail binding collectively drives microtubule patterns
Jashaswi Basu, Kajal Singh, Anita Jannasch, Chaitanya A. Athale
Stop-and-go dynamics and nonlinear velocity shifts result from the inhibitory effects of nonmotile anchors, determining the specific curvature and architectural complexity of the resulting network.
Actin and vimentin jointly control cell viscoelasticity and compression stiffening
James P. Conboy, Mathilde G. Lettinga, Pouyan E. Boukany, Fred C. MacKintosh, Gijsje H. Koenderink
Nearly equal contributions from both networks drive cellular stiffness and strain-stiffening under uniaxial compression, revealing a mechanical synergy essential for maintaining structural integrity across diverse environments.
Lipid droplets are rigid and physically suppress phagocytosis, unless cell compression or stretching activates actomyosin
Michael P. Tobin, Irena L. Ivanovska, Steven H. Phan, Tianyi Bai, Jeneille Deans, Guilherme P.F. Nader, Dennis E. Discher
Interfacial tension from liquid–liquid phase separation enables these small droplets to displace the macrophage cytoskeleton, a mechanical interference that is only overcome when external or internal forces trigger a compensatory contractile response.
Lipid scrambling via TMEM16F mediates the formation and release of extracellular vesicles
Trieu Le, Maria Eugenia Perez Collado, Yu Meng Li, Amra Saric, Joost C.M. Holthuis, Sergio Grinstein, Spencer A. Freeman
Inhomogeneity-induced membrane curvature drives vesicle detachment, a mechanism critical for the clearance of apoptotic cells and the signaling of anti-inflammatory tissue responses.
Kinematics and morphological correlates of descent strategies in arboreal mammals suggest early upright postures in euprimates
severine.toussaint@mnhn.fr (Dionisios Youlatos), severine.toussaint@mnhn.fr (John A Nyakatura), severine.toussaint@mnhn.fr (Severine LD Toussaint)
Comparative analysis of extant and extinct species demonstrates that primates prioritize stability through tail-first and lateral descent postures, utilizing specific kinematic adjustments like slower speeds and asymmetrical gaits to compensate for morphological trade-offs between body mass and limb length.
Piezo2 tension sensitivity and its modulation by alternative splicing
Sindoni, M.; Sharp, W.; Grandl, J.
Exon 35 acts as a key regulatory domain that increases responsiveness to membrane tension and cellular indentation, enabling tissue-specific variants to operate across distinct mechanical ranges.
Molecular mechanism of cholesterol-dependent membrane fusion in SARS-CoV-2 entry
Li, Wei, Wu, Mengdan, Feng, Shirong, Su, Jiaming, Niu, Qian, Lin, Weijun, Fan, Jiaqi, Cui, Lele, Xiang, Yijuan, Li, Hao, Li, Kaiyu, Su, Zhaoming, Lu, Guangwen, Lai, Ying
Oligomerization of spike proteins via interactions between cholesterol and the palmitoylated cysteine-rich region enhances viral docking to host membranes to facilitate cellular entry.
Enhanced bacterial chemotaxis in confined microchannels: Optimal performance in lane widths matching circular swimming radius
Yue, C.; Zhang, C.; Zhang, R.; Yuan, J.
Escherichia coli exploits collisions between its intrinsic clockwise circular paths and microchannel sidewalls to align its motion and maximize chemotactic efficiency when confinement dimensions correspond to its natural swimming radius.
A two-step clockwork mechanism opens a proteo-lipidic pore in PIEZO2
Li, Shu, Wijerathne, Tharaka, Bhatt, Aashish, Jiang, Wenjuan, Lacroix, Jerome, Han, Wei, Luo, Yun Lyna
Multiscale molecular dynamics simulations and electrophysiology characterize the membrane tension-induced transitions that govern the channel’s dynamic gating behavior.
Linking spinal circuit reorganization to recovery after thoracic spinal cord injury
smd395@drexel.edu (Andrew B Lockhart), smd395@drexel.edu (David SK Magnuson), smd395@drexel.edu (Ilya A Rybak), smd395@drexel.edu (Natalia A Shevtsova), smd395@drexel.edu (Simon M Danner)
Lateral hemisection and midline contusion injuries utilize distinct compensatory mechanisms such as detour pathways or local network reorganization, yet both depend on the reactivation of sublesional lumbar rhythm-generating circuits and balanced commissural connectivity to restore functional gait.
Slow spatial migration can help eradicate cooperative antimicrobial resistance in time-varying environments
Hernandez-Navarro, L.; Distefano, K.; Täuber, U. C.; Mobilia, M.
Synchronization between environmental shifts and population turnover exploits stochastic bottlenecks to maximize extinction probabilities within a metapopulation.
Boundary aggregation of rod-shaped active agents
Jui-Lin Hsu, Chiao-Chen Chuang, No Chen, Chien-Jung Lo, Cheng-Hung Chang
Surface-swarming experiments characterize the spatial distribution and orientation of motile units to clarify the mechanisms governing their accumulation at confining geometries.
A novel AI-coupled flow chamber method quantifying erythrocyte osmotic fragility
Fırat, Ipek Seda, Alaçayır, Özgür, Creutz, Till, Artmann, Gerhard Michael, Damiati, Samar, Artmann, Ayşegül Temiz
BioExP provides an automated and reproducible alternative to traditional osmotic fragility testing by accurately detecting shifts in membrane stability from biological modulators like LPS and HgCl2 while utilizing real-time imaging and minimal sample volumes.
Electrophysiology in nanoscale compartments
Howell, M. R.; Xu, R. J.; Cohen, A. E.
Stochastic channel gating and rapid shifts in ionic concentrations within sub-micron environments drive membrane voltage dynamics that diverge fundamentally from the deterministic predictions of traditional conductance-based models.
Revealing pH-dependence and independence of the characteristics of a β sheet-forming antimicrobial peptide
Niknam Hamidabad, M.; Mansbach, R.
Deprotonation of specific lysine residues, most notably at the C-terminus, drives the structural transition of GL13K into a stabilized \(\beta\)-hairpin configuration as pH levels increase.
Quantitative mapping of nanoscale EGFR-Grb2 assemblies by DNA-PAINT
Kaminer, A.; Li, Y.; Barth, H.-D.; Dietz, M. S.; Heilemann, M.
EGF stimulation triggers a reduction in surface receptor density alongside a transition toward higher-order oligomers and the progressive recruitment of adaptor proteins to individual signaling sites.
Nonlinear elasticity and transition to macroscopic irreversibility in composite hydrogels
Ippolyti Dellatolas, Thibaut Divoux, Emanuela Del Gado, Irmgard Bischofberger
Attractive interactions between nanofillers and the polymer network drive the material’s mechanical reinforcement and dictate the threshold for permanent deformation even at low filler concentrations.
Adenocarcinoma cell mechanobiology is altered by the loss modulus of the surrounding extracellular matrix
Smith, A. M.; Pardi, B. M.; Sousa, I.; Gopinath, A.; Andresen Eguiluz, R. C.
A549 cells exhibit significant shifts in migration speed and focal adhesion size when exposed to varying loss moduli, demonstrating that time-dependent mechanical cues independently regulate epithelial cell behavior compared to purely elastic environments of identical stiffness.
Bringing calorimetry (back) to life
Faezeh Khodabandehlou, Christian Maes, Édgar Roldán
Nonequilibrium heat capacity in active biophysical models of ciliar motion and molecular motors exhibits complex dependencies on biological parameters and can reach negative values.
Self-Viscophoresis: Autonomous Motion by Biasing Thermal Fluctuations via Self-Generated Viscosity Asymmetry
Bokusui Nakayama, Yusuke Takagi, Ryoya Hirose, Masatoshi Ichikawa, Marie Tani, Ibuki Kawamata, Eiji Yamamoto, Akira Kakugo
Asymmetric particles in thermoresponsive solutions create local viscosity gradients that anisotropically damp random fluctuations, allowing for reversible control of the direction and dimensionality of their transport.
PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation
Sverzhinsky, Aleksandr, Xue, Huijun, Langelier, Marie-France, Muniz Corrêa, Marcelo V., Del Mundo, Joshua, Classen, Scott, Hammel, Michal, Rothenberg, Eli, Pascal, John M.
Striking mobility of the catalytic domain relative to the DNA-binding regions facilitates the rapid detection of and response to damage sites.
Phasor analysis of RGB camera data enables fluorescence microscopy unmixing and brightfield segmentation in a commercial microscope
Schuty, B.; Garcia, M. J.; Khuon, S.; Malacrida, L. S.
Discrete Fourier transforms applied to pixel-level color intensities facilitate the unsupervised resolution of overlapping signals to quantify alveolar collapse and identify melanoma-specific spectral signatures.
Supercoiled DNA recognition and cleavage control in topoisomerase VI
Richman, Daniel E., Wendorff, Timothy J., Rashid, Fahad, Beck, Curtis, Yan, Qianyun, Johnson, Haley R., Eckerty, Ryan A., Fogg, Jonathan M., Baker, Matthew L., Zechiedrich, Lynn, Berger, James M.
Structural transitions between cleaved and uncleaved states reveal that the enzyme preferentially targets deformable DNA sites to activate its catalytic mechanism.
Novel sterol-spiropyran derivatives: synthesis and photoactivity in Langmuir monolayers
Negus, Theo, Perry, Alexis, Petrov, Peter G.
Light-induced conformational switching within the monolayer modulates surface pressure and molecular organization with kinetics governed by compressional elasticity, providing a mechanism for the optical control of lipid membrane properties and morphology.
Large-scale exploration of protein space by automated NMR
Muentener, T.; Abramson, D.; Stern, E.; Hertel, I.; Jankevicius, G.; Mas, G.; Folkers, G. E.; Wicky, B. I. M.; Hiller, S.
Experimental characterization of hundreds of de novo proteins reveals unexpected local dynamics missing from computational models, establishing a high-throughput foundation for understanding the sequence-structure-dynamics relationship.
Decoupling phase separation and fibrillization preserves activity of biomolecular condensates
Mahendran, Tharun Selvam, Singh, Anurag, Srinivasan, Sukanya, Jennings, Christian M., Neureuter, Christian, Gindra, Bhargavi H., Parekh, Sapun H., Banerjee, Priya R.
Small molecule metabolites selectively inhibit the age-related conversion of protein condensates into amyloid fibrils, thereby maintaining their biochemical functionality.
Morphology of Compound Viscoelastic Drops in Extensional Flows
Malay Vyas, Uddipta Ghosh
Interfacial dynamics within these multi-layered systems govern the precise encapsulation and release mechanisms required for advanced drug delivery and biotechnological applications.
Single molecule counting detects low-copy glycine receptors in hippocampal and striatal synapses
christian.specht@inserm.fr (Bert Brône), christian.specht@inserm.fr (Christian G Specht), christian.specht@inserm.fr (Clémence Mille), christian.specht@inserm.fr (Serena Camuso), christian.specht@inserm.fr (Souad Youjil Abadi), christian.specht@inserm.fr (Yana Vella)
Integration with gephyrin scaffolds and presence at functionally relevant densities reveal the precise organization of these receptors in telencephalic regions where their existence was previously controversial.
Supercoiling DNA with a free end.
Daniela Moretti, Giada Forte, Giuseppe Gonnella, Davide Marenduzzo, Cristian Micheletti, Antonio Suma
Coarse-grained Brownian dynamics simulations and mean-field theory characterize the spatio-temporal evolution and steady-state profiles of twist and writhe in open-ended genetic filaments.
Non-muscle actinopathy-associated loss-of-function actin variants modulate cytoskeletal reorganization
Graczer, E.; Dakos, K.; Bozo, T.; Paszty, K.; Di Donato, N.; Kellermayer, M.; Varga, A.
G302A and S338-I341 variants reduce cellular stiffness and compromise mechanical stress responses in patient-derived fibroblasts by disrupting cofilin phosphorylation and myosin light chain signaling.
Peptides from coronin 1 inhibit fusion by balancing the activation barrier and hemifusion stability
Swaratmika Pandia, Manbit Subhadarsi Panda, Hirak Chakraborty
AG-22 and mTG-23 peptides disrupt the membrane merger process by modulating the temperature-dependent kinetic evolution and transitions of fusion intermediates.
Multi-barrier unfolding of the double-knotted protein, TrmD-Tm1570, revealed by single-molecule force spectroscopy and molecular dynamics
Bruno da Silva, F.; Niewieczerzal, S.; Lewandowska, I.; Fortunka, M.; Sikora, M.; Silbermann, L.-M.; Tych, K. M.; Sulkowska, J. I.
Native contacts within the double-knotted SPOUT protein facilitate only partial self-folding and four distinct mechanical unfolding pathways, indicating that complete formation of its complex topology likely requires chaperone assistance.
Dislocation dynamics on deformable surfaces
Marcello De Donno, Luiza Angheluta, Marco Salvalaglio
An extension of the amplitude-phase-field crystal framework to curved geometries demonstrates that surface deformations drive dislocation motion through curvature-induced self-propulsion and modified defect interactions.
Turning the Fluorescent Protein Barrel into a Programmable Electrostatic Device Reveals Differential Bleaching States of the Chromophore
Frankiv, N.; Leong, L. M.; Baker, B. J.
Reciprocal coupling between \(\beta\)-sheet residues and internal sidechains dictates the polarity and kinetics of optical signals by modulating chromophore protonation and isolating photophysically distinct, light-sensitive fluorescence components.
The mechanics and physics of tofu: Understanding hydrated soft solids through feature networks
Boes, B.; Simon, J.-W.; Holthusen, H.; Kuhl, E.
Automated model discovery identifies universal constitutive laws revealing that the material’s poroviscoelastic response scales nonlinearly with hydration levels, challenging traditional bi-phasic assumptions.
Why Life is Hot
Schilling, T.; Warren, P.; Poon, W. C. K.
Coupling cellular chemical reaction networks to out-of-equilibrium reservoirs enables the optimization of diverse fitness functions, such as precision and robustness, at the inevitable cost of substantial heat dissipation.