Feb 23 26
Featured Papers
Topological control of spontaneous failure in active nematic solids
Sheng Chen, Matthew Ricci, A. Pasha Tabatabai, Zachary Gao Sun, Sven Witthaus, Suraj Shankar, Mor Nitzan, Michael P. Murrell
Tailored defect patterns guide the initiation and propagation of fractures by localizing internally generated stresses within the material’s elastic matrix.
A tunable autonomous RNA-fueled micro-engine
Kun Wang, Wenjun Chen, Buming Guo, Qiuyan Huang, Guolong Zhu, Heng Ni, Lei Zhang, Melanie Perez, Ruojie Sha, Nadrian C. Seeman, Paul M. Chaikin
RNase H-mediated enzymatic cleavage and sequence-specific RNA binding drive autonomous, reversible conformational cycles that power the movement of 500 nm particles at programmable speeds.
Squeaking at soft–rigid frictional interfaces
Adel Djellouli, Gabriele Albertini, Jackson Wilt, Vincent Tournat, David Weitz, Shmuel Rubinstein, Katia Bertoldi
High-frequency stick-slip oscillations driven by nonlinear friction generate audible acoustic emissions when elastomeric materials slide against rigid surfaces.
CLIPPER Regulates LPIN1-Mediated Mitochondrial Biogenesis and Heart Regeneration
Francesco Paolo Ruberto, Daniel Maric, Tatjana Kleele, Mohamed Nemir, Isabelle Plaisance, Luca Braga, Hashim Ali, Chang Jie Mick Lee, Thong Beng Lu, Alexandre Sarre, Parisa Aghagolzadeh, Roger S.-Y. Foo, Suliana Manley, Mauro Giacca, Thierry Pedrazzini
Silencing this conserved long noncoding RNA triggers midzone mitochondrial fission and metabolic shifts that reduce oxidative DNA damage, thereby enabling cardiomyocyte proliferation and functional recovery after myocardial infarction.
Non-inertial scan angle multiplier for expanded fields-of-view
Che-Hang Yu, Yiyi Yu, Joseph S. Canzano, Yuandong Fei, Filip Tomaska, Spencer LaVere Smith
Decoupling scan speed from mirror inertia increases system étendue and throughput while maintaining diffraction-limited performance and beam quality across a broad wavelength range.
Partition Coefficients Reveal Changes in Properties of Low-Contrast Biomolecular Condensates
Varma, K.; Matthias, D.; Shapiro, C. B.; Bailey-Darland, S.; Matsuzawa, T.; Lorenz, C.; Bate, T.; Thornton, S. J.; Duraivel, S.; Style, R. W.; Sethna, J. P.; Dufresne, E. R.
Small molecules added to simplified systems reduce biochemical enrichment to physiological levels, inducing significant fluctuations and material property shifts that are characterizable through a reformulated theory of critical phenomena.
Some Papers
Self-consistent automatic retrieval of single cell rotation enables highly reliable holo-tomographic flow cytometry
Pirone, D.; Miccio, L.; Bianco, V.; Ferraro, P.; Memmolo, P.
An iterative reprojection-based optimization algorithm determines precise rotation sequences from reconstructed refractive index data, eliminating the need for prior information and increasing the throughput of label-free 3D imaging.
Hydrodynamics of Dense Active Fluids: Turbulence-Like States and the Role of Advected Activity
Sandip Sahoo, Siddhartha Mukherjee, Samriddhi Sankar Ray
Heterogeneous activity fields coupled to flow dynamics generate sharp interfacial fronts and localized vortices, revealing that universal spectral behavior in active fluids is inherently local and time-dependent.
Universal Persistent Brownian Motions in Confluent Tissues
Alessandro Rizzi, Sangwoo Kim
Traction forces and junctional tension fluctuations produce distinct structural and dynamical signatures that allow for the identification of dominant active force mechanisms in fluid-state tissues.
Geometrical preference of anchoring sites in the unicellular organism Stentor coeruleus
Syun Echigoya, Takuya Ohmura, Katsuhiko Sato, Toshiyuki Nakagaki, Yukinori Nishigami
Calcium-induced asymmetric body deformation drives wall-following behavior through hydrodynamic interactions, enabling the organism to locate and select narrow corners for attachment via purely biophysical processes.
Non-uniform filament turnover, contractility, and bundle formation in disordered actomyosin networks
Alexander K.Y. Tam, Alex Mogilner, Dietmar B. Oelz
Distinct filament turnover mechanisms, such as treadmilling and branching, sustain steady-state contraction by preventing the network from reaching a stationary, non-contractile bundled state.
Hypoxia-Driven Changes in Nuclear Morphology as a Determinant of Cell Migration
Prema Kumari Agarwala, Rohit Joshi, Abhijit Majumder, Shobhna Kapoor
Cobalt chloride-induced environments drive pancreatic cancer cell invasion by reducing cell spread area, enhancing filopodia formation, and decreasing actin anisotropy to modify cellular and nuclear mechanics.
Autonomous Chemo-mechanical Oscillations in Crosslinked Filamentous-Actin Gels
Ken-Ichi Sano, Ryuzo Kawamura, Yoshihito Osada
Artificial cytoskeletal networks recreate the rhythmic mechanical behaviors necessary for cellular functions such as motility and structural regulation.
Centromeres and Telomeres as Rheological Probes of the Human Cell Nucleus
Alexis S. Clavijo, Steven Ionov, Alexandra Zidovska
Dynamical self-organization of the genome is governed by physical principles inherent to its behavior as a living polymer in live cells.
Mechanochemical feedback between confinement and actin crosslinking drives the shape dynamics of liquid-like droplets
Mansour, Daniel, Jordan, Dominique, Walker, Caleb, Chandrasekaran, Aravind, Lee, Christopher T., Graham, Kristin, Stachowiak, Jeanne C., Rangamani, Padmini
Multivalent crosslinkers modulate the internal filament architecture to regulate the morphological evolution of protein-based condensates.
Nanoscale imaging of expanded cells and proteins with spontaneously blinking dyes
Sauer, M.; Taban, D.; Jungblut, M.; Budiarta, M.; Helmerich, D. A.; Kiesel, C.; Doose, S.; Kollmannsberger, P.; Plutkiss, S.; Lavis, L.; Rizzoli, S.; Shaib, A. H.; Krah, D.; Beliu, G.
A single-step expansion method enables single-molecule localization microscopy in 6–14x expanded samples without re-embedding, resolving the molecular architecture of nuclear pore complexes and recombinant proteins.
A Unifying Thermodynamic Model for Phase Separation and Aging of Biopolymers
Michels, J. J.; Caria, J.; Lemke, E. A.
Time-dependent changes in the average valency of reversible folding sites govern the kinetic hardening and viscoelastic evolution of protein condensates within a multi-component extension of associating polymer theory.
Nanopore-based massively parallel sensing for peptide profiling and protein identification
Wang, Ji, Chen, Junyi, Pan, Hailin, Luo, Fengqin, Qin, Wenbing, Zeng, Huixian, Yuan, Xilong, Qiao, Yuchen, Zhang, Yunfeng, Zhang, Yishuo, Wang, Dapeng, Shen, Liang, Zhai, Zhiwei, Zhu, Qianhua, Deng, Yuqing, Sheng, Xiaojing, Xie, Qingqing, Zhang, Yuning, Yan, Xu, Zeng, Tao, Shen, Mengzhe, Bai, Yinqi, Teng, Bo, LI, Yuxiang, Liu, Chuanyu, Wang, Ou, Dong, Yuliang, Liu, Siqi, Xu, Xun
Integration of library preparation with AI-driven analysis overcomes previous technical bottlenecks to facilitate precise peptide identification and antibody validation.
On the Statistical Mechanics of Active Membranes: Some Selected Results
Sreekanth Ramesh, Prashant K. Purohit, Yashashree Kulkarni
Analytical expressions for the tension-area relation, fluctuation amplitudes, normal vector correlations, and persistence length provide a theoretical basis for interpreting the mechanical behavior and experimental assays of biological membranes operating far from equilibrium.
Tensile Expansion Microscopy Applies Mechanical Force to Super-resolve Fixed and Image Live Cellular Samples
Kisley, L.; Venkataramani, V.; Latham, D. R.; Arampongpun, R.; Zammali, M.; Shrikanth, T.; Mohapatra, A.; Guerrero, J. A.; Andresen Eguiluz, R. C.; Mathur, D.; Sanchez, L.
Continuous stretching of tough double-network hydrogels via an electromechanical iris enables real-time monitoring of biological dynamics with high reproducibility and minimal distortion.
Persistence-Driven Void Formation in Active-Passive Mixtures
Giulia Janzen, Liesbeth M. C. Janssen, Nuno A. M. Araújo, Rastko Sknepnek, D. A. Matoz-Fernandez
Increasing persistence triggers a transition from uniform melting to a localized mechanical instability, where stress accumulation drives collective, mosh-pit-like rearrangements at the boundaries of nucleated voids.
Coupling between Phase Separation and Geometry on a Closed Elastic Curve: Free Energy Minimization and Dynamics
Hanchun Wang, Ronojoy Adhikari, Michael E. Cates
Elastic bending and stretching energies either suppress phase separation or stabilize multi-interface metastable states that are absent on rigid circular domains.
Chaos in Liquid Crystal Directrons
Praveen Kumar Singh, Salman Ahmad Khan, Soumik Das
Multi-directron interactions and electric field thresholds trigger a transition from directed motion to a biomimetic chaotic state characterized by randomized trajectories, dynamic assembly, and spontaneous fission.
Activated kinesin-1 assembles into a dimer-of-dimers
Chiba, K.
KIF5C undergoes reversible tetramerization via its C-terminal tail upon the relief of autoinhibition, forming a more processive motor complex with an increased affinity for microtubules.
Dynamic control of IDP interaction network via diverse binding pathways
Kim, Jae-Yeol, Chung, Hoi Sung
Three-color single-molecule FRET reveals the structural mechanisms underlying heterogeneous partner exchange.
Some More Papers
Allosteric activation of the glutamate receptor mGlu2 by the serotonin receptor 5-HT2A
Gai, Siyu, Lin, Li, Meng, Jiyong, Wu, Yichen, Xue, Li, Xu, Chanjuan, Sun, Qian, Ricarte, Adrià, Dalton, James, Renault, Pedro, Giraldo, Jesús, Pin, Jean-Philippe, Rondard, Philippe, Liu, Jianfeng
Molecular mechanisms within heteromeric complexes facilitate the integration of intracellular signaling through functional cross-talk between diverse G protein-coupled receptors.
Quantum-augmented graph differential geometry enhances accuracy in protein-protein interaction prediction
Karthick, V., Alshammari, Fahad Sameer, Jayasimman, I. Paulraj, Besi, P. Roselyn, Akgul, Ali
QGDM integrates quantum superposition and entanglement effects to identify 1,247 novel human protein-protein interactions with a 91.8% experimental validation rate.
Spatiotemporal mapping of microscale stiffness during collagen polymerization and crosslinking by optical multifrequency time-harmonic elastography
Frank Sauer, Jakob Jordan, Tom Meyer, Pedro Dantas de Moraes, Guillaume Flé, Josef Alfons Käs, Ingolf Sack
Optimized point-wise shear wave excitation enables rapid mechanical profiling of extracellular matrix-derived networks within small sample volumes.
Non-linear visco-elasto-plastic rheology of a viscous vertex model
Shalabh Kumar Anand, Matthias Merkel
Mean-field constitutive relations bridge cell- and tissue-scale mechanics by incorporating active anisotropic cellular stresses and providing a general framework to derive macroscopic behavior from cell-based models.
HOP2–MND1 chaperones a diffusing DMC1–ssDNA complex to survey dsDNA for homology recognition during meiotic recombination
Bingkai Cheng, Yanan Li, Yi Zhao, Yuting Zhang, Xia Zhang, Lishuang Chen, Hao Yang, Xiaoxuan Song, Zhiyun Ren, Cong Liu, Jingdong Xue, Bing Li, Chao Liu, Wei Li, Bo Sun
Clamping of ssDNA–dsDNA junctions by the HOP2–MND1 complex stabilizes an expanded DNA bubble, enabling the diffusing presynaptic filament to achieve the sequence alignment necessary for recombination.
An information theory approach to quantifying the sequence-dependent response of nucleic acid motors with applications to nanopore DNA sequencing
Craig, Jonathan M., Laszlo, Andrew H., Brinkerhoff, Henry, Thomas, Christopher A., Marx, Sinduja K., Lebo, Eric F., Abell, Sarah J., Franzi, Michaela C., Huang, Jesse R., Kim, Hwanhee C., Carrasco, Jessica D., Gundlach, Jens H.
Mutual information analysis of helicase kinetics improves the base-calling accuracy of all standard DNA nucleotides.
Spatial resource dynamics control resistance escape
Appold, N.; Citak, T.; Palm, A.; Kayser, J.
Intermittent treatment pulses reconfigure growth zones and resource availability, establishing a critical dosing threshold that balances overall population reduction with the sustained physical confinement of emerging resistant mutants.
The influence of cell morphology on the dynamics and stability of model bacterial communities
Lim, I. X.; Halabeya, F.; Milstein, J.
Coccus cells more effectively invade and fixate within confined microchannels compared to bacillus cells, which maintain quasi-stability through mechanical alignment and restricted inter-lane movement.
Structure and polydispersity of single lipid vesicles by small-angle X-ray scattering at European XFEL
Neuhaus, Charlotte, Stammer, Moritz L., Alfken, Jette, Osterhoff, Markus, Komorowski, Karlo, Major, András, Bielecki, Johan, Rafie-Zinedine, Safi, de Wijn, Raphael, Letrun, Romain, E, Juncheng, Bean, Richard, Salditt, Tim
Radial electron density profiles extracted from individual diffraction hits resolve the lipid bilayer structure while circumventing the limitations of radiation damage and ensemble averaging.
Counteraction of HMGB1 at ss-dsDNA junctions maintains liquidity of protamine-DNA co-condensates
Ahlawat, V.; Kota, D.; Zhou, H.-X.
The acidic C-terminal tail of HMGB1 prevents the formation of rigid protamine-DNA tangles, creating a liquid environment that allows repair machinery to access double-strand breaks during the sperm chromatin transition.
Estimation of Absolute Protein-DNA Binding Free Energy using Streamlined Geometric Formalism
Mukherjee, S.; Srivastava, D.; Patra, N.
Evaluation of three specific complexes yields chemically accurate results and identifies key intermolecular forces while maintaining modest computational requirements.
Oligo DNA-based quantum dot (QD) single-particle tracking for multicolor single-molecule imaging
Sakuragi, S.; Kato, N.; Uchida, T.; Zhao, B.; Katagiri, T.; Enomoto, M.; Kato, R.; Yoshimura, H.; Oyama, C.; Katayama, I.; Chikuma, A.; Teramura, Y.; Bannai, H.
Complementary 20-mer sequences incorporating polyA-polyT linkers overcome conjugation limitations to facilitate the simultaneous observation of distinct lipid and protein diffusion dynamics in the same living cell.
Synaptic spine head morphodynamics from graph grammar rules for actin dynamics
Hur, M.; Bartol, T.; Rangamani, P.; Sejnowski, T.; Mjolsness, E.
Dissipative stochastic simulations delineate the epistatic relationships between actin-binding proteins and their collective impact on the structural remodeling of the postsynaptic membrane.
Exploring Conformational Transitions of RNA Dimers via Machine Learning Potentials
Medrano Sandonas, L.; Tolmos Nehme, M.; Cofas-Vargas, L. F.; Olivos-Ramirez, G. E.; Cuniberti, G.; Poblete, S.; Poma, A. B.
Equivariant MACE potentials trained on high-level quantum data accurately capture the interplay of base stacking and backbone flexibility while demonstrating superior sampling of structural transitions compared to existing general-purpose models.
Decoding the Allosteric Paradox: A Dual Framework Integrating AI Cofolding Models with Landscape-Guided Interpretable AI Framework of Ligand-Protein Binding
Parikh, V.; Foley, B.; Gatlin, W.; Ludwick, M.; Turano, L.; Verkhivker, G.
Leading AI architectures consistently fail to predict allosteric complexes because these sites maintain neutral frustration landscapes that lack the distinct energetic and evolutionary signatures found in orthosteric pockets.
Calcium activation mechanism of a noncanonical aromatic L-amino acid decarboxylase from psilocybin mushroom Psilocybe cubensis
Li, Tianjie, Reynolds, Erin E., Wang, Ziqi, Torrens-Spence, Michael P., Weng, Jing-Ke, Wang, Yi
Integrated molecular simulations and biochemical assays define the structural transitions and ion-binding dynamics that govern the enzyme’s catalytic regulation.
An Information-theoretic Collective Variable for Configurational Entropy
Ashley Z. Guo, Kaelyn Chang, Nicholas J. Corrente
Data compression-based metrics quantify instantaneous structural organization and phase behavior in molecular dynamics simulations without requiring system-specific order parameters or prior knowledge.
Micellar effects on Ostwald ripening in emulsions: Transition from cubic to quadratic particle size growth
Alexey Kabalnov
Solubilizate-micelle exchange dynamics and the oil atmosphere distribution parameter determine the kinetic crossover point, with the resulting rate acceleration being more pronounced for nonionic surfactants than for ionic ones.
Spectral entropy of the discrete Hasimoto effective potential exposes sub-residue geometric transitions in protein secondary structure
Yiquan Wang
Abrupt, first-order-like kinematic transitions enable a dual-probe spectral framework to improve boundary detection and map flexible regions implicated in protein functional dynamics.
[Limits of optimal decoding under synaptic coarse-tuning]
(http://arxiv.org/abs/2602.21758v1) Ori Hendler, Ronen Segev, Maoz Shamir
Strong synaptic imprecision restricts the signal-to-noise ratio of optimized linear readouts to a saturated level comparable to naive population averaging, suggesting that robust neural computation occurs along a low-dimensional manifold aligned with simple decoding strategies.
Temporal stimulus segmentation by reinforcement learning in populations of spiking neurons
Luisa Le Donne, Lik Chun Chan, Robert Urbanczik, Walter Senn, and Giancarlo La Camera
Synaptic plasticity governed by reward feedback allows neural populations to autonomously discover the boundaries and identities of specific signals embedded in ongoing sensory activity.
XY Model with Persistent Noise
Xia-qing Shi, Hugues Chaté, and Benoît Mahault
Active crystals maintain quasi-long-range order and resist melting even when subjected to the large internal deformations caused by their inherent fluctuations.
Hydrodynamic Interactions Destroy Motility-Induced Phase Separation in Active Suspensions
Tingtao Zhou and John F. Brady
Long-range fluid couplings actively destabilize the aggregation of both biological and synthetic microswimmers, contradicting previous models that neglected the role of fluid dynamics.
Self-avoiding tethered surfaces are always flat
A. D. Chen, M. C. Gandikota, M. J. Kim, A. Cacciuto
Fully flexible elastic membranes maintain a size exponent of \(\nu=1\) in the thermodynamic limit for any finite degree of self-avoidance, regardless of whether surface area is removed through lattice perforations.
Analyses of bent spindles reveal the mechanics of anaphase B in fission yeast
Paula Real-Calderón, Thomas G. Fai, Rafael R. Daga, Joël Lemière, Fred Chang
Spindle buckling under compressive stress quantifies the balance between motor-generated sliding forces and the flexural rigidity of the microtubule bundle during nuclear separation.
Solo regulates the localization and activity of LARG for actin cytoskeletal remodeling in cell-substrate adhesions
Aoi Kunitomi, Yusuke Toyofuku, Chikaya Fujimori, Shuhei Chiba, Nahoko Higashitani, Atsushi Higashitani, Shinichi Sato, Kensaku Mizuno, Kazumasa Ohashi
Interaction between the Solo C-terminus and LARG facilitates localized RhoA signaling, driving the formation of contractile stress fibers and the maturation of focal adhesions under mechanical stress.
[Confinement-Induced Symmetry Breaking of Active Surfaces]
(http://arxiv.org/abs/2602.21519v1) Da Gao, Alexander Mietke, Rui Ma
Hydrodynamic modeling of the cell cortex demonstrates that ellipsoidal boundaries destabilize symmetric division and drive the emergence of polarized geometries at a critical threshold of spatial restriction.
[Measuring elastic properties of granular hydrogels: Effects of capillary interaction and ionic conditions]
(http://arxiv.org/abs/2602.21457v1) Jiayin Zhao, Haiyi Zhong, Yixiang Gan
Neglecting capillary-induced liquid bridges results in a systematic underestimation of Young’s modulus that increases as sample size or intrinsic stiffness decreases, a discrepancy resolved by a modified constitutive model incorporating ionic salinity.
A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9
Ahsan, M.; Saha, A.; Ramos, D.; Strohkendl, I.; Knight, A. L.; Skeens, E.; Lisi, G. P.; Taylor, D. W.; Palermo, G.
Divalent metal binding at the HNH-RuvC interface triggers the conformational activation and catalytic coupling of the enzyme’s nuclease domains across varying ionic environments.
[Mechanism of MEK1 activation by phosphorylation]
(https://www.cell.com/biophysj/fulltext/S0006-3495(26)00154-2?rss=yes) Everett Jin, Levent Sari, Milo M. Lin
Molecular dynamics simulations reveal the structural and dynamical transitions driven by phosphorylation at residues S218 and S222 that underlie the enzyme’s cooperative activation process.
[Ligand Binding Free Energy Landscapes at the Tubulin Colchicine Site from Coarse-Grained Metadynamics]
(https://www.biorxiv.org/content/10.64898/2026.02.24.707696v1) Grazzi, A.; Brown, C. M.; Sironi, M.; Marrink, S.-J.; Pieraccini, S.
Martini 3-based simulations improve statistical convergence over all-atom methods and achieve binding free energy estimates within 3–10 kJ mol⁻¹ of experimental values while significantly reducing computational costs.
[Liquid–liquid phase separation by caged coacervating peptides]
(https://www.nature.com/articles/s41598-026-40774-2) Bando, Akinari, Kitamatsu, Mizuki, Kanazaki, Yuuki, Tojo, Rika, Watanabe, Kazunori, Ohtsuki, Takashi
Squid-inspired histidine-rich peptides modified with photodeprotectable groups facilitate the light-triggered release of encapsulated molecular cargo through the rapid disassembly of coacervate droplets.
[Engineering the mechanosensitivity of single DNA molecules via high-throughput microfluidic force spectroscopy]
(https://www.biorxiv.org/content/10.64898/2026.02.24.707783v1) DeJong, M. P.; Bian, Y.; Ortiz-Cardenas, J. E.; Figueroa, B.; Pant, A.; Posadas-Barrera, E.; Brixi, L.; Bauer, M. S.; Dunn, A. R.; Fordyce, P. M.
Multiplexed measurements of hundreds of DNA variants reveal that multivalent interactions can produce structures that are kinetically stable yet mechanically fragile, enabling high-throughput sequence-function mapping of molecular responses to force.
[Machine Learning Approaches to Quantify Nanoscale Variations in the Mechanical Properties of Soft Nanoparticles]
(http://pubs.rsc.org/en/Content/ArticleLanding/2026/SM/D5SM00943J) Benjamin Baylis, John Dutcher
AFM-FS data obtained from specimens on rigid substrates facilitates a comparative evaluation of two distinct computational frameworks for interpreting complex force-distance relationships.
Cryogenic electron tomography reveals herpesvirus capsid assembly intermediates inside the cell nucleus
Oliver, Stefan L., Chen, Muyuan, Engel, Leeya, Hecksel, Corey W., Zhou, Xueting, Schmid, Michael F., Arvin, Ann M., Chiu, Wah
Vertex-specific structural differences between genome-filled and empty particles provide insights into the maturation process within the native cellular environment.
AI-BioMech: Deep Learning Prediction of Mechanical Behavior in Aperiodic Biological Cellular Materials
Sadia, H.; Dias, M. A.; Alam, P.
Semantic segmentation architectures leverage transfer learning to replace traditional finite element simulations, mapping stress and strain distributions directly from 2D images with high computational efficiency and experimental accuracy.
How brain pulsations drive solute transport in the cranial subarachnoid space: insights from a toymodel
Neff, A.; Vallet, A.; Dvoriashyna, M.
Lagrangian mean velocity, integrating steady streaming and Stokes drift, governs long-term transport by significantly enhancing solute dispersion and clearance efficiency across distinct physiological regimes.
A gated hydrophobic funnel within BAX binds bioactive lipids to potentiate pro-apoptotic function
Gelles, Jesse D., Chen, Yiyang, Luna-Vargas, Mark P. A., Viacava Follis, Ariele, Al Noman, Md Abdullah, Kabir, Md, Bayiokos, Stella G., Mohammed, Jarvier N., Sebastian, Tara M., Pham, Ngoc Dung, Shi, Yi, Jin, Jian, Kriwacki, Richard W., Chipuk, Jerry Edward
Cooperative binding of 2-trans-hexadecenal and BIM to a specialized cavity triggers the allosteric activation of BAX before its insertion into the mitochondrial membrane.
Illumination optimization and low-power trapping of Limnospira indica PCC 8005 using bulk acoustic waves in microgravity
Dupont, Bérénice, Benoit-Gonin, Xavier, Vincent-Bonnieu, Sébastien, Aider, Jean-Luc, Ardré, Maxime
Acoustically induced layering of these helical microorganisms significantly reduces energy consumption and improves light penetration, facilitating more efficient biomass and oxygen production for space-based life support systems.
[Exploring the Energy Landscape of Hairpin Folding using the TIS-DNA model]
(https://www.biorxiv.org/content/10.64898/2026.02.24.707746v1) Baratam, K.; Chakraborty, D.
Non-specific chain collapse and strand alignment initiate a single-funnel progression toward the native state, followed by ordered loop formation and a downhill nucleation of native contacts.
From Global Flocking to Local Clustering: Interplay between Velocity Alignment and Visual Perception of Active Particles
Mohit Gaur, Arnab Saha, Subhajit Paul
Non-reciprocal interactions within a restricted vision cone trigger a transition from system-wide alignment to fragmented, locally ordered clusters where density accumulation arises as a direct consequence of localized velocity coherence.
[Controlling inertial active Brownian motion via stochastic resetting]
(http://arxiv.org/abs/2602.21134v1) Manish Patel, Amir Shee
Enhanced spatial localization and non-Gaussian steady states emerge from the competition between momentum relaxation and restart frequency, yielding a regime where rare long excursions are non-monotonically maximized.
[A constitutive model for discontinuous shear thickening in epithelial tissues]
(http://arxiv.org/abs/2602.20886v1) Tanmoy Ghosh, Kabir Ramola, Saroj Kumar Nandi
Finite yield stress in the unjammed regime and stochastic fluctuations drive the transitions between discontinuous shear thickening, continuous shear thickening, and Newtonian behavior as the target shape index and temperature increase.
[The Jammed Phase of Infinitely Persistent Active Matter]
(http://arxiv.org/abs/2602.20776v1) M. C. Gandikota, Rituparno Mandal, Pinaki Chaudhuri, Bulbul Chakraborty, Chandan Dasgupta
Critical active forcing for yielding scales with virial pressure according to a robust power law, while a redistributed contact force network maintains statistics consistent with passive systems despite the abrupt emergence of active plasticity.
[Landscape of Target State Directed Processes in Living Systems]
(http://link.aps.org/doi/10.1103/cx3h-q6d2) Nicolas Lenner, Matthias Häring, Stephan Eule, Jörg Großhans, and Fred Wolf
Reverse-time stochastic dynamics provides a foundational framework for understanding goal-oriented biological behaviors by distinguishing them from the traditional forward-time models used in stochastic thermodynamics.
[Programming Shapes with Competing Layered Patterns]
(http://arxiv.org/abs/2602.20655v1) Wan Yee Yau, Carl D. Modes
Incompatible growth gradients in bilayer systems dictate final three-dimensional morphologies based on curvature strength and aspect ratios, enabling the replication of biological morphogenesis such as dental epithelium and Drosophila development.
Rapid pronucleus assembly using cytoplasmic RNAs in fertilized eggs of Xenopus laevis
Mizuki Ikeda, Yuto Tanaka, Tatsuya Shohoji, Yuki Hara
Negatively charged RNAs facilitate sperm chromatin decompaction by electrically displacing positively charged proteins, with specific RNA lengths and concentrations optimizing the rate of this remodeling process.
Binding properties of marine sulfated glycans to coagulation (co)-factors using surface plasmon resonance spectroscopy
Al. Ahmed, Hoda, Pomin, Vitor H.
Fucosylated chondroitin sulfates and sulfated fucans utilize antithrombin-independent mechanisms and metal-ion-enhanced interactions with heparin cofactor II and factor Xa to offer a potentially safer therapeutic profile than traditional heparin.
Collective fate decisions and cell rearrangements underlie gastruloid symmetry breaking
Oriola, D.; Torregrosa-Cortes, G.; Samatas, S.; Arato, K.; Fernandez-Munuera, D.; Hahn, E. M.; Anlas, K.; Garcia-Ojalvo, J.; Trivedi, V.
Pluripotent cells modulate the timing of development through differentiation delays, while lineage-specific surface tensions drive the radial sorting required for robust, autonomous axis formation.
Deviations in whole body angular momentum are largely corrected before foot placement
Berkelmans, S.; Bruijn, S. M.; Afschrift, M.
Mediolateral foot placement is primarily governed by linear momentum dynamics because whole-body angular momentum deviations are largely resolved before the foot lands.
[All-optical mapping of cAMP transport reveals rules of sub-cellular localization]
(https://www.biorxiv.org/content/10.1101/2023.06.27.546633v2) Xiang, K. M.; Park, P.; Koren, S. A.; Hayward, R. F.; Cohen, A. E.
Micron-scale signaling domains arise from a balance between rapid diffusion (~130 µm²/s) and enzymatic degradation, refuting the existence of nanoscale sequestration or distinct membrane-associated pools.
[Transsaccadic working memory in healthy ageing and neurodegenerative disease]
(https://elifesciences.org/articles/109581) Anna Scholcz, Gabriel Davis Jones, Masud Husain, Rob Udale, Sanjay G Manohar, Sijia Zhao, Sofia Toniolo, Thomas Parr, Verena Klar
Encoding and decay failures, rather than impaired saccadic updating, drive the spatial working memory deficits observed in Alzheimer’s and Parkinson’s patients.
Size tuning of neural response variability in laminar circuits of macaque primary visual cortex
Alessandra Angelucci, Lauri Nurminen, Maryam Bijanzadeh
Diverse cortical mechanisms decouple internal fluctuations from suppression, causing far-surround stimulation to increase noise in superficial layers and sub-receptive field stimuli to elevate it in deeper layers.
Effects of sodium chloride on circadian period and temperature compensation of KaiC phosphorylation
Kim, Eugene, Adams, Makayla, Tyree, Soren, Kim, Yongick
Increasing concentrations of NaCl shorten the oscillation period and disrupt temperature compensation by perturbing the conformational states and oligomerization of the KaiB protein.
Unique protein dynamics distinguish the highly homologous LXR alpha and beta isotypes
Kesaban Roy Sankar Choudhuri, Denise Okafor
Ligand discrimination within nearly identical binding pockets arises from these distinct conformational variations, providing a mechanism for the development of isoform-selective modulators.
Stochastic Mechanism of Dominant Follicle Selection: Selection of One Suppresses Selection of Others
Lyu, Z.; Kolomeisky, A.
Negative feedback between estradiol and follicle-stimulating hormone establishes a narrow temporal window that prevents the maturation of multiple follicles once an initial selection occurs.
The N-Myc MB0-MBI region interacts specifically and dynamically with the N-lobe of Aurora kinase A
Hultman, Johanna, Morad, Vivian, Tanner, Eliane, Kenney, Tristan M. G., Pietras, Zuzanna, Khare, Lalit Pramod, Derbyshire, Dean, Resetca, Diana, Arrowsmith, Cheryl H., Aili, Daniel, Ekström, Simon, Penn, Linda Z., Wallner, Björn, Ahlner, Alexandra, Sunnerhagen, Maria
Allosteric promotion of kinase activation through an inhibitable binding mode offers a therapeutic strategy for restricting neuroendocrine tumor growth.
[Synthetic gene circuits that selectively target RAS-driven cancers]
(https://elifesciences.org/articles/104320) Gabriel Valentin Senn, Leon Nissen, Yaakov Benenson
Integrating multiple sensors into a modular framework facilitates cell-line-specific optimization and the precise expression of cytotoxic proteins to induce robust death in cells harboring oncogenic mutations.
Characterizing MINFLUX imaging performance with DNA origami
Clowsley, A. H.; Bokhobza, A. F. E.; Janicek, R.; Kołataj, K.; Bleuer, G.; Di Michele, L.; Acuna, G. P.; Soeller, C.
Repeat-domain docking strands on DNA origami enable the correction of residual drift during extended 3D MINFLUX acquisitions to achieve ~2 nm localization precision in both synthetic and biological samples.
Breakdown and Restoration of Hydrodynamics in Dipole-conserving Active Fluids
Anish Chaudhuri, Lokrshi Prawar Dadhichi, Arijit Haldar
Activity stabilizes linear behavior in dimensions \(d \geq 2\) and defines novel universality classes that make these systems significantly more experimentally accessible than their passive counterparts.
Chemotaxis of cell aggregates: morphology and dynamics of migrating active droplets
Giulia L. Celora, Benjamin J. Walker, Mohit P. Dalwadi, Philip Pearce
Proliferation-driven transitions between distinct traveling-wave patterns are determined by the balance of internal stress and chemical coupling strength, as dictated by exponentially small asymptotic terms at the contact lines.
Arc-length characterization of finite, radial growth patterns
Andreas A. Hennig, Ilaria Beechey-Newman, Natalya Kizilova, Erika Eiser
Distinguishing between diverse formation mechanisms and identifying pattern centers provides a robust analytical alternative where traditional linear chord methods are ineffective.
Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers
Alexander Zhilkin, Muralika Medaparambath, Dan Mendels
Harmonic Linear Discriminant Analysis (HLDA) identifies residue-level scores and statistical separations from minimal local sampling to predict the kinetic impact of point mutations without requiring exhaustive simulations.
Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide
Muralika Medaparambath, Alexander Zhilkin, Dan Mendels
Harmonic Linear Discriminant Analysis of short, unbiased molecular dynamics trajectories identifies mutation-sensitive residues and predicts thermodynamic stability shifts by correlating eigenvalue changes with free-energy differences.
[Dielectric response in proteins: The proteotronics approach]
(http://arxiv.org/abs/2602.19899v1) E. Alfinito, M. Beccaria
A user-friendly calculation method for relative permittivity facilitates the study of hydrated proteins in proteotronics workflows and produces results consistent with classical macroscopic models.
A label-free method to quantify early-stage amyloid aggregation under flow via intrinsic phenylalanine fluorescence
Gaëlle Audéoud, Louis Moine, Laura Bonnecaze, Maxime Lavaud, Lucie Khemtemourian, Yacine Amarouchene, Thomas Salez, Marion Mathelié-Guinlet
Tracking the conversion of monomers into transient 2–10 nm oligomers facilitates the investigation of cytotoxic intermediates in tryptophan-free peptides, such as PSMα3 and hIAPP, under near-physiological conditions.
Effects of near-field hydrodynamic interactions on bacterial dynamics near a solid surface
Baopi Liu, Lu Chen, Haiqin Wang
Translational and rotational velocities during stable circular motion, as well as surface residence times, are governed by the specific fluid forces acting between the bacterium and the boundary.
Generalized Model for Static Contact Angles and Hysteresis on Micro/Nanostructured Surfaces
Carlos E. Colosqui
Random or periodic local topographies are integrated into a compact framework to determine the upper limits of droplet pinning across arbitrary surface geometries.
A Comprehensive Atlas and Machine-Learning Framework for Predicting IDR-Protein Binding Affinity
Adhikari, S.; Choudhuri, S.; Mondal, J.
IBPC-Kd and the IDRBindNet graph-transformer model identify global shape complementarity and electrostatic asymmetry as the primary determinants for quantifying dissociation constants across diverse biological and de novo designed interfaces.
Functionally Relevant Protein Dynamics Monitored by Time-Resolved Quasielastic Neutron Scattering
Tatsiana Burankova, Thomas Hauß, Jacques Ollivier, Ruep E. Lechner, Norbert A. Dencher, Jörg Pieper
Picosecond-scale fluctuations in bacteriorhodopsin modulate in real time during the protein’s functional cycle when triggered by in-situ light excitation.
Quantifying the effects of cell death and agar density on yeast colony biofilms using an extensional-flow mathematical model
Alexander Tam, Jennifer M. Gardner, Jin Zhang, Vladimir Jiranek, Daniel Netherwood, Campbell Gourlay, Benjamin Binder, Edward Green
Interplay between substrate-mediated friction and localized mortality dictates the structural evolution and spreading kinetics of the microbial population.
Diverse regulation of functional dimerization of a sugar transporter by different interfacial lipids
Zhang, Yan, Zhao, Weijing, Duan, Mojie, Shen, Yang, Li, Jianping, Xie, Huayong, Tong, Qiong, Zhao, Yongxiang, Yang, Jun
Solid-state NMR and molecular dynamics simulations reveal the specific molecular mechanisms by which individual lipid species modulate the structural transitions and conformational landscape of the protein within lipid bilayers.
Bound or unbound: Mapping and monitoring receptor oligomerization using time-resolved fluorescence
Greife, A.; Liu, R.; Koehler, P. S.; Heinze, K. G.; Hemmen, K.; Peulen, T.-O.
An open-source analytical framework integrates multimodal FRET and brightness measurements to determine protein association constants and distance distributions within the heterogeneous environment of living cells.
Protein-induced membrane strain drives supercomplex formation
Alexander Jussupow, Hyunho Kim, Maximilian C Pöverlein, Ville RI Kaila
Specific recruitment of cardiolipin and quinone to sites of reduced membrane thickness creates a thermodynamic environment that stabilizes assembly while modulating protein dynamics and respiratory flux.
Squirmers with arbitrary shape and slip: modeling, simulation, and optimization
Kausik Das, Hai Zhu, Marc Bonnet, Shravan Veerapaneni
A Helmholtz decomposition framework defines slip velocities to characterize helical trajectories and identifies energy-efficient motion profiles governed by the body’s geometric symmetries.
Microgel Translocation Through Narrow Capillaries
Subhadip Biswas, Buddhapriya Chakrabarti
Internal network topology and elasticity determine a critical entry diameter and a force-dependent stalling point caused by densification, defining the mechanical boundaries between successful transport and arrest.
Training overdamped dynamics
Marc Berneman, Daniel Hexner
Rayleighian-based local update rules enable materials to autonomously adapt their microscopic damping parameters to achieve targeted rate-dependent mechanical responses.
Critical Scaling and Metabolic Regulation in a Ginzburg–Landau Theory of Cognitive Dynamics
Gunn Kim
Biological intelligence manifests as a macroscopic order parameter sustained by energy flux, where a universal susceptibility exponent of 3/2 aligns with observed cortical avalanches and defines healthy mental states as metabolically pinned configurations near the threshold of instability.
Process for Standardizing and Assessing the Parameters Governing MS2 Virus-Like Particle Reassembly around Nucleic Acid Cargo
de Castro Assumpcao, D.; Vinokour, E. S.; Mills, M. M.; Liang, S.; Mills, C. E.; Carvalho da Costa, A.; Kennedy, N. W.; Tullman-Ercek, D.
Size exclusion chromatography-based quantification and factorial experimental design identify protein concentration and ionic strength as the dominant factors influencing yield, establishing a robust framework for standardized and reproducible particle reconstruction.
Entropy Quantum Computing for Fixed-Backbone Protein Design
Emami, B.; Dyk, W.; Haycraft, D.; Robinson, J.; Nguyen, L.; Miri, M.-A.; Huggins, D. J.
Dirac-3 achieves near-optimal energy solutions with near-linear runtime scaling, identifying a practical performance crossover where photonic optimization surpasses the super-polynomial growth of exact classical methods as problem complexity increases.
Sampling Mismatch and Correction for Ptychographic Single-Particle Analysis
Li, T.; Li, S.; Yan, Z.; Shen, Y.; Li, X.
Accurate calibration of scanning step and detector pixel sizes eliminates phase reversals and signal distortions, enabling ptychographic reconstructions of biological macromolecules to reach ~1.5 Å resolution.
Serum modulates the aggregation - toxicity landscape of the staphylococcal toxin PSMα3
Bonnecaze, L.; Duchalet, A.; Moine, L.; Vial, A.; Cardenas, M.; Martin, C.; Molinari, M.; Marsaudon, S.; Mathelie-Guinlet, M.
Soluble intermediates formed during fibrillation drive cytotoxicity through membrane-disrupting interactions that are inhibited by serum lipoproteins.
Discovery of MA48, a Small Molecule Inhibitor of CAPON (NOS1AP)-NOS1 Protein-Protein Interaction
Abdo, A.; Nada, H.; Gabr, M.
MA48 disrupts the CAPON-nNOS interaction in living cells with low-micromolar affinity, providing a foundational small molecule lead for the development of neurodegenerative disease therapeutics.
Interactions of Phototropism and Gravitropism in Cyanobacteria
Gates, C.; Mundoor, H.; Smalyukh, I.; Cameron, J. C.
Polyphosphate bodies serve as intracellular sensors that regulate the spatial distribution of chlorophyll and phycobilins in response to external force, providing a mechanism for directional gravity sensing in prokaryotes.
[The Untangle Challenge for accurate ensemble models]
(https://www.biorxiv.org/content/10.64898/2026.02.21.706873v1) Hopkins, M. S.; Terwilliger, T. C.; Afonine, P.; Ginn, H. M.; HOLTON, J. M.
Density misfit barrier traps create topological local minima that cause structural tangling, preventing refinement algorithms from simultaneously satisfying experimental data and chemical geometry restraints.
E. coli extracellular matrix: a tunable composite with hierarchical structure
Siri, M.; Mangiarotti, A.; Seewald, A.; Rosenthal, N.; Amini, S.; Raguin, E.; Fratzl, P.; Bidan, C. M.
Synergistic interactions between curli amyloid fibers and pEtN-cellulose dictate mechanical behavior by forming a sub-micron architecture where the rigid protein network constrains cellulose swelling.
Sloppiness and Action Constraint in Cell State Transitions: Are Single Cells Sloppy?
Wang, Y.; Ying, J.; Xiao, H.; Huang, M.; Zhang, L.; Wang, W.
Critical transitions depend on a small number of sensitive parameters that constrain cellular trajectories to follow a principle of least action.
[Geometric Limits of Mitotic Pressure Under Confinement]
(http://arxiv.org/abs/2602.18909v1) Amit Singh Vishen
A confinement-induced minimum in furrow radius saturates mitotic pressure and axial force, allowing cell division across diverse mechanical environments to collapse onto a universal scaling curve where material properties and active forces determine the specific operating point.
Fine-Tuning α-Synuclein Phase Separation through Sequence-Optimized Peptide Modulators
Ikenoue, T.; Konuma, T.; Ikegami, T.; Suga, H.
A systematic framework based on deep mutational scanning identifies the molecular rules of solubility and multivalency needed to engineer de novo peptides that precisely regulate the thermodynamics and material properties of protein condensates.
Formation of a swelling gel underlies a morphological transition in Bacillus subtilis biofilms
Saha, A.; Jones, J. M.; Plummer, A.; Larkin, J. W.
Poly-γ-glutamate and exopolysaccharides act as swelling agents and cross-linkers, respectively, to drive a sol-gel transition that generates the internal strain necessary for macroscopic wrinkle formation.
A closed-loop mathematical structure of mechanics-turnover coupling for mechanical adaptation in living systems
Matsumoto, E.; Deguchi, S.
Integral feedback within the Feedback Adaptive Turnover-mediated Environment-Dependent (FATED) framework defines the minimal conditions for homeostasis and provides a universal analytical expression for calculating adaptation timescales across diverse biological scales.
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 MIET enables the simultaneous measurement of lateral molecular diffusion and vertical membrane undulations with nanometer axial sensitivity and microsecond temporal resolution in various cellular organelles.
Stoichiometric binding of Cyclophilin-A to the HIV-1 capsid modulates its mechanoelastic properties
Rey, J. S.; Bryer, A. J.; Perilla, J. R.
Increased binding stoichiometry promotes structural failure at lower deformations and overrides intrinsic ductility differences, indicating that balanced recruitment is necessary to preserve the mechanical flexibility required for nuclear translocation.
Discovery and dynamic pharmacology of μ-opioid receptor positive allosteric modulators
O’Brien, E. S.; Wang, J.; Tanguturi, P.; Li, M.; White, E.; Shiimura, Y.; Paul, B.; Appourchaux, K.; Krishna Kumar, K.; Huang, W.; Majumdar, S.; Traynor, J. R.; Streicher, J. M.; Chen, C.; Kobilka, B.
DNA-encoded library screening identified a novel scaffold that potentiates endogenous and synthetic agonists by modulating the intracellular conformational transitions associated with activation.