Apr 06 26
Featured Papers
Global stabilization of the transcriptome in mitotic cells
Ekaterina Khalizeva, Arash Latifkar, Kehui Xiang, David P Bartel, Jimmy Ly, Iain M Cheeseman
PABPC1&4-mediated repression of deadenylation increases mRNA half-lives more than fourfold to buffer transcript levels and sustain cell viability during extended periods of transcriptional inactivity.
The dynamics of centromere assembly and disassembly during quiescence
Océane Marescal, Kuan-Chung Su, Brittania Moodie, Noah J.L. Taylor, Iain M. Cheeseman
Cells transcriptionally downregulate most centromere proteins during entry into arrest and postpone CENP-A deposition until the G1 phase following the first post-exit mitosis, a transition distinguished by PLK1 levels.
When a Bath Is Not Enough: State-Dependent Energy Injection and Nonmonotonic Dissipation in Cytoskeletal Matter
Michael Murrell
Feedback between a system’s mechanical configuration and its energy input drives emergent behaviors like selective routing and relaxation-driven contractility, demonstrating that active biological systems internally regulate their own power consumption rather than relying on a fixed external source.
Active Hydrodynamic Theory of Euchromatin and Heterochromatin
S. Alex Rautu, Alexandra Zidovska, David Saintillan, Michael J. Shelley
Contractile stresses from cross-linking proteins drive mechanically induced phase separation and nuclear boundary wetting of condensed regions, while transcription-induced fluctuations generate long-range coherent flows and continuous morphological deformations.
Mechanics of disclination emergence in three-dimensional active nematics
Yingyou Ma, Christopher Amey, Aparna Baskaran, Michael F. Hagan
A principal-plane framework characterizes loop nucleation from bend instabilities and identifies an activity-dependent effective stiffness that governs both defect morphology and steady-state behavior.
Robotectonics: Emergent Phototactic Aggregation-Disaggregation in Swarms
Fabio Giardina, S. Ganga Prasath, L. Mahadevan
Decentralized collectives leverage local transport behaviors to autonomously remodel their environment, demonstrating how complex coordination can arise from the physical coupling of agents and their surroundings without global planning.
Active mechanics of sea star oocytes
Foster, P. J.; Zampetaki, A.; Liu, J.; Fürthauer, S.; Fakhri, N.
A precise balance between myosin-driven active stress and cortical viscosity, regulated by the relative density of molecular motors and passive crosslinkers, maximizes the rate of cellular deformation during surface contraction waves.
Some Papers
Diffusive spreading across dynamic mitochondrial network architectures
Keaton B. Holt, Camryn Zurita, Lizzy Teryoshin, Samantha C. Lewis, Elena F. Koslover
Molecular homogenization transitions from an interaction-limited “social network” to a diffusion-limited “physical network” depending on the balance between organelle remodeling rates and internal transport speeds.
Cell loss disrupts mechanical homeostasis to drive retinal pigment epithelium ageing-like phenotype in vitro
Piskova, Teodora, Kozyrina, Aleksandra N., Astrauskaitė, Giedrė, Mabrouk, Mohamed Elsafi, Schepl, Sebastian, Yam, Stacy Lok Sze, Ravithas, Ragul, Wagner, Wolfgang, Vassalli, Massimo, Di Russo, Jacopo
Vision-supporting phagocytosis diminishes as a result of structural remodeling, proving that physical changes alone are sufficient to impair specialized cellular functions.
Wrinkles, rucks, and folds formed in a heavy sheet on a frictional surface
Keisuke Yoshida, Hirofumi Wada
Interactions between elasticity, gravity, and interfacial friction dictate the physical principles and morphological transitions governing these localized surface deformations. The Soft Matter Journal is impossible to access, totally useless.
Biogenic bubbles enable microbial escape from physical confinement
Babak Vajdi Hokmabad, Thomas Appleford, Hao Nghi Luu, Meera Ramaswamy, Maziyar Jalaal, Sujit S. Datta
Fermentation-driven CO\(_2\) production hydrodynamically entrains immotile cells into rising vertical columns, creating persistent conduit networks that facilitate long-range dispersal and genetic mixing.
Energy-precision trade-off in mitotic oscillators revealed by ATP modulation in artificial cells
Wang, S.; Yourston, L.; Maryu, G.; Kim, Y.; Walker, D.; Kadiyala, U.; Yang, Q.
Embryonic cell cycles prioritize a metabolic compromise that balances rapid division speed with sufficient temporal coherence, positioning physiological ATP levels at an energetic optimum for speed rather than maximum fidelity.
Phase coherence and disorder-induced wave propagation in micromotor arrays
Romane Braun, Alexis Poncet, Alexandre Morin, Denis Bartolo
Assemblies of thousands of 3D-printed rotary motors organize into antiferromagnetic patterns and leverage structural imperfections to propagate signals, offering a synthetic model for understanding collective dynamics in living systems.
Design of Fluorescent Membrane Scaffold Proteins for Nanodiscs
Cleveland, E.; Wolf, A. R.; Chen, S.; Mohona, F. A.; Kailat, I.; Tran, B. H.; Babu, L. S.; Lin, Y.-C. T.; Marty, M. T.
Engineered scaffold protein variants incorporating C-terminal fluorescent tags and HaloTag fusions maintain standard nanodisc structure and stoichiometry while providing a versatile platform for diverse imaging and functional applications.
More Papers
VGLL4-driven TEAD4 multimerization orchestrates DNA binding and YAP recruitment
Ren, Zhiyun, Zhao, Yilin, Yu, Wentao, Zhang, Xia, Song, Xiaoxuan, Bao, Yanling, Hu, Meng, Chen, Lishuang, Yang, Hao, Cheng, Bingkai, Liu, Cong, Jin, Yunyun, Zhang, Lei, Sun, Bo
Stoichiometric modulation by VGLL4 stabilizes TEAD4 multimerization to regulate its dynamic engagement with DNA and the subsequent recruitment of YAP within the Hippo pathway.
Ising models of cooperativity in muscle contraction
Elaheh Saadat, Matthieu Caruel, Stefano Gherardini, Ilaria Morotti, Matteo Marcello, Marco Caremani, Marco Linari, Ivan Latella, and Stefano Ruffo
Coupled structural transitions within both thin and thick filaments govern the sharp activation profile of sarcomeres in response to calcium binding.
Electrostatic interactions constrain generalization of porous-media models for intracellular diffusion in mammalian cells
Debabrata Dey, Gideon Schreiber
Variations in electrostatic attraction and repulsion between diffusing particles and the crowded cytoplasmic matrix create charge-specific transport barriers that prevent universal geometric frameworks from accurately predicting molecular movement across diverse cell types.
Snooping helices: The elastic path finding algorithm of growing hyphae
Antoine Rittaud, Elodie Couttenier, Sophie Bachellier-Bassi, Christophe d’Enfert, Igor M. Kulić, Catherine Villard
Candida albicans navigates and penetrates host tissues by minimizing the elastic energy of its confined growth tip before it solidifies into a permanent, oscillatory morphology.
Conformational equilibria in the activation of cystine-knot hormone receptors
Zhen Gong, Wayne A. Hendrickson
Dimeric models of varying stoichiometries, synthesized from nematode and human structural data, define the quantifiable energetic transitions that govern G-protein signal transmission.
Mechanism of lipid-dependent cold sensitivity in a model ion channel
Li, Chieh-Chin, Nimigean, Crina M.
An intersubunit salt bridge modulated by membrane lipids facilitates cooperative protein–membrane interactions that drive temperature-dependent gating.
Principles of gamma synchrony predict figure–ground perception in texture stimuli
Mario Senden, Mark Jonathan Roberts, Maryam Karimian, Peter De Weerd
The theory of weakly coupled oscillators explains how stimulus-dependent variations in frequency and coupling strength account for human performance and perceptual learning during scene segmentation.
GTPase-activating protein DLC1 spatio-temporally regulates Rho signaling
Giliane Rochat, Jakobus van Unen, Laurent Dubied, Lucien Hinderling, Maciej Dobrzynski, Max Heydasch, Olivier Pertz
DLC1 controls the global rate of Rho deactivation and utilizes mechanosensitive focal adhesion association to provide the local feedback necessary for robust adhesion disassembly.
Val109 and Ile170 contribute to channel function in Guillardia theta-derived anion channelrhodopsins
Yokoyama, Takanori, Sugano, Eriko, Tabata, Kitako, Kakizaki, Taira, Maruoka, Shu, Endo, Yuka, Ozaki, Taku, Fukuda, Tomokazu, Bai, Lanlan, Tomita, Hiroshi
Distances between key residues and the dimensions of the ion tunnel bottleneck dictate the photocurrent magnitude and closing kinetics of these optogenetic silencers.
Adaptive Ratchets and the Evolution of Molecular Complexity
Tom Röschinger, Roberto Morán-Tovar, Simone Pompei, and Michael Lässig
Recognition sites evolve more rapidly when coupled to time-varying targets.
Physical constraints on the rhythmicity of the biological clock
YeongKyu Lee and Changbong Hyeon
The KaiABC protein circuit utilizes energy dissipation from ATP hydrolysis to establish and maintain stable biochemical oscillations within a non-equilibrium framework.
MDFIC2 is a sensory neuron–specific PIEZO channel auxiliary subunit
Zijing Zhou, Fei Dai, Delfine Cheng, Xiaonuo Ma, Seyedeh Farzaneh Omidkhoda, Jack Clarke, Huijing Zhang, Michael Laden, Yang Guo, Jinyuan Vero Li, Renjing Liu, Emily S. Wong, Yixiao Zhang, Charles D. Cox
MDFIC2 converts PIEZO1 and PIEZO2 into high-threshold, slowly inactivating mechanoreceptors by binding to a conserved pocket within the channel pore modules via its posttranslationally modified distal C-terminus.
Microscopic measurement of the local deformation field establishes the mechanistic origin of the fatigue threshold for soft brittle materials
Umut Altuntas, Chenzhuo Li, John Martin Kolinski
Strain concentrations at the crack tip define the energetic limit required to transition from reversible deformation to irreversible crack growth during cyclic loading.
Deoxy-Piezo1 hyperactivity elevates pump-leak fluxes and lactate production in sickle cells
Virgilio L. Lew, Simon D. Rogers
Hemoglobin S polymers lock Piezo1 channels in an open state throughout deoxygenated transits, with the channels closing only when the cells return to oxygenated bloodstreams.
Challenges in replay detection by TDLM in post-encoding resting state
Gordon B Feld, Juliane Nagel, Lennart Wittkuhn, Raymond J Dolan, Simon Kern, Steffen Gais
Hybrid simulations reveal that TDLM requires an exceptionally high density of events to detect spontaneous neural sequences, indicating that current analytical pipelines lack the statistical power to identify memory replay at physiologically plausible rates in MEG resting-state data.
Density of states weighted decoherence probe formalism for charge transport in DNA
Hashem Mohammad and M. P. Anantram
Atomistic quantum modeling of phase-breaking scattering captures the influence of environmental interactions to enhance the accuracy of predicted electronic properties.
Generalized free energy and excess/housekeeping decomposition in nonequilibrium systems: From large deviations to thermodynamic speed limits
Artemy Kolchinsky, Andreas Dechant, Kohei Yoshimura, and Sosuke Ito
A variational approach to fluctuation statistics provides a formal potential for nonconservative systems, linking the internal components of energy dissipation to the fundamental constraints on transition rates.
Logarithmic theory of visuomotor stabilization
Leonardo Demarchi
Logarithmic processing of optic flow enables robust, scale-invariant navigation by decoupling the confounding effects of motion speed and environmental distance on visual feedback.
Simulation-based inference captures non-Markovian effects as exemplified in protein production kinetics through cell division
Pedro Pessoa, Juan Andres Martinez, Vincent Vandenbroucke, Frank Delvigne, Steve Pressé
Conditional normalizing flows approximate the intractable likelihoods of history-dependent protein inheritance to reveal that yeast glc3 gene expression is brief and transient under nutrient stress.
Negative design enables cell-free expression and folding of designed transmembrane β-barrels
Giacomo Pedrelli, Marvelous Chikerema, Andrei Sokolovskii, Tamas Lazar, Alexander V. Shkumatov, Alexander N. Volkov, Anastassia A. Vorobieva
Incorporating prolines or polar residues into β-strands suppresses aggregation-prone intermediates and facilitates spontaneous assembly into lipid bilayers, overcoming the misfolding common in sequences optimized solely for thermodynamic stability.
The LOK C-Terminus is an IBAR-like Domain that Facilitates Membrane Binding and Ezrin Colocalization
Jeriann R. Beiter, Dovydas Vasiliauskas, Gillian M. Hodge, Hannah E. Schneiderman, Monica C. Pillon, Sahithya Sridharan Iyer, Michelle C. Mendoza, Andrew T. Lombardo, Gregory A. Voth
Apical membrane recruitment enables LOK to precisely phosphorylate its substrates to control membrane tension and mediate the epithelial-to-mesenchymal transition.
Interpreting tissue stiffening with lung tumorigenesis by imaging architectural resembling of extracellular matrix components
Wang, Chuncheng, Qian, Shuhao, Li, Wenyue, Zhou, Lingxi, Chen, Lingmei, Meng, Jia, Jiang, Rushan, Niu, Bo, Sun, Ke, Ding, Zhihua, Wang, Xiaozhao, Zhuo, Shuangmu, Liu, Zhiyi
Label-free multiphoton microscopy and a quantitative resemblance metric resolve the specific structural remodeling of elastin and collagen fibers.
Balloon regime: Drop elasticity leads to complete rebound
Diego Díaz, Arivazhagan G. Balasubramanian, Kasra Amini, Xiaomei Li, Fredrik Lundell, Shervin Bagheri, and Outi Tammisola
Vertical filaments emerging from the receding contact line expand into thin-walled structures that pull the liquid volume away from superhydrophobic substrates during high-speed impacts.
Unraveling hydrogel resistance to particle deposition: Adhesion versus elastohydrodynamic lift
Aleksandr Leontev, Axel Rosenhahn, and Viatcheslav Freger
Repulsive elastohydrodynamic forces generated by the deformation of the soft interface counteract particle adhesion to determine the antifouling efficiency of hydrogel coatings.
Competitive binding of transcription factors as activator-repressor in stochastic gene expression
Amit Kumar Das and Debabrata Biswas
An analytical framework identifies missing experimental parameters to characterize the emergence of phenotypic switching and fluctuations in expression levels within the regulatory network.
Munc13 serves as a molecular filter for SNARE sorting and assembly in active zone condensates
Hong Zhang, Yu Zhang, Zhifei Zhao, Zelin Cao, Kexu Zhao, Mengshi Lei, Shen Wang, Cong Ma
Munc13-1 clusters Syb2 into vesicle nanodomains within RIM1/RIM-BP2 condensates to increase local protein density and ensure the rapid, spatiotemporally precise exocytosis of neurotransmitters.
Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome
George Wanes, Udayan Mohanty, Paul C. Whitford
Millimolar increases in magnesium concentration stabilize the unrotated configuration and reduce rotation kinetics by an order of magnitude by increasing the free-energy barrier between subunits.
Heat- and PIP2-dependent TRPM4 activity underlies mutually exclusive human diseases
Yuhua Tian, Soohyeon Bae, Xuesong Wu, Kyle C. Rouen, Adriana Hernández-Gonzalez, Yanxiao Han, Abdullah Al Tekreeti, Simon Vu, Irene Chen, Ellen Li, Igor Vorobyov, Vladimir Yarov-Yarovoy, Byung-Chang Suh, Samuel T. Hwang, Jie Zheng
Skin-disease-associated variants bypass lipid-mediated regulation to increase channel activity at cooler surface temperatures, whereas heart-disease-linked mutations increase channel density in a manner that is only functionally preserved at core body temperature.
Symmetry-breaking motility of an active hinge in a crowded channel
Leonardo Garibaldi Rigon, Y. Baek
Spontaneous conformational changes driven by interactions with the surrounding medium allow internal activity to be converted into persistent unidirectional transport.
Rational design of amphiphilic pyrrolidinium derivatives: structure–activity correlation and alkyl chain tuning for superior antimicrobial activity
Elmira A. Vasilieva, Darya A. Kuznetsova, Roman A. Babkin, Denis M. Kuznetsov, Anna P. Lubina, Alexandra D. Voloshina, Dilyara N. Valeeva, Lucia Ya. Zakharova
CPS-\(n\)-6 homologs with alkyl chain lengths of 12 to 18 carbons demonstrate how specific hydrophobic tail modifications regulate self-assembly and biological performance.
Diffusion of rod-like particles in complex fluids
Władysław Sokołowski, Huma Jamil, Karol Makuch
Generalized transport theories account for the breakdown of the Stokes-Einstein relation by evaluating the coupling between anisotropic geometry and the viscoelastic properties of the medium.
Ignition Criteria for Trigger Waves in Cell Signaling
Brandon H. Schlomann, William S. DeWitt, Yuanzhao Zhang, and Kasturi Shah
Analytic expressions for one-dimensional systems and numerical solutions for two and three dimensions define the critical thresholds for initiation within a minimal biochemical framework.
Conservation Laws and Slow Dynamics Determine the Universality Class of Interfaces in Active Matter
Raphaël Maire, Andrea Plati, Frank Smallenburg, and Giuseppe Foffi
Active hard disks undergoing phase separation into gas and liquid, crystal, or glass states exhibit distinct interfacial scaling properties that depend on the specific physical state of the condensed matter.
The microtubule GTP-tubulin cap size is modulated during cell division
Anna C. Cassidy, Dylan T. Burnette, Marija Zanic
Global regulation of these stabilizing terminal structures tunes polymer stability to facilitate the rapid network remodeling and accurate chromosome segregation required at specific stages.
A minimal model for the role of Rim4 in regulating meiotic exit in budding yeast
V. Abigail Marquez Davila, Pallavi Gadgil, Anna Zike, Gisela Cairo, Renyu Wang, Sima Setayeshgar, Soni Lacefield
Timely release of sequestered mRNAs ensures that division terminates after exactly two rounds of chromosome segregation and prevents further cell-cycle oscillations.
Matrix stiffness and stress relaxation regulate osteogenesis through histone demethylases KDM4B and KDM6B
Ian M. Tayler, Amy Zhu, Abhishek Sharma, Neha Saxena, Siddharth S. Dey, Ryan S. Stowers
Mechanosignaling pathways translate physical cues from stiff, fast-relaxing hydrogel matrices into the epigenetic upregulation of enzymes necessary for the differentiation of bone marrow-derived mesenchymal stem cells.
Apoptosis Induction, Disruption of Cytoskeleton Remodeling and EMT Inhibition as Major Mechanism(s) Underlying the Pleiotropic Action of Withania somnifera in Breast Cancer
Aditi Srivastava, Tanveer Ahamad, Aqib Sarfraz, Sahabjada Siddiqui, Feroz Khan, Anchal Trivedi, Mohd. Faheem Khan, Aparna Misra, Hari Shankar, Mohsin Ali Khan, Rumana Ahmad
Viscosalactone B, Withanolide E, and Withaferin A target coronin1A and vimentin to trigger oxidative stress and cell cycle arrest in MDA-MB-231 cells.
Phospholipase D1 and Phosphatidic Acid are required for MVE Fusion and Exosome Secretion
Melodie T. Nguyen, Broderick L. Bills, Andre C. Allen, Megan L. Hulser, Sisiyan Jiang, Michelle K. Knowles
Real-time tracking of individual CD63+ multivesicular endosomes via total internal reflection fluorescence microscopy reveals the spatiotemporal dynamics of lipid-mediated membrane remodeling during vesicle fusion and exosome release.
Quantitative Prediction of Oil–Water Interfacial Tension in Surfactant Systems Using Dissipative Particle Dynamics
Rachel Hendrikse, Carlos Amador, Mathew Davies, Mark Richard Wilson
Direct parameterization against experimental data enables the model to accurately capture the interfacial behavior of pure and mixed ionic surfactant systems.
TriRNASP: A knowledge-based potential with three-body effects for accurate RNA structure evaluation
Tongwei Yuan, En Lou, Zouchenyu Zhou, Ya-Lan Tan, Zhi-Jie Tan
Integrating coarse-grained three-body correlations with Kullback-Leibler divergence and atom clash penalties enables more precise assessment of candidate models generated by RNA structure prediction methods.
Implicit Membrane for Helical Peptide Selectivity Towards Bacterial Membranes
Sofía Blasco, Erin Spearing, Martina Drabinová, Vendula Rašková, Robert Vácha
Distinct lipid arrangements between cell types provide a structural basis for engineering therapeutic agents that eradicate pathogens while minimizing collateral damage to mammalian tissues.
Dynamics of emulsion drop impact, spreading and evaporation: Effect of internal phase gelation
Mario Cordova-Gonzalez, Parisa Bazazi, S. Hossein Hejazi
Internal phase gelation regulates the energy dissipation and structural transitions that dictate the droplet’s deformation limits and final deposition morphology on solid surfaces.
The Central Coupler of the AAA+ ATPase ClpXP Controls Intersubunit Communication and Couples the Conversion of Chemical Energy into the Generation of Force
Sosa, R. P.; Florez, A.; Kim, J.; Tong, A. B.; Kang, Z.-h.; Li, A.; Kuriyan, J.; Bustamante, C. J.
The central coupler triggers ATP hydrolysis in adjacent subunits via a conserved residue triad and synchronizes this energy release with the downward stroke of translocating loops to drive rapid and thermodynamically efficient protein unfolding.
Deciphering Coccolith Formation: Advanced Microscopy Insights from the Biomineralisation of Gephyrocapsa huxleyi
Triccas, A.; Verezhak, M.; Ihli, J.; Guizar-Sicairos, M.; Holler, M.; Laidlaw, F.; Singleton, M.; Chamard, V.; Wood, R.; Grunewald, T. A.; Nudelman, F.
Physical confinement of individual calcite units during growth dictates the morphological evolution and final 3D architecture of the mineralized scales throughout the entire developmental process.
Investigating a Relation between Amyloid Beta Plaque Burden and Accumulated Neurotoxicity Caused by Amyloid Beta Oligomers
Kuznetsov, A. V.
Variations in protein degradation efficiency and microscopic assembly kinetics create a non-linear accumulation of irreversible damage, explaining why individuals with equivalent pathological loads experience divergent cognitive outcomes.
Proton tunneling at the ryanodine receptor Ca2+ activation site provides temperature-invariant noise for robust Ca2+-induced Ca2+ release
Maltsev, A. V.; Lakatta, E. G.; Maltsev, V. A.
Cardiac pacemaker rhythmicity and signaling fidelity are maintained across temperature fluctuations because quantum-mediated noise prevents the irregular signaling that arises from temperature-dependent classical stochasticity.
Spatially patterned, spectral single-molecule microscopy
Beckwith, J. S.; Cullinane, B.; Heraghty, D. F.; Krokowski, S.; Jones, C. L.; Yang, S.; Gregory, R. C.; Floto, R. A.; Santos, A. M.; Davis, S.; Vendruscolo, M.; Klenerman, D.; Lindo, V.; Sankaran, P. K.; Lee, S.
Commercially available color CMOS detectors, when combined with direct fitting of raw pixel responses, enable the simultaneous recovery of molecular positions and spectral fingerprints without the need for complex beam-splitting or dispersive optical architectures.
Serial femtosecond crystallography reveals the pH-driven allosteric mechanism of hexamer glargine
AYAN, E.; Shankar, M. K.; Telek, E.; Kang, J.; Fintor, K.; Yabuuchi, T.; Yabashi, M.; Tosha, T.
Structural transitions from compact near-neutral assemblies to plastic, molten-like acidic states mechanistically link glargine’s isoelectric precipitation to its prolonged pharmacological release.
Recovering membrane interaction kinetics of single molecules from 3D tracking data
Lundin, E.; Volkov, I. L.; Johansson, M.
Quantifying the circular curvature of 3D trajectory segments within a hidden Markov modeling framework enables the discrimination of cytosolic and membrane-bound states in rod-shaped bacteria without relying on diffusion-rate changes or direct colocalization.
Molecular basis of protein-glycan cross-linking by CpCBM92A revealed by NMR spectroscopy
Trooyen, S. H.; Ruoff, M. S.; McKee, L. S.; Courtade, G.
Three distinct binding sites with specialized affinities for specific glucan linkages and chain lengths coordinate the simultaneous engagement of multiple carbohydrate polymers.
Comparative performance of three optical biosensing platforms for SARS-CoV-2 antibodies detection in human serum
Agostino Occhicone, Alberto Sinibaldi, Peter Munzert, Jordan N. Butt, Ethan P. Luta, Diego M. Arévalo, Francesco Michelotti, Benjamin L. Miller
Bloch surface wave and microring resonator technologies provide rapid, label-free antibody quantification that matches clinical benchmarks and maintains high repeatability across different biochip batches.
Spatially Structured Cohesion from Extremal Alignment in Topological Active Matter
Julian Giraldo-Barreto, Viktor Holubec
Orientation-dependent neighborhood selection generates a density-coupled cohesive bias that stabilizes finite, structured flocks without the need for explicit attractive forces.
Mode-coupling theory for aging in active glasses: relaxation dynamics and evolution towards steady state
Soumitra Kolya, Nir S. Gov, Saroj Kumar Nandi
Quench distance from the activity-modified critical point determines the exponent \(\delta\), demonstrating that increased self-propulsion slows the growth of relaxation times while the effect of persistence time depends on the specific nature of the activity.
Influence of Plaque Characteristics on Stent Biomechanical Outcomes - A Case Study on Double Kissing Crush Coronary Stenting
Andrea Colombo, Dario Carbonarob, Mingzi Zhang, Chi Shen, Ankush Kapoor, Nigel Jepson, Claudio Chiastra, Susann Beier
Plaque composition significantly alters arterial wall stress, lumen restoration, and local hemodynamics while modifying the relative performance of different stent platforms.
Generation-Establishment Tradeoffs Shape the Temporal Window of Recombinant Evolution
Anthony, S. J.; Wells, H. L.; Mitra, U.; Newton, P. K.
The interplay between density-dependent generation and competitive suppression creates a non-monotonic hazard landscape with a unique interior maximum, dictating exactly when population dynamics allow new lineages to establish..
DNA-Functionalized Nanoparticles for Multicolor Cathodoluminescence Imaging
Conway, J. B.; Abdul Rehman, S.; Prigozhin, M. B.
Lanthanide nanoparticles maintain their distinct emission signatures throughout standard electron microscopy staining and drying protocols, enabling simultaneous multiplexed protein labeling and high-resolution ultrastructural imaging in mammalian cells.
Direct Membrane Penetration of Oligoarginines by Fluorescence and Cryo-electron Microscopy Combined with Molecular Simulations
Baxova, K.; Morandi, M.; Scher, N.; Kula, P.; Tichacek, O.; Schachter, I.; Busko, P.; Zahradnik, J.; Vazdar, M.; Koikkara, J.; Allolio, C.; Avinoam, O.; Jungwirth, P.
Nonaarginine drives cellular entry through a mechanism of membrane folding and multilamellar stacking, producing structural deformations that vary in complexity according to the size of the accessible membrane reservoir.
Subdiffusive random growth of bacteria
Wei, J.; Lin, J.
Complex viscoelastic mechanics of the cell wall, rather than biological regulation, dictate short-timescale growth noise by inducing strong negative temporal correlations through power-law-distributed relaxation times.
Localized ribosome access and distal tuning via the Listeria prfA RNA thermometer
O’Steen, M. R.; Chen, J. V.; Beier, D. H.; Walter, N. G.; Keane, S. C.
Hierarchical unfolding enables the ribosome binding site to open selectively at 37 °C while the upper helix remains structured, establishing a quantitative link between localized structural dynamics and translational activation.
Curvature-mediated prewetting organize mitochondrial nucleoid
Hu, X.; Shu, L.; Zhang, G.; Jiang, Y.; Yin, Y.; Xu, Y.; Wang, Y.; Shang, Y.; Cao, J.; Li, T.; Fang, S.; Guo, S.; Li, D.; Jiang, D.; Weber, C. A.; Liu, C.; Chen, Z.; Zhao, X.; Ge, Y.
Negatively high-curvature regions lower the nucleation energy barrier for TFAM to drive localized protein condensation at physiological concentrations, establishing membrane geometry as a thermodynamic switch for spatial cellular organization.
Partial EMT Drives Persistent Collective Migration via Collision Guidance in Heterogeneous Populations
Jeong, H.; Kim, J.; Sim, J.-Y.; Leggett, S. E.; Wong, I. Y.
TGF-beta-stimulated populations utilize a distinct post-contact alignment mechanism to maintain rapid coordination and physically displace neighboring epithelial or mesenchymal monolayers.
Membrane structural properties in Staphylococcus aureus are tuned by the carotenoid 4,4’-diaponeurosporenoic acid
Munera-Jaramillo, J.; Lopez, G.-D.; Suesca, E.; Ibanez, E.; Cifuentes, A.; Carazzone, C.; Leidy, C.; Manrique-Moreno, M.
This biosynthetic intermediate increases the lipid phase transition temperature and reduces interfacial hydration to enhance molecular order, acting in a functionally distinct yet complementary manner to staphyloxanthin in the regulation of lipid packing.
Dimerisation and twist reversal of the Lewy fold in α-synuclein mutants with Parkinson’s disease and dementia
Zhang, H.; Murzin, A. G.; Macdonald, J. A.; Hinton, T. V.; Peak-Chew, S.; Franco, C.; Cullinane, P. W.; Warner, T.; Okuzumi, A.; Real, R.; Nishioka, K.; Taniguchi, D.; Kaneda, D.; Morris, H.; Houlden, H.; Ghetti, B.; Jaunmuktane, Z.; Yang, Y.; Scheres, S.; Goedert, M.
Pathogenic A53T and G51D substitutions produce left-handed filament configurations lacking island A density, whereas H50Q retains a right-handed wild-type fold and M83 transgenic mice develop structures resembling multiple system atrophy rather than human Lewy bodies.
Linear odd electrophoresis of a sphere in a charged chiral active fluid
Reinier van Buel, Bogdan Cichocki, Jeffrey C. Everts
Directional asymmetries in the electrophoretic mobility tensor persist even under thin electric double layer conditions, distinguishing transport in these chiral active systems from the isotropic behavior found in Newtonian fluids.
Frictional sliding strength of knotted and capstan configurations along the axis of a cylinder
Javier Sabater, Ji-Sung Park, Jérôme Crassous, Sébastien Neukirch, Pedro M. Reis
Superlinear scaling in sliding resistance originates from the mechanical coupling between normal forces and evolving contact arclength during tightening, transitioning to linear behavior only after full contact with the cylinder is established.
Intrinsically disordered ligands for the control of receptor uptake by endocytosis
Park, S.; Sarro, I.; Kamatar, A.; Wang, L.; Rangamani, P.; Lafer, E. M.; Stachowiak, J.
Engineered protein chimeras utilize sequence-encoded attractive or repulsive interactions to either drive receptor clustering for internalization or maintain surface expression, offering a programmable platform for modulating cellular behavior.
Theoretical estimate of the effective pKa of titratable lipids using continuum electrostatics
Sur, S.; Grossfield, A.
Salt concentration and membrane composition modulate surface potential to drive ionization shifts, with the largest deviations from solution values occurring at high lipid densities.
Mechanism underlying the ultralow energy-consumption rapid ion dehydration for the high flux of KcsA potassium channels
Wang, Y.; Song, B.; Jiang, L.
Resonant energy transfer from coherently oscillating ions in the filter drives a tunneling-like motion of K+ ions, allowing them to shed their hydration shells through a two-stage coupling process between the channel cavities and the filter.
Electrostatic Actuation Induces Competing Adhesion and Vibration Regimes at Fingertip Contact
Kenanoglu, C. U.; Wiertlewski, M.; Vardar, Y.
Time-resolved measurements of the fingertip-surface interface demonstrate that electrostatic tactile feedback follows an inverted U-shaped frequency response, where low-frequency vibrations decrease interfacial shear stress and high-frequency viscoelastic effects shift the system toward an adhesion-dominated regime.
The low-field effect in radical pairs: a zero-field singlet-triplet basis picture
Woodward, J. R.
Sequential recruitment of dark triplet states into the singlet-accessible manifold reveals the underlying mechanism of magnetic sensitivity and provides a framework for estimating its maximum potential in arbitrary spin systems.
Critical amino acid residues in the N-terminal domain of NADPH-dependent assimilatory sulfite reductase flavoprotein mediate octameric assembly
Walia, N.; Pedrete, T.; Ahmadizadeh, F.; Rahman, E.; Garg, Y.; Washburn, B.; Pye, C.; Liu, F.; Randolph, P. S.; Weiss, K. L.; Nagy, G.; Bleiholder, C.; Stroupe, M. E.
A 52-residue segment containing Gln22, Tyr39, Phe40, and Gln47 functions as a portable, chemically robust motif for engineering stable octameric complexes in heterologous protein systems.
Molecular basis for ligand-gating of the human GluD1 receptor
Mondal, A. K.; Wang, H.; Weaver, M. G.; Zheng, I.; Kormshchikov, N.; Ahmed, F.; Twomey, E. C.
GABA and D-serine binding to the ligand-binding domain triggers cation influx through a non-swapped transmembrane ion channel architecture.
Protein Language Models Encode Evolutionary Grammar but Conflate Topological and Thermodynamic Phases
Wang, Y.; Cai, M.; Ma, Y.; Wang, X.; Wei, K.
ESM-2’s latent manifold prioritizes macroscopic physicochemical composition over microscopic backbone geometry, resulting in the homogenization of structurally distinct proteins that share similar evolutionary sequence statistics.
PI(4,5)P2-dependence of GABAA receptor channel function revealed by optogenetic manipulation of a binding site
Mori-Kreiner, R.; Andriani, R. T.; Strasdeit, T.; Zhou, J.; Miyashita, N.; Yonezawa, Y.; Kawai, T.; Kloecker, N.; Okamura, Y.
High-affinity binding at the α1 K311 residue accelerates receptor activation and safeguards inhibitory signaling against acute membrane phospholipid fluctuations across multiple classes of inhibitory ion channels.
Tuning siRNA packing order in lipid nanoparticles modulates oligonucleotide functional delivery
Breuer, A.; Kyriakakis, G.; Dreisler, M. W.; Schulz, F. H.; Bolis, G.; Margaritaki, S.; Papageorgiou, V.; Spacho, N.; Hatzakis, N. S.
Low-order siRNA arrangements within lipid nanoparticles promote superior gene silencing compared to more compact packing, identifying specific N/P ratios and lipid compositions that maximize therapeutic potency.
Energetic analysis of Na+/K+-ATPase using bond graphs
Ai, W.; Hunter, P. J.; Pan, M.; Nickerson, D. P.
Physiological efficiency reaches approximately 75% through chemical and electrical energy storage, with a sharp decline in chemoelectrical transduction occurring once the free energy of ATP hydrolysis falls below a critical threshold of -48 kJ/mol.
Two-dimensional active polar semiflexible polymer under shear flow
A. Lamura, R. G. Winkler
Filaments exhibit negative viscosity at low shear rates and tumbling dynamics with a stronger Weissenberg number dependence than passive polymers, while their spatial extension follows a characteristic scaling exponent determined by their semiflexibility.
Hydrodynamic Switching Fronts Polarize Deformable Particle Trains
Linzheng Huang, Hengdi Zhang, Zaicheng Zhang, Zaiyi Shen
Directionally biased interactions driven by individual particle asymmetry enable inclination states to relay through the train as propagating fronts, resulting in either uniform polarization or persistent domains depending on boundary conditions.
Diffusion from particle-coated drops: the subtle role of particle size
Alexandros T. Oratis, Matteo Camagna, Timo J. J. M. van Overveld, Valeria Garbin
Interfacial particle monolayers impose minimal resistance to solute transport unless their coverage reaches extreme fractions beyond the close-packing limit.
Free chiral self-propelled robots compared to active Brownian circle swimmers
Thomas Kiechl, Amy Altshuler, Anton Lüders, Yael Roichman, Thomas Franosch
Overdamped Langevin equations accurately predict mean-squared displacement and intermediate scattering functions, while revealing that translational noise primarily affects short-term real-space propagation.
Inertial chiral active Brownian particle: Transition from Gaussian to platykurtic distribution
M Muhsin, S Deion, M Sahoo
Resonance between the harmonic trapping frequency and the particle’s inherent chiral frequency maximizes the steady-state mean square displacement and minimizes position kurtosis, creating a nearly uniform probability distribution near the potential center.
Taylor dispersion in a soft channel
Aditya Jha, Masoodah Gunny, Joshua D Mcgraw, Yacine Amarouchene, Thomas Salez
Elastic wall deformation in response to hydrodynamic pressure increases the effective advection velocity and the dispersion coefficient under both steady and pulsatile flow conditions.
Haematocrit and Shear Rate Modulate Local Cell-free Layer Thickness and Platelet Margination in Blood Flow Along a Sinusoidal Wall
Eleonora Pero, Giovanna Tomaiuolo, Stefano Guido, Claire Denham, Timm Krueger
Low-hematocrit conditions promote platelet accumulation at surface crests to drive high-amplitude growth, while higher concentrations facilitate a more uniform distribution along the vessel topography.
Linear Viscoelasticity of Semidilute Unentangled Flexible Polymer Solutions
Amit Varakhedkar, P. Sunthar, J. Ravi Prakash
Brownian dynamics simulations identify a concentration-dependent crossover from Zimm to Rouse behavior resulting from the screening of hydrodynamic and excluded volume interactions, yielding quantitative predictions of experimental response through a successive fine-graining approach.
Reciprocal-space mapping of diffuse scattering by serial femtosecond crystallography reveals analog-specific disorder in insulin analogs
AYAN, E.; Kang, J.; Tosha, T.; Yabashi, M.; Shankar, M. K.
Detemir exhibits strong pseudo-translational signatures while aspart shows pronounced merohedral twinning under near-physiological conditions, highlighting distinct modes of structured heterogeneity that inform the stability and design of these clinical therapeutics.
Allosteric Mechanisms Underlying Long QT Syndrome Type 2 (LQT2) Associated Mutations in hERG Channels
Deyawe Kongmeneck, A.; San Ramon, G.; Delisle, B.; Kekenes-Huskey, P.
Structural destabilization of the selectivity filter by S4 helix mutations governs the trafficking-deficient phenotype, which can be mitigated by compensatory second-site variants like Y652C.
Disruption of Drosophila melanogaster Larval Locomotion Caused by Silver Ions
Stewart, M.; Pradhan, H.; Zhuang, X.; Wang, Y.
Dose- and time-dependent reductions in crawling speed and accumulated distance stem from impaired peristaltic rhythms that trap the organisms in a prolonged stop phase.
Molecular dynamics simulations illuminate the role of sequence context in the ELF3-PrD-based temperature sensing mechanism in plants
Lindsay, R. J.; Sahoo, A.; Viegas, R. G.; Leite, V. B. P.; Wigge, P. A.; Hanson, S. M.
Heat-induced disruption of long-range contacts exposes sticky aromatic residues and promotes the formation of polyQ-dependent helices that drive the reversible condensation required to regulate growth-related transcription.
Ion-Containing Bottlebrush Elastomers as Pressure-Sensitive Electroadhesives
Hao Dong, Intanon Lapkriengkri, Nadia Chapple, Hyunki Yeo, Alexandra Zele, Hiba Wakidi, Thuc-Quyen Nguyen, Michael L. Chabinyc, Christopher M. Bates, Megan T. Valentine
Complementary anionic and cationic polymer networks leverage mobile ion migration to achieve reversible, high-strength adhesion at operating potentials below 2 V.
A Modular 3D-Printed Design to Investigate Prebiotic Chemical Systems in Hot Spring Pools
Arslan Siddique, Dev Chauhan, Alethea Dutton, Kavish Reddy, Soumya Kanti De, Albert C. Fahrenbach, Tracie Barber, Martin Van Kranendonk, Anna Wang
Interconnected chambers replicate fluctuating environmental conditions and fluid exchange to facilitate the spontaneous formation and organic encapsulation of diverse lipid vesicle morphologies.
On phenomenology of physical effects in axons
Jüri Engelbrecht, Kert Tamm, Tanel Peets
Hybrid mathematical models incorporating observables like temperature fluctuations and phenomenological inductance provide a more realistic representation of the coupled electrical, mechanical, and thermal processes driving signal transmission.
Label-Free 4D Holotomography with Depth-Adaptive Segmentation for Quantitative Analysis of Lipid Droplet Dynamics in Hepatic Organoids
cho, j.; lee, h.; oh, c.; park, j.; park, s.; koo, b.-k.; Park, Y.
Mouse hepatic organoids exhibit distinct lipid accumulation strategies depending on fatty acid treatment, where oleic acid promotes droplet enlargement and linoleic acid increases droplet frequency, while palmitic acid triggers rapid structural collapse.
Doubling the Field of View in Common-Path Digital Holographic Microscopy via Wavelength Scanning and Polarization Gratings
Piekarska, A.; Rogalski, M.; Stefaniuk, M.; Trusiak, M.; Zdankowski, P.
The multi-shear replica-removal algorithm leverages wavelength-dependent shear variations to separate overlapping object information, facilitating high-quality quantitative phase imaging of dense biological structures and dynamic processes.
Binding Structures, Mechanical Properties, and Effects on Cellular Behaviors of Extracellular Matrix Proteins on Biomembranes
Ivanovskaya, V.; Ruffing, J.; Phan, M. D.
Collagen and elastin facilitate cell migration through rigid scaffolding and minimal membrane disruption, respectively, while fibronectin restricts motility via complex structural rearrangements and excessive adhesion forces, providing a mechanical basis for engineering cell-specific scaffolds.
Unravelling the plausible metal-dependent catalytic mechanism of Inositol monophosphatase ortholog from Pseudomonas aeruginosa through the lenses of macromolecular crystallography and enzyme kinetics
Yadav, V. K.; Jena, A. K.; Mukerji, M.; Mishra, A.; Bhattacharyya, S.
A triad of magnesium ions and an active-site Threonine/Aspartate dyad activate water molecules to perform a nucleophilic attack on the substrate’s phosphorus atom, driving the formation of a trigonal bipyramidal transition state and subsequent product release.
Osmotic pressure gradients in E. coli biofilms revealed by in-situ sensors
Zhang, W.; Schneck, E.; Bertinetti, L.; Bidan, C. M.; Fratzl, P.
Radial increases in osmotic pressure from the biofilm’s interior to its periphery govern colony morphology and growth by driving matrix swelling, nutrient transport, and mechanical stress distribution.
Quantitative comparison of fluorescent reporters by FCS excitation scan
Schneider, F.; Trinh, L. A.; Fraser, S. E.
Systematic benchmarking across multiple living systems identifies mNeonGreen as the most effective reporter among ten common variants for quantitative imaging and diffusion studies.
Osmotically Induced Shape Changes in Membrane Vesicles
Pereira, R. G.; Mukherjee, B.; Gautam, S.; D’Agnese, M.; Biswas, S.; Meeker, R.; Chakrabarti, B.
A self-consistent framework incorporating solute conservation reveals that spherical instability is driven by global free-energy competition rather than linear mechanical criteria, correcting classical stability predictions by several orders of magnitude.
Nucleolar Condensation Orchestrates rRNA-dependent Mobility and Spatiotemporally Enriches rDNA-binding of Human Chromatin Remodeler BRG1
Ng, W. S.; Engl, W.; Zhao, Z. W.
Patterned charge blocks within the C-terminal intrinsically disordered region drive the protein’s partition into the fibrillar center, creating a dynamic environment that coordinates its local diffusion and genomic recruitment.
Structured local mismatch placement and internal packaging in cardiomyocytes during hyperthermal sarcomeric oscillations
Shintani, S. A.
Identical minimal local reconfigurations are organized by a shared rephasing compass that dictates mismatch placement and are internally processed through distinct redistribution routes ranging from compact to broad.
Efficient Double Helix Detection with Steerable Filters
Barentine, A. E. S.; Balaji, A.; Moerner, W. E.
A localization analysis pipeline utilizing seven convolutions achieves state-of-the-art 3D tracking performance with significantly lower computational overhead than deep-learning approaches.
Exact Generalized Langevin Dynamics of Pair Coordinates in Elastic Networks
Shunsuke Ando, Tomoya Urashita, Soya Shinkai, Tomoshige Miyaguchi
Analytical formulas for memory kernels and restoring forces provide a rigorous framework for reducing high-dimensional many-body motions into exact stochastic descriptions of inter-bead distance fluctuations.
Emergent Rotation of Passive Clusters in a Chiral Active Bath
Divya Kushwaha, Abhra Puitandy, Shradha Mishra
Aggregated clusters develop persistent rotational states and superdiffusive angular dynamics only within specific regimes of size ratio and packing fraction where coherent torque and structural order coexist.
Long distance attraction between particles in a soap film
Youna Louyer, Megan Delens, Nicolas Vandewalle, Benjamin Dollet, Isabelle Cantat, Anaïs Gauthier
Non-reciprocal forces driven by boundary-dependent film deformations result in asymmetric interactions that vary in magnitude and direction depending on each particle’s position relative to the frame.
Gerrymandering in the heart: How tissue heterogeneities promote premature ventricular contractions
Daisuke Sato, Donald M. Bers
Spontaneous subcellular calcium waves generate transient inward currents that overcome the suppressive electrical load of surrounding healthy cells to initiate triggered activity.
Active Transport as a Mechanism of Microphase Selection in Biomolecular Condensates
Le Qiao, Peter Gispert, Lukas S. Stelzl, Friederike Schmid
Active redistribution of proteins along cytoskeletal networks generates an effective long-range repulsion that arrests coarsening, allowing for programmable control over condensate size and morphology through motor binding rates and transport velocities. Doesn’t cite Bez :( .