Mar 02 26
Featured Papers
The coarsening of biomimetic condensates in an active fluid is non-self-similar
Jeremy Laprade, Layne B. Frechette, Christopher Amey, Adrielle T. Cusi, Aparna Baskaran, W. Benjamin Rogers, Guillaume Duclos
Active fluctuations disrupt the scale-invariant growth typical of passive systems, forcing the droplet size distribution to evolve through distinct morphological regimes over time.
RNA-specific local translation is patterned by condensates for multinucleate cell growth
Zachary M. Geisterfer, Ameya P. Jalihal, Sierra J. Cole, Amy S. Gladfelter
Immiscible liquid droplets sort distinct transcript species to prevent their diffusion and maintain spatial autonomy within a shared cytosol.
Dynamic Instabilities and Pattern Formation in Chemotactic Active Matter
Hongbo Zhao, Qiwei Yu, Andrej Košmrlj, Sujit S. Datta
Collective chemical signaling competes with motility-induced phase separation to either inhibit phase growth or generate non-equilibrium structures like traveling waves and spirals through distinct bifurcation mechanisms.
Rotational 3D printing of active-passive filaments and lattices with programmable shape morphing
Mustafa K. Abdelrahman, Jackson K. Wilt, Yeonsu Jung, Rodrigo Telles, Gurminder K. Paink, Natalie M. Larson, Joanna Aizenberg, L. Mahadevan, Jennifer A. Lewis
Helical mesogen alignment and spatial material patterning provide independent control over local bending and torsion, enabling the computational design and predictable execution of complex, out-of-plane transformations.
Autophoresis of a Janus particle near a planar wall: a lubrication limit
Tachin Ruangkriengsin, Günther Turk, Howard A. Stone
The size of the active cap determines whether a tilted particle returns to an axisymmetric state or continues to reorient, establishing the conditions for rotational stability in the near-contact regime.
Some Papers
Stretching drives Membrane Homogenization of Phase-Separated Supported Lipid Bilayers
Perlman Illouz, A.; Meyer, R.; Köster, S.; Golani, G.; Sorkin, R.
Equibiaxial tension triggers a second-order phase transition characterized by power-law scaling of the order parameter, establishing a mechanical mechanism for the physical regulation of lateral membrane organization.
Large-scale simulations reveal evolutionary constraints on intrinsically disordered regions imposed by full-length protein architecture
Jiang, Y.; Liu, X.; Zhao, L.; Lu, Z.-Y.
Structural coupling between ordered and disordered segments leads to the evolutionary selection of compact-rigid or extended-flexible states that correspond to distinct regulatory roles in DNA and RNA interaction.
Enhanced 2D structured illumination microscopy: super-resolution with optical sectioning and reduced reconstruction artifacts
Steinecker, S. M.; Ortkrass, H.; Schuerstedt-Seher, J. C.; Kiel, A.; Kralemann-Koehler, A.; Schulte am Esch, J.; Huser, T.; Mueller, M.
Integrating coarse and fine illumination patterns suppresses out-of-focus background and optimizes resolution to enable high-fidelity imaging of thick biological specimens across visible and near-infrared wavelengths.
Experimental and simulated FRAP for the quantitative determination of protein diffusion in helical cells
Sakib, S.; Fradin, C.
Half-compartment simulations establish the relationship between recovery kinetics and specific morphological parameters, identifying an mNeonGreen diffusion coefficient of 4.9 ± 2.2 μm² s⁻¹ in Paramagnetospirillum magneticum.
Mechanical regulation of cellular energy metabolism in cancer microenvironments
Toth, J. M.; Jaganathan, A.; Basir, R.; Pieuchot, L.; Shen, Y.; Reinhart-King, C. A.; Shenoy, V. B.
A newly developed cellular metabolic potential within a chemo-mechanical model quantifies the energetic costs of stress fiber assembly and predicts stiffness-dependent AMPK activation and glucose uptake in contractile cells.
High-Throughput Single-Cell Spectroscopy Using Phasor Analysis of Spectral Flow Cytometry
Pannunzio, B.; Cespedes, P.; Diaz, M.; Ali, D.; Rial, A.; Malacrida, L. S.
phSFC translates fit-free hyperspectral signatures to a high-throughput platform, enabling the statistically robust resolution of membrane order and lipid phase behavior in complex biological samples.
Scaling Relations of Multicomponent Phase Coexistence Boundaries
Daoyuan Qian, Julia Acker, Rob M. Scrutton, Charlotte M. Fischer, Seema Qamar, Tomas Sneideris, Alexander Borodavka, and Tuomas P. J. Knowles
Two distinct regimes govern the partitioning of complex mixtures into multiple domains, enabling the quantitative characterization of condensate behavior.
Slowing translation to avoid cellular depletion of active ribosomes at slow growth rates
Dotan Goberman, Anjan Roy, and Rami Pugatch
A trade-off between peptide elongation speed and the metabolic cost of manufacturing ribosomes prevents the autocatalytic collapse of the translation system as growth approaches zero.
Electrorheoimaging of a nonequilibrium emulsion: Microstructures and multistate switchable viscosities
Majid Bahraminasr and Anand Yethiraj
Stepwise adjustments to electric field strength transform internal droplet configurations into discrete structural phases that offer a wide range of controllable flow resistances.
Rupture-Repair Cycles in Regenerating Hydra Tissues
Oded Agam, Erez Braun
Mechanically triggered Ca2+ signaling modulates actomyosin contraction to halt rupture propagation, shifting the statistics of tissue pressure releases from a controlled exponential scale to a scale-free power-law regime when the repair response is inhibited.
Anisotropic Diffusion in Lyotropic Chromonic Liquid Crystal using Fluorescence Recovery After Photobleaching
Kyu Hwan Choi, Jiyong Cheon, Joonwoo Jeong, Sho C. Takatori
Divergent transport patterns of intercalating and non-intercalating dyes demonstrate that microstructural evolution regulates molecular motion through competing mechanisms of steric confinement and directed channeling.
ATP synthase activity boosts membrane proton acceptance and lateral diffusion
Hendrik Flegel, Ambili Ramanthrikkovil Variyam, Nadav Amdursky, Claudia Steinem
Localized proton transfer along the lipid bilayer surface sustains ATP synthesis by bypassing the bulk aqueous phase, explaining how bioenergetic coupling persists under low delocalized driving forces.
Riding the Wave: Polymers in Time-dependent Nonequilibrium Baths
Bhavesh Valecha, Jens-Uwe Sommer, Abhinav Sharma
Structural length and topology determine the direction of steady-state transport, with long, ring, and star configurations moving with the signal while short and fully connected structures drift against it.
Entropic Tug of War: Topological Constraints Spontaneously Rectify the Dynamics of a Polymer with Heterogeneous Fluctuations
Adam H. T. P. Höfler, Iurii Chubak, Christos N. Likos, and Jan Smrek
Translational symmetry breaking drives persistent directional transport in dense molecular environments, providing a physical framework for understanding the movement of living chromatin.
Cell-Cell Adhesion as a Double-Edged Sword in Tissue Fluidity
Anh Q. Nguyen, Pradip K. Bera, Jacob Notbohm, Dapeng Bi
Energetic adhesion energy facilitates collective migration by lowering neighbor-exchange barriers, whereas dissipative junctional viscosity promotes jamming by resisting cell rearrangements and modulating tissue relaxation timescales.
Organization of core mitochondrial replication components into multiphasic condensates
Yao, Y.; Tangade, A. S.; Livingston, Q.; Mondal, A.; Parikh, N.; Mittal, J.; Feric, M.
Specific binding preferences between proteins and single- or double-stranded DNA determine the internal architecture of mt-nucleoids, explaining how the replication machinery spontaneously coordinates its complex molecular environment.
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 operate at a metabolic optimum that balances rapid division with timing coherence, as oscillation speed peaks near physiological energy levels while precision scales monotonically with available fuel.
Spatial Triple-Correlation Spectroscopy (S3CS) Reveals Heterotrimer Dynamics in Live Cells
Julissa Sanchez-Velasquez, Tao Sun, Xiaomeng Zhang, Elizabeth Hinde
Integration of three-channel line-scan microscopy with a spatial triple-correlation function quantifies protein assembly and transport relative to subcellular architecture while distinguishing ternary complexes from individual subunits.
The kinetics and mobility of a ParA ATPase drive carboxysome distribution in Halothiobacillus neapolitanus
Azaldegui, C. A.; Swasthi, H. M.; Hu, L.; Pulianmackal, L. T.; Rivett-Trznadel, H.; Liu, J.; Vecchiarelli, A. G.; Biteen, J. S.
McdA utilizes DNA-stimulated ATPase activity and McdB-mediated displacement to establish nucleoid gradients that prevent organelle aggregation via a Brownian ratchet mechanism.
How wind and currents shape the drift velocity of macrophytes and macroplastic particles - from experiment to model
Gronwald, F.; Zhao, Z.; Karez, R.; Bouma, T. J.; Weinberger, F.
Buoyancy and morphological traits dictate how wind-induced turbulence and current speeds influence drift velocity, allowing for the validation of existing surface transport models and the creation of a new predictive equation for negatively buoyant specimens that interact with the bottom.
Entropic size control of self-assembled filaments
Maximilian C. Hübl and Carl P. Goodrich
Promiscuous binding interactions between subunits enable the scalable programming of a preferred equilibrium size by balancing binding free energy against configurational entropy.
More Papers
Tubulin transforms Tau and α-synuclein condensates from pathological to physiological
Lucas, Lathan, Tsoi, Phoebe S., Quan, My Diem, Choi, Kyoung-Jae, Ferreon, Josephine C., Ferreon, Allan Chris M.
Microtubule recruitment within these assemblies suppresses the formation of toxic oligomers and amyloids, preventing the neurite degeneration that occurs when tubulin levels decline.
Optimizing spatial organization of FtsZ rings for large-scale constriction in synthetic cells
Panevska, Anastasija, Šakanović, Aleksandra, Paccione, Gianfranco, Rivas, Germán, Schwille, Petra
Truncated FtsN cytosolic domains facilitate the assembly and regulation of closed equatorial protein networks on giant vesicle membranes.
Quantification of Cholesterol Incorporation in Giant Unilamellar Vesicles Produced by a Modified cDICE Method
Marcos Arribas Perez, Gijsje H. Koenderink
Precise maintenance of target molar ratios resolves the common discrepancy between initial lipid mixtures and final membrane contents typically encountered in droplet-based production techniques.
Robust ciliary flows protect early Xenopus embryos from pathogens independent of multiciliated cell patterning
Baby, A.; Briole, A.; Yadav, A.; Cheylan, I.; Thome, V.; Boutin, C.; D’Ortona, U.; Viallat, A.; Favier, J.; Loiseau, E.; Kodjabachian, L.
Collective ciliary beating generates a resilient liquid shield that ensures effective pathogen clearance by prioritizing functional robustness over precise spatial patterning or energy optimization.
Rheb membrane orientation dynamics and functional consequences elucidated by molecular simulations, single-molecule-FRET and signaling assays
Hutchins, C. M.; Pagba, C.; Verma, G.; Jakubec, J.; Du, G.; Jayaraman, V.; Gorfe, A.
Transitions between two primary orientation states and two intermediates on endo-membranes regulate mTORC1 activation, establishing spatial dynamics as a functional control mechanism for lipid-modified small GTPases.
A universal protein ladder for standardisation of diverse FRET assays
Smith, E. R.; Gelder, K. L.; Hunter-Craig, L.; Bose, D. A.; Craggs, T. D.; Twelvetrees, A. E.
Modular repeating TPR motifs and self-labeling enzymes establish a consistent calibration curve that links molecular distances from in vitro single-molecule experiments to intracellular imaging across diverse expression systems and experimental platforms.
Constructing a single-objective oblique plane microscope (OPM) for fast, multi-colour, high-resolution volumetric fluorescence imaging
Zhang, Z.; Hong, W.; Wu, Y.; Dey, A.; Shevchuk, A.; Klenerman, D.
Step-by-step instructions for assembly and characterization using off-the-shelf parts lower the technical threshold for implementing this complex remote-refocusing light-sheet technique.
Adaptations in Plasmodium tubulin determine distinct microtubule architectures, mechanics and drug susceptibility
Bangera, Mamata, Wu, Jiangbo, Beckett, Daniel, Fachet, Dominik, Ferreira, Josie L., Voth, Gregory A., Reber, Simone, Moores, Carolyn A.
Evolutionary divergence in the parasite’s tubulin subunits modulates the intrinsic stiffness and assembly dynamics of the resulting microtubule filaments.
Vesicle dynamics in synapsin-induced condensates by passive X-ray microrheology
Titus Czajka, Andras Major, Hendrik Bruns, Marco Cammarata, Christian Hoffmann, Dragomir Milovanovic, Tim Salditt
X-ray photon correlation spectroscopy quantifies collective dispersion relations in biomolecular systems while overcoming experimental challenges such as radiation damage and low scattering signals.
Clathrin is an Intrinsic Driver of Membrane Fission
Bouzos, N.; Foley, S. L.; Potamianos, A.; Jacobs, C. O.; Johnson, M. E.; Zeno, W. F.
Lattice mechanics and triskelion geometry determine clathrin’s capacity for membrane remodeling, revealing that weakened lattice assembly paradoxically facilitates fission by enabling greater curvature generation.
Association and dissociation of Na + between bulk, cluster and micelle sites in aqueous sodium decanoate solutions elucidated by 23Na NMR relaxation experiments and quadrupolar relaxation modelling
Pär Håkansson, Pau Mayorga Delgado, Anne Selent, Ritu Ghanghas, Ilari Ainasoja, Sanna Komulainen, Jiri Mares, Perttu Lantto, Nonne L. Prisle, Ville-Veikko Telkki
Counter-ion partitioning between various surfactant aggregate states regulates the water activity and thermodynamic properties of the aqueous system.
Dissecting Gap Junctional and Ephaptic Contributions to Electrical Conduction in a Novel Cardiomyocyte Pair Model
Wu, X.; Swanger, S. A.; Meier, L. E. B.; Dennison, C. L.; Weinberg, S. H.; Poelzing, S.; Gourdie, R. G.
Physiological sodium concentrations promote ephaptic-dominated intercellular activation at the cardiac perinexus, whereas low sodium conditions favor gap junctional coupling, as demonstrated by a unique “Intercalated Disc Signature” in paired-cell sodium currents.
Mechanisms of gene regulation by SRCAP and H2A.Z
Tollenaere, Armelle, Ugur, Enes, Dalla Longa, Susanna, Deluz, Cédric, Assenheimer, Devin, Gebhardt, J. Christof M., Leonhardt, Heinrich, Suter, David M.
SRCAP prevents the activation of lineage-specific genes by maintaining H2A.Z occupancy and sterically hindering pioneer transcription factor binding through a mechanism independent of its histone-exchange activity.
Using Particle Shape to Control Defects in Colloidal Crystals on Spherical Interfaces
Gabrielle Nicole Jones, Philipp Schoenhoefer, Sharon C. Glotzer
Monte Carlo simulations of non-spherical hard particles demonstrate how specific geometric anisotropies can manipulate the distribution and type of topological defects that arise from geometric frustration on curved surfaces.
Transition from traveling fronts to diffusion-limited growth in expanding populations
Louis Brezin, Kyle J. Shaffer, and Kirill S. Korolev
Analytical solutions for reaction-diffusion equations reveal sublinear fronts that advance as the square root of time.
Theory of Rapid Behavioral Inferences Under the Pressure of Time
Ann M. Hermundstad and Wiktor F. Młynarski
Variability within random stimulus sequences serves as a mechanism for animals to improve the reliability of inferences necessary for survival-critical tasks.
Compositional memory matters for early molecular systems
Ledoux, B.; Kuwabara, R.; Ichihashi, N.; Mizuuchi, R.; Lacoste, D.
Partial compartmentalization enables the accumulation of compositional memory across replication cycles, stabilizing the coevolutionary dynamics of early molecular replicators and parasites against the error catastrophe.
Absorption dipole effects on MINFLUX single molecule localization
Stallinga, S.; Wang, W.; Rieger, B.
Fixed absorption dipoles tilted out of the imaging plane and primary optical aberrations introduce systematic localization errors that can be minimized by employing hexagonal probing patterns or iterative area reduction.
Linker histones consolidate heterogenous nucleosome fiber contacts by linking together multiple nucleosomes
Adhireksan, Zenita, Sharma, Deepti, Bao, Qiuye, Lee, Phoi Leng, Padavattan, Sivaraman, Davey, Gabriela E., Hansen, Jeffrey C., Davey, Curtis A.
Different H1 variants employ diverse binding modes to support dynamic chromatin organization within crowded environments.
Effects of Counter Ion Protonation on the Ultrafast Excited State Dynamics in Archaerhodopsin-3
Krystyna Herasymenko, Danushka Walisinghe, Masae Konno, Vincent Ledentu, Miquel Huix-Rotllant, Xuchun Yang, Nicolas Ferré, Keiichi Inoue, Massimo Olivucci, Stefan Haacke
Electrostatic interactions between the protein environment and the protonated Schiff base retinal create a mutation-induced energy barrier that suppresses sub-picosecond photo-isomerization and increases fluorescence quantum yield.
A molecular grammar for programmable multiphase protein-RNA vesicles
Ramachandran, V.; Potoyan, D. A.
Asymmetries in interaction strengths, chain lengths, and molecular stoichiometry dictate the spontaneous emergence of diverse internal architectures, including hollow vesicles, from well-mixed protein-RNA systems.
Intrinsically disordered SERBP1 regulates translation through topology-driven G-quadruplex recognition.
Baudin, A.; Dinh, H. H.; Breunig, K.; Lei, X.; Xu, X.; Penalva, L. O.; Libich, D. S.
An encircling RGG box mechanism stabilized by C-terminal serines functions as a phosphorylation-sensitive switch to control mTOR expression and glioblastoma cell growth.
Swapped and non-swapped TRAAK states co-exist in membranes at a ratio influenced by temperature
Ma, Yue, Ackermann, Katrin, Waheed, Qaiser, Postis, Vincent, Smith, Terry K., Bode, Bela E., Pliotas, Christos
Electron paramagnetic resonance (EPR) spectroscopy quantifies the distribution of the channel’s extracellular cap conformations to define the structural equilibrium of the protein within lipid membranes.
Chlorpromazine inhibits EAG1 channels by altering the interdomain coupling
Kyle Kihn, Ze-Jun Wang, Xi Chen, Mahdi Ghorbani, Purushottam B. Tiwari, Jeffery B. Klauda, Tinatin I. Brelidze
The intracellular tetrameric ring formed by interacting PAS and CNBH domains regulates the transition of the voltage sensor domain between closed and open states.
Arginine versus Lysine: Molecular Determinants of Cation-π Interactions in Biomolecular Condensates
Armentia, L.; Lopez, X.; De Sancho, D.
Arginine promotes phase separation more effectively than lysine primarily due to its lower dehydration penalty and its ability to maintain consistently stronger cation-π interactions regardless of the surrounding dielectric medium.
Analytical Time-Dependent Dynamics of Stochastic Gene Expression with sRNA–mRNA Interactions
Zhenhua Yu, Yiling Wang, Zhenyu Wang, Zhanpeng Shu, Zhixing Cao
A generalized probability-generating-function framework transformed via Laurent series expansion provides the time-dependent joint distribution of molecular counts, overcoming mean-field limitations in regimes of strong antagonism.
Adhesion differentials control the rheology of biomimetic emulsions
Quentin Guigue, Marc Besse, Raphael Voituriez, Alexis M. Prevost, Elie Wandersman, Matthias Merkel, Lea-Laetitia Pontani
Geometric analysis of imaging data collected under cyclic shear reveals how the interplay between packing and internal forces drives the large-scale tissue deformations fundamental to morphogenesis.
Distributional invariance and proportional scaling in axonal conduction
Laurie D. Cohen, Shimon Marom
The ratio of terminal to initial conduction velocities follows a right-skewed distribution that remains invariant across varying branch lengths, neuronal positions, and hierarchical levels.
Validating folding energy estimates as a method for variant interpretation
Elwes, C.; Alcraft, R.; Lister, H.; Smith, P. A.; Shorthouse, D.; Hall, B. A.
Aggregating stability estimates across multiple protein structures and filtering outlier residues significantly improves the quantitative accuracy of FoldX-based folding energy predictions for biophysical variant interpretation.
The Geometry of Cognitive Difficulty: A Dynamical Manifold Theory in Excitable Neural Networks
Panda, N.
Structured reorganization of neural state space, quantified through metrics like energetic cost and geometric curvature, reveals that cognitive difficulty manifests as a multidimensional manifold rather than a simple scalar increase in activation.
Noninvasive Laser SCOS Monitoring of Rat Brain Hemodynamics During Intracerebral Injection
Fernandes, M.; Huang, Y. X.; Xu, I.; Noguera Saigua, C.; Li, J.; Mahler, S.
The system’s ability to distinguish between saline and flow-modulating fluid recovery profiles validates its utility for characterizing the physiological impact and clearance of cerebral therapeutic agents.
Quantifying the effect of magnesium ions on nucleosome stability in chromatin fibers
Luuk J.C. Daris, Lieke A. Lamers, Kes van Blitterswijk, Camila Delgado Zuvanic, Jorine M. Eeftens
Single-molecule force spectroscopy reveals how magnesium ions modulate nucleosome stability across two distinct regimes of mechanical chromatin fiber unfolding.
From Prefix to Path: Learning Temporally Consistent Biomolecular Dynamics from Limited Initial Data
Choudhuri, S.; Adhikari, S.; Mondal, J.
Transformer-based autoregressive modeling reconstructs long-range metastable transitions and accurate free-energy landscapes by extrapolating continuous trajectories from brief segments of molecular dynamics simulations.
Anomalous Ion Confinement Penalties and Giant Ion-Screening Effects in One-Dimensional Nanopores
Kevin Leung
Hydration free energy penalties for confined ions deviate significantly from Born Equation predictions and undergo background electrolyte screening that exceeds Debye-Hückel estimates by nearly an order of magnitude.
Kinetic Theory of Chiral Active Disks: Odd Transport and Torque Density
Raphael Maire, Alessandro Petrini, Umberto Marini Bettolo Marconi, Lorenzo Caprini
Tangential impulses during dissipative collisions generate an antisymmetric stress and analytically predictable coefficients, establishing a tractable Boltzmann-Enskog framework for the systematic coarse-graining of chiral active matter.
Study of flow of crystals and deformable particles in a channel and the effective segregation of soft and hard particles
Padmanabha Bose, Smarajit Karmakar
High-density stiff assemblies of two-dimensional polymeric rings develop fluid layers at channel boundaries, while narrow confinement acts as the primary driver for partitioning particles according to their individual flexibility.
How Different are Self and Nonself?
Andreas Tiffeau-Mayer, Jonathan A. Levine, Christopher J. Russo, Quentin Marcou, William Bialek, and Benjamin D. Greenbaum
Peptidome modeling across species reveals that self and nonself sequences are nearly indistinguishable, implying that the immune system effectively targets antigens closely resembling the organism’s own proteome.
Machine-Learning-Inferred and Energy-Landscape-Guided Analyses Reveal Kinetic Determinants of CRISPR/Cas9 Gene Editing
Lei Jin, Risi Liyanage, Dongsheng Duan, and Shi-Jie Chen
R-loop unfolding rates serve as a key predictor of cleavage efficiency, enabling more accurate forecasting of on- and off-target gene editing outcomes through random forest modeling.
Bias in the AlphaFold3 prediction of ligand-induced domain motion in enzymes
Hao Yu, Ayse A. Bekar-Cesaretli, Maria Lazou, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda
The relative abundance of specific structural states in the training data determines predicted conformations, leading to a memorization effect where the model defaults to the most frequent PDB state regardless of ligand presence or affinity.
Stress-dependent growth in breast cancer arises from a mechano-osmotic coupling and cell-sizing checkpoint
Irish Senthilkumar, Jef Vangheel, Vatsal Kumar, Laoise McNamara, Bart Smeets, Enda Howley, Eoin McEvoy
Extracellular loading restricts tumor expansion by generating hydrostatic forces that oppose osmotic pressure from biomolecule synthesis, preventing cells from reaching the critical volume threshold required to trigger mitosis.
Adding noise and scaling forces to speed up the Langevin clock
Prithviraj Basak, Stephen Whitelam, John Bechhoefer
Maintaining systems closer to thermal equilibrium during time-dependent protocols enables more precise free-energy recovery and accelerates performance in stochastic thermodynamic computing devices.
Introducing a fusogenicity metric for lipid nanoparticle formulation
Zheng, L.; Baliga, M.; Gallagher, S. F.; Gao, A. Z.; Rueben, J.; Go, Y. K.; Deserno, M.; Leal, C.
The ratio of Gaussian and bending moduli (\(Q\)), derived from small angle X-ray scattering, captures spontaneous curvature to provide a predictive framework for optimizing the drug release efficiency of delivery vehicles like SM-102 and ALC-0315.
Progressive Backmapping of Highly Coarse-Grained Protein Models
Zhu, Y.; Remington, J. M.; Song, S.; Yang, B.; Magee, B. P.; Schneebeli, S. T.; Li, J.
Stepwise reconstruction through intermediate resolutions enables the accurate recovery of all-atom details in massive protein complexes, including entire viral assemblies comprising hundreds of subunits.
Aromatic ring transforms DNA binding modes of an octahedral rhodium complex
Guðfríður Björg Möller, Micah J. McCauley, Liam J. Price, Grace Ferris, Ioulia Rouzina, Megan Núñez, Mark C. Williams
The chrysi complex selectively binds mismatched DNA sites through metalloinsertion, whereas the phi complex functions as a classical intercalator within well-matched base pairs.
Mechano-sensitivity of multi-component caveolae
Sarkar, N.; Lamaze, C.; Sens, P.
Synergistic interactions between Cavin proteins and EHD2 neck rings create a switch-like mechanical response that triggers the abrupt release of molecular components once a specific tension threshold is exceeded.
HaloTag-based approach to quantify subcellular localization of TRPV3 channels.
Alexander Holloway, Joshua Chiang, Afroza Khan, Eric N. Senning, Andrés Jara-Oseguera
Accurate measurement of surface expression in live cells facilitates investigations into how endogenous factors and disease-linked mutations influence channel trafficking and skin health.
Molecular assembly of the KCNQ1-KCNE1-BACE1 complex
Martin, A.; Bienert, V.; Haefner, S.; Stockinger, F.; Möhwald, A.; Freimuth, M.; Karch, S.; Broichhagen, J.; Sandoz, G.; Alzheimer, C.; Huth, T.
BACE1 recruits two molecules per channel tetramer to a binding site distinct from KCNE1, utilizing its extracellular domain to slow gating while allowing for the formation of a functionally additive tripartite complex.
Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage
Benyuan Jiang, Jiajun Zhang, Qing Nie, Songhao Luo, Zhenquan Zhang, Zhiwei Huang, Zihao Wang
DeepTX identifies how specific modulations of burst size and frequency govern divergent outcomes such as differentiation, apoptosis, and survival across various genotoxic treatments.
Characterizing the Impact of Nucleoid-Associated Proteins on HU-DNA Interactions by Live-Cell Single-Molecule Tracking
Fuller, D. E. H.; Dai, X.; McCarthy, L.; Way, L.; Wang, X.; Biteen, J. S.
Dps and H-NS modulate HU mobility and chromosomal interactions by driving growth-phase-dependent changes in nucleoid compaction and organization.
The Integration Host Factor is a pH-responsive protein that switches from DNA bending to DNA bridging in acidic biofilm-like conditions
Dinesh Parthasarathy, Saminathan Ramakrishnan, Georgia Tsang, Auro Varat Patnaik, Sabrina M. C. Hardy, Willem Vanderlinden, Jamieson Howard, Braden Bylett, James R. Law, Mark Leake, Agnes Noy, Davide Michieletto
Residue protonation at pH levels below 5 exposes positively charged surface patches that enable the protein to mechanically stabilize the biofilm matrix through intermolecular DNA crosslinking.
Will a Large Complex System be a Maxwell Demon?
Matthew P Leighton
Maxwell demon behavior in random stochastic systems becomes exponentially less likely as degrees of freedom increase, implying that large-scale demons must result from selection rather than chance.
Guiding isotropic active fluids with anisotropic friction
Cody D. Schimming, Brian A. Camley
Positive topological defects in the substrate aggregate active fluids into clusters that transition from stationary clumps to revolving or steered units when azimuthal symmetry is broken.
Flocking by stopping: A mechanism of emergent order in collective movement
Yogesh Kumar KC, Arshed Nabeel, Srikanth Iyer, and Vishwesha Guttal
Intermittent pauses in activity enable simple pairwise interactions to generate stable global alignment by mitigating the disordering effects of social noise.
Transport-generated signals uncover geometric features of evolving branched structures
Fabian H. Kreten, Ludger Santen, and Reza Shaebani
A noninvasive diagnostic framework analyzes time-resolved data from a single observation site to recover global properties without tracking individual particle trajectories.
Functional significance of morphological variation in the mechanosensory lateral line system of fishes and its biomimetic potential
Ishu Aggarwal, Jacqueline F. Webb, Patrick R. Onck, Ajay Giri Prakash Kottapalli
Cupula geometry and material properties dictate mechanical responses to water flow, explaining how specific morphological shifts across species and developmental stages influence sensory perception and provide design principles for aquatic sensors.
The role of the tryptophan-rich allosteric network and sodium egress in GPCR activation
Zhenzhou Qi, Duy Phuoc Tran, Andrejs Tučs, Roopan Thiara, Louis-Philippe Picard, Koji Tsuda, Aditya Pandey, Adnan Sljoka, Akio Kitao, Robert Scott Prosser
The human adenosine A2A receptor samples a precoupled state upon the release of sodium from its conserved pocket, a process mediated by a mechanical signal propagation pathway linking the W246 toggle switch to the G-protein interface.
Stochastic modeling of long-legged ant A. gracilipes locomotion in laboratory experiments
Jack Featherstone, Anouk Béraud, Meta Virant-Doberlet, Antonio Celani, Mahesh Bandi
Active Brownian and run-and-tumble frameworks accurately replicate observed trajectory statistics through consistent probability distributions for turn angles, run durations, and waiting periods.
Base-pair scale dynamics of a repair helicase on DNA lesions reveal varied damage-sensing mechanisms
Troitskaia, A.; Lasitza-Male, T.; Caldwell, C. C.; Spies, M.; Chemla, Y. R.
XPD pauses and retreats when encountering cyclobutane pyrimidine dimers on the translocated strand, an interaction mediated by two specific structural regions sensitive to DNA modifications.
Beyond fish in formation: A two-tier approach for biomechanical studies of collective movement
Zhang, Y.; Ramesh, D.; Lauder, G.
Schooling fish achieve energy conservation by dynamically modulating their positioning and swimming kinematics in response to hydrodynamic stimuli from neighboring individuals.
High-pH NMR to Identify Macromolecular Hydrogen-Bonds and Foldons
Alexandrescu, A.; Rua, A. J.; Shah, S.; Farirchild, D.; Bezsonova, I.
Amide proton persistence at pH 10–11 identifies structural interactions with significantly higher accuracy than traditional H/D exchange and reveals hierarchical unfolding pathways in proteins that are otherwise difficult to characterize.
Experimentally calibrated multiscale model predicts schedule dependent drug combination effects
Hayoun-Mya, Othmane, Montagud, Arnau, Valencia, Alfonso, Ponce-de-Leon, Miguel
Interactions between tissue-level transport and intracellular signaling dictate the sequence of molecular target engagement, revealing that inhibiting the PI3K/AKT axis before MEK maximizes efficacy by preventing pro-survival signaling rebounds and locking cells into an apoptotic state.
Velocity sensitivity of mechanotransduction in the afferent terminal underlies vibration detection in the Pacinian corpuscle
Chikamoto, Akitoshi, Meng, Melissa, Gracheva, Elena O., Bagriantsev, Sviatoslav N.
Direct electrophysiological recordings localize the transduction of stimulus speed to the nerve terminal situated within the organ’s inner core.
Disentangling mucus rheology and transport efficiency in human airways
Briole, A.; Mao, Q.; D’Ortona, U.; Favier, J.; Viallat, A.; Loiseau, E.
Hydration of the thin fluid layer at the cilia-mucus interface, rather than bulk mechanical properties, governs the success or failure of mucociliary clearance.
Vimentin promotes actin assembly by stabilizing ATP-actin subunits at the barbed end
Paty, L.; Kalvoda, L.; Varela-Salgado, M.; Tran, Q. D.; Lenz, M.; Jegou, A.; Romet-Lemonne, G.; Leduc, C.
Vimentin stimulates actin filament nucleation and rapid growth through a direct interaction with ATP-actin monomers that occurs independently of its terminal domains or filamentous structure.
Morphological parameters can capture emergent properties of dynamic disordered cytoskeletal networks
Ghosh, S.; Houston, L.; Vasquez, A.; Ghosh, K.; Prasad, A.
Curvature and texture descriptors collectively distinguish between dynamic trajectories of simulated biopolymer networks, identifying subtle transitions that traditional nematic order parameters fail to capture.
Quantifying the effects of cell death and agar density on yeast colony biofilms using an extensional-flow mathematical model
Tam, A. K. Y.; Netherwood, D. J.; Gardner, J. M.; Zhang, J.; Gourlay, C. W.; Jiranek, V.; Binder, B. J.; Green, J. E. F.
Strengthened biofilm-substratum adhesion and reduced nutrient uptake are the primary mechanisms by which denser agar inhibits colony expansion, identifying adhesion as the most consistent regulator of yeast growth.
Dynamin optimizes protein-membrane interactions for fission
Spencer, Russell K. W., Müller, Marcus
Leaflet splaying from PH domain insertion minimizes the energetic barrier to tube collapse by creating chevron-shaped deformations that localize the fission site and eliminate the need for protein detachment.
A simple method for computationally unstructuring proteins: some findings
Powell, A.
Fold topology determines structural susceptibility, with alpha helical regions demonstrating robustness and unstructuring typically initiating at exposed termini.
Extrapolating molecular dynamics simulations to zero time step and across thermodynamic space
Kush Coshic, Gerhard Hummer
A linear thermodynamic model of integration errors enables the removal of numerical artifacts from simulations and the estimation of key properties such as heat capacity, compressibility, and thermal expansion coefficients.
Ionic Liquid-Driven Modulation of DNA Brush Morphology on Nanoparticle Surfaces
Anuj Chhabra, Sandip Mandal, Yugang Zhang, Oleg Gang, Prabal K. Maiti, Sunita Srivastava
Imidazolium-based ionic liquids drive a transition from electrostatic-dominated behavior in single-stranded segments to hydrophobic groove-binding-induced compaction in double-stranded regions.
General theory for group resetting with application to avoidance
Juhee Lee, Seong-Gyu Yang, Hye Jin Park, and Ludvig Lizana
Collective dynamics within potential landscapes dictate the timing of stochastic returns, extending existing mathematical frameworks beyond single-particle systems to encompass multi-body ensembles.
Two-phase quadratic integrate-and-fire neurons: Exact low-dimensional description for ensembles of finite-voltage neurons
Rok Cestnik
Realistic spike waveforms are integrated into analytically tractable population dynamics by modeling neurons with continuous membrane potentials.
Hyperuniformity of Weighted Particle Systems
Salvatore Torquato, Jaeuk Kim, Michael A. Klatt, Roberto Car, and Paul J. Steinhardt
Internal degrees of freedom are integrated into the mathematical framework of hyperuniformity to characterize complex particle arrangements.
Elastohydrodynamic instabilities of a soft robotic arm in a viscous fluid
Mohamed Warda and Ronojoy Adhikari
Constant mechanical loading triggers spontaneous transitions between steady and periodic states through the non-linear coupling of structural deformations and drag forces.
Role of chloride concentration in modulating seizure transitions in excitatory and inhibitory networks
Qianchen Gong, Yingpeng Liu, Yan Zhang, Muhua Zheng, and Kesheng Xu
Shifts in GABAergic reversal potentials driven by ionic accumulation govern the transition between distinct firing regimes during the progression and termination of pathological discharges.
Euler-Helfrich problem for open vesicles bounded by elastic filaments
Chengyao Zhang and Xin Yi
Spherical harmonics-based energy minimization characterizes the morphological transformations and mechanical stability emerging from the coupling between membrane geometry and boundary elasticity.
Influence of Bubble Lifetime on the Drying of Catalytically Active Sessile Droplets
Meneka Banik, Ranjini Bandyopadhyay
Marangoni convection triggered by oxygen bubbles counteracts outward capillary advection to redirect particle transport, shifting deposition patterns from the droplet periphery toward the center.
Allosteric gating of radical transport in ribonucleotide reductase
Jiali Gao, Xiaohua Chen
Structural rearrangements at the subunit interface align a sequence of redox-active tyrosine residues to enable the long-range proton-coupled electron transfer required for catalytic activation.
Ostwald’s Rule of Stages in One-Dimension
Jiajun Chen, Ying Xia, Mingyi Zhang, Yu Huang, James J. De Yoreo
Phase boundary fluctuations facilitate a dissolution-reprecipitation mechanism that drives the kinetic transition from metastable to stable peptide structures on graphite, demonstrating that sequential crystallization occurs even in the absence of a thermodynamic nucleation barrier.
A hyperelastic theory for nonlinear hydrogel diffusiophoresis
Chinmay Katke, C. Nadir Kaplan
Reaction-transport dynamics and polymer-solute interactions drive large-scale deformations that can be accelerated up to 40 times by optimizing stimulus concentration, solute size, or fluid flow.
Amendable decisions in living systems
Neri, I.; Pigolotti, S.
Optimal reversible strategies enable living systems to achieve zero error probability in finite time, explaining decision-making performance across scales ranging from human visual perception to cellular differentiation.
Anomalous diffusion of nanoparticles in semidilute hyaluronic acid solutions
Mitra, H.; Nakate, P.; Stevenson, M. J.; Ardekani, A. M.
The ratio of particle size to polymer mesh size determines the degree of hindered mobility, enabling a predictive framework for transport through target-specific biological environments.
Temperature and intrinsic Ca2+ reshape TRPM4 pharmacology
Hu, J.; Ievleva, S.; Park, S. J.; Lee, J.; Cheng, J.; O’Dea, G.; Sheng, J.; Du, J.; Lü, W.
Ligand recognition within TRPM4’s binding pockets shifts functionally under physiological conditions, transforming the putative inhibitor TPPO into a potent activator and revealing that environmental variables are critical for identifying selective therapeutic modulators.
Role of mechanical allostery in kindlin-mediated integrin activation
Zhang, Weiwei, Yang, Haibin, Yang, Zihang, Bian, Yunqiang, Wei, Zhiyi, Yao, Mingxi, Zhang, Jian, Li, Wenfei, Yu, Cong, Wang, Wei
Physiological forces overcome the slow in vitro kinetics of kindlin dimerization by lowering the free-energy barrier of its rate-limiting closed-to-open transition.
Protein trafficking and synaptic demand configure complex and dynamic synaptome architectures of individual neurons
Sorokina, Oksana, Bulovaite, Edita, Sorokin, Anatoly, Grant, Seth G. N., Armstrong, J. Douglas
Minimal cell biological processes governing protein transport and local demand are sufficient to generate the complex, age-dependent spatial organization of synaptic proteins observed across diverse neuronal types.
Efficient sampling of large-scale transition pathways and intermediate conformations in sub-mesoscopic protein complexes
Scaramozzino, Domenico, Lee, Byung Ho, Orellana, Laura
eBDIMS2 utilizes an improved coarse-grained algorithm to simulate the complex structural dynamics and functional transitions of high-order protein assemblies.
RNA i-Motif Formation at Neutral pH
Preciado-Carrillo, Z.; Fountain, S.; Wright, E. P.; Guneri, D.; Abdelhamid, M. A.; Craggs, T. D.; DING, Y.; Waller, Z. A. E.
Single-molecule experiments identify a persistent 1% folded population at physiological pH despite global unfolding in bulk measurements, suggesting these structures may remain biologically relevant within cells.
A fast and accurate calculation method for light induced isomerization of retinal proteins in real time
Althoff, P.; Labudda, K.; Hoeweler, U.; Luebben, M.; Gerwert, K.; Koetting, C.; Rudack, T.
Quantum mechanically refined force field parameters integrated into a classical molecular mechanics framework enable the simulation of retinal photoisomerization on its natural 500-femtosecond timescale, accurately identifying the branched photocycle and asymmetric excited state potential of Channelrhodopsin-2.
Fast MAS NMR Spectroscopy Can Identify G-Quartets and Double-Stranded Structures in Aggregates Formed by GGGGCC RNA Repeats
Zager, S.; Medved, N.; Cevec, M.; Cercek, U.; Rogelj, B.; Plavec, J.; Kragelj, J.
A dynamic equilibrium between Watson-Crick and Hoogsteen base-pairing motifs determines the structural composition of the RNA aggregates and shifts in response to divalent cations or nuclear extracts.
Multistep loss of catalytic and ligand binding abilities of hexameric purine nucleoside phosphorylase
Narczyk, Marta, Bzowska, Agnieszka
Dissociation constants for the enzyme shift as specific activity decreases, reflecting intermediate states that remain capable of processing transition-state analogs despite losing the ability to catalyze natural substrates.
Vibrational contribution to the sub-terahertz dielectric response of kinesin and its hydration shell
Pandey, Saurabh K., Cifra, Michal
Antiparallel dipole variations between the protein and its surrounding water layer create a non-additive reduction and blue-shift in low-frequency absorption, characterizing the mechanistic influence of hydration on the motor domain’s dielectric properties.
Elucidating the mechanism of cefpodoxime-BSA interaction via a combination of multi-spectroscopic methods and molecular docking simulations
El Gammal, Reem N., Elmansi, Heba, El-Emam, Ali A., Hammouda, Mohammed E. A., Belal, Fathalla
Hydrophobic interactions drive the spontaneous formation of a static ground-state complex at subdomain IIA, yielding a moderate binding affinity that determines the drug’s pharmacokinetic distribution and elimination.
The Role of Conformational Changes in TcmN Aromatase/Cyclase in Polyketide Biosynthesis
Valadares, V. S.; Granja, A. C. S.; Martins, L. C.; Padmanabha Das, K.; Cino, E. A.; Magalhaes, M. T. Q.; Valente, A. P.; Arthanari, H.; Moraes, A. H.
A ligand-gated breathing mechanism regulates the transition between open and closed states to accommodate bulky intermediates and facilitate product release while preventing protein aggregation.
Altered ciliary morphology reduces mechanosensation in a cystic kidney model as indicated by a mathematical model
Kumamoto, Kanako, Kagami, Hiroyuki, Saitoh, Sei, Yamada, Shiori, Matsumoto, Mami, Ohno, Nobuhiko
Increased urine flow potentially mitigates cyst development by restoring mechanical drag forces that are otherwise diminished by the elongated and structurally compromised cilia characteristic of early-stage disease.
Revealing properties for enhanced quantum sensing in engineered proteins
Antill, L. M.; Baidoo, J.; Gerhards, L.
Localized reorganization of the donor microenvironment and significantly slowed dipolar dephasing govern the magnetosensitivity of AsLOV2-derived variants while preserving their core structural integrity.
Local GPCR density tips the balance of μ-opioid receptor trafficking
Holsey, M. D.; Bondar, A.; Geggier, P.; Dukas, G. V.; Webb, C. M.; Govindaraju, A.; Mathiasen, S.; Canals, M.; Lambert, N. A.; Asher, W. B.; Javitch, J. A.
Shared recruitment of GRK2/3 and β-arrestin across an affinity matrix of class A receptors enables receptor internalization, whereas class B GPCRs inhibit this process by sequestering these same regulatory proteins.
Impact of Image Representation on Deep Learning-Based Single-Cell Classification by Holographic Imaging Flow Cytometry
Pirone, D.; Cavina, B.; Giugliano, G.; Nanetti, F.; Reggiani, F.; Miccio, L.; Kurelac, I.; Ferraro, P.; Memmolo, P.
A Pareto analysis of six processing pipelines demonstrates that deep-learning-accelerated methods and intermediate image representations significantly reduce computational overhead while maintaining high classification accuracy compared to full phase reconstruction.
Computational Synthetic Inner Membrane Reveals Cardiolipin-Leak Control of ATP Output
Petalcorin, M. I. R.
Respiratory capacity and membrane potential serve as the dominant controllers of energy flux, defining a narrow cardiolipin performance window of 0.18 for maximizing ATP synthesis in programmable membranes.
Aberration-aware 3D localization microscopy via self-supervised neural-physics learning
Fu, S.; Shi, W.; Katrukha, E. A.; Chen, X.; Fei, Y.; Fang, K.; Wang, R.; Zhang, T.; Ma, D.; Li, Y.
LUNAR enables calibration-free, high-density volumetric nanoscopy at large imaging depths by simultaneously inferring molecular parameters and system distortions through an integrated, adaptive optimization process.
Antiparallel Cell Circulation Emerging from Self-Aligned Tension Gradients
Karimata, R.; Hashimura, H.; Horiguchi, S. A.; Fujimori, T.; Sawai, S.; Okuda, S.
Reciprocal mechanical interactions between cells that couple their orientation to their velocity drive the organization of stable bidirectional lanes and the spontaneous phase separation of motile cells from nonmotile neighbors.
Social Information Quality and Environmental Volatility Shape Collective Foraging Behavior
Chirkov, V.; Kurvers, R. H. J. M.; Deffner, D.; Romanczuk, P.
Agents utilizing payoff-based information develop flexible strategies that adapt to shifting resource landscapes, while those relying on positional cues produce rigid behaviors that fail as instability increases.