<?xml version="1.0" encoding="UTF-8" ?>
<rdf:RDF xmlns:admin="http://webns.net/mvcb/" xmlns="http://purl.org/rss/1.0/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:prism="http://purl.org/rss/1.0/modules/prism/" xmlns:taxo="http://purl.org/rss/1.0/modules/taxonomy/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:syn="http://purl.org/rss/1.0/modules/syndication/">
<channel rdf:about="https://biorxiv.org">
<admin:errorReportsTo rdf:resource="mailto:biorxiv@cshlpress.edu"/>
<title>bioRxiv Subject Collection: Biophysics</title>
<link>https://biorxiv.org</link>
<description>
This feed contains articles for bioRxiv Subject Collection "Biophysics"
</description>

<items>
<rdf:Seq>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.20.739612v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.20.739462v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.20.739664v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.20.739653v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.20.739477v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.20.739429v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.18.739361v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.16.739021v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739201v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739215v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.18.739347v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739187v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.16.738902v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739185v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739057v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739191v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739178v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739107v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.17.739112v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.12.738114v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.14.738422v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.15.738578v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.16.738946v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.15.738743v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.16.738899v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.16.739031v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.15.738683v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.15.738799v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.16.738963v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.16.738959v1?rss=1"/>
</rdf:Seq>
</items>
<prism:eIssn/>
<prism:publicationName>bioRxiv</prism:publicationName>
<prism:issn/>

<image rdf:resource=""/>
</channel>
<image rdf:about="">
<title>bioRxiv</title>
<url>https://www.biorxiv.org/sites/default/files/bioRxiv_article.jpg</url>
<link>https://www.biorxiv.org</link>
</image>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739612v1?rss=1">
<title>
<![CDATA[
A Composite Endomembrane Suspension Governs Cytoplasm Rheology 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739612v1?rss=1
</link>
<description><![CDATA[
The cytoplasm of eukaryotic cells is populated by dense disordered suspensions of filamentous and granular endomembranes, yet how they contribute to the mechanical behavior of the cell interior remains unknown. We combined active micro-rheology, cell-like encapsulation and simulations to study the material properties of marine egg extract fractions enriched in distinct endomembrane components. We characterized the cytoplasm as a composite suspension made of yolk granules interspaced by sheets and tubules of endoplasmic reticulum (ER) bathed in cytosolic fluid, that occupies ~38% of cell volume. Remarkably, while isolated cytosol, yolk or ER fractions had characteristics of Newtonian fluids, their combination yielded the emergence of viscoelasticity and glass-like dynamics closely resembling that of in vivo cytoplasm. Our data suggest that the ER acts as a sterically excluding backbone that drives the formation of load-bearing yolk flocculation structures to endow the cytoplasm with solid-like properties at volume fractions far below random close packing. This work establishes a generic framework to understand the material properties of composite endomembrane suspensions, and delineates a novel strategy by which eukaryotic cells may tune the physical state of their cytoplasm.
]]></description>
<dc:creator><![CDATA[ Arjona, M. I., khosravanizadeh, A., Municio-Diaz, C., Mioche, M., Dmitrieff, S., Salle, J., Marteil, A., Durieu, C., Pontani, L. L., Wandersman, E., MINC, N. ]]></dc:creator>
<dc:date>2026-07-21</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739612</dc:identifier>
<dc:title><![CDATA[A Composite Endomembrane Suspension Governs Cytoplasm Rheology]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739462v1?rss=1">
<title>
<![CDATA[
An Atomistic Description of Heterotypic Lipid Exchange by Sec14-like Phosphatidylinositol Transfer Proteins 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739462v1?rss=1
</link>
<description><![CDATA[
Lipid transfer proteins (LTPs) are core regulators of the membrane dynamics, lipid signaling and intracellular communication networks that connect every organelle in the eukaryotic cell. ATP-independent lipid exchange reactions are a hallmark activity of these proteins. These remarkable reactions are essential for the important biological functions of LTPs but how lipid exchange is executed is not at all understood. Herein, we focus on phosphatidylinositol transfer proteins (PITPs) of the highly conserved and highly expanded Sec14/CRAL-Trio-like protein superfamily that potentiate phosphatidylinositol-4-phosphate (PtdIns4P) signaling in eukaryotic cells. Using an integrated structural approach, we describe in atomistic detail the lipid exchange reaction of Sec14-like PITPs. The molecular concepts we identify not only yield insights into how these PITPs integrate metabolic activity with PtdIns4P signaling in cells but also provide a framework for interpreting the functional mechanisms of other LTPs of the Sec14/CRAL-Trio superfamily.
]]></description>
<dc:creator><![CDATA[ Nguyen, T., Chen, X.-R., Singh, P., Green, S., Cahill, M. C., Shaffer, J. M., Khan, D., Molugu, T., Kidwell, A., Iyer, P., Zhaliazka, K., D'Arcy, S., Bankaitis, V., Igumenova, T. ]]></dc:creator>
<dc:date>2026-07-21</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739462</dc:identifier>
<dc:title><![CDATA[An Atomistic Description of Heterotypic Lipid Exchange by Sec14-like Phosphatidylinositol Transfer Proteins]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739664v1?rss=1">
<title>
<![CDATA[
Anionic lipids regulate PLCβ membrane recruitment 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739664v1?rss=1
</link>
<description><![CDATA[
Phospholipase C-{beta} (PLC{beta}) enzymes are essential effectors of G protein-coupled receptor signaling that hydrolyze phosphatidylinositol 4,5-bisphosphate (PIP2) at the plasma membrane to generate the second messengers inositol trisphosphate and diacylglycerol. PLC{beta}s play essential roles in diverse physiological processes, including cardiac and neuronal function, macrophage activation, and the pathogenesis of diseases such as hypertrophic cardiomyopathy. PLC{beta} enzymes are unique in that they are aqueous-soluble and must partition onto the membrane surface to access their substrate, making membrane association a critical regulatory step. For example, we recently demonstrated that G{beta}{gamma} activates PLC{beta} by membrane recruitment and orientation of the catalytic core on the membrane surface. Although PLC{beta} membrane recruitment is required for function, the molecular determinants governing this process remain incompletely understood. Using a quantitative membrane partitioning assay, we show that robust membrane association of PLC{beta} requires anionic phospholipids, whereas polar phospholipids cannot substitute. Membrane partitioning exhibits a steep dependence on anionic lipid abundance, which is mediated by electrostatic interactions between negatively charged lipids and basic residues within the distal C-terminal domain of PLC{beta}. We further demonstrate that anionic lipids cooperate with G{beta}{gamma} to regulate PLC{beta} membrane recruitment, such that the magnitude of G{beta}{gamma}-dependent recruitment is dictated by membrane anionic lipid content. These findings reconcile previous discrepancies regarding G{beta}{gamma}-mediated PLC{beta} membrane recruitment and establish membrane electrostatics as a key regulatory input that integrates lipid composition with G protein signaling to regulate PLC{beta} activity.
]]></description>
<dc:creator><![CDATA[ Crawford, M. A., Bennett, M. B., Qin, Y., Cano, K. E., Gonzalez, T. G., Mojidra, R., Falzone, M. E. ]]></dc:creator>
<dc:date>2026-07-21</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739664</dc:identifier>
<dc:title><![CDATA[Anionic lipids regulate PLCβ membrane recruitment]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739653v1?rss=1">
<title>
<![CDATA[
Solid-state NMR Reveals Mobility-Based Organisation of the Schizosaccharomyces pombe Cell Wall 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739653v1?rss=1
</link>
<description><![CDATA[
Fungal cell walls are hierarchically organised polysaccharide networks whose mechanical and functional properties depend on both chemical composition and molecular organisation. Although glucan synthases are essential for cell wall biosynthesis, how individual synthases shape the supramolecular architecture and dynamics of intact walls remains poorly understood. Here, we combine mobility-resolved 13C solid-state NMR spectroscopy with targeted genetic perturbation of the glucan synthases Ags1, Bgs1, and Bgs4 to determine how synthase activity governs the molecular organisation of the Schizosaccharomyces pombe cell wall. We first establish a molecular-level reference for the wild-type wall by identifying the major glucan and mannan environments and resolving polysaccharides according to their mobility directly in intact cells. The rigid wall scaffold is dominated by unbranched {beta}-1,3-glucan and -1,3-glucan, whereas branched glucans and mannans occupy more dynamic molecular environments. Comparison with thermosensitive glucan synthase mutants reveals distinct, mutation-dependent reorganisation of both the rigid structural scaffold and the mobile polysaccharide matrix. Quantitative analysis further shows that, despite retaining broadly similar glucan compositions, the Ags1, Bgs1, and Bgs4 mutants redistribute carbohydrates among rigid, intermediate, and mobile molecular environments in distinct ways. These mutation-specific mobility fingerprints demonstrate that glucan synthases regulate not only polysaccharide biosynthesis but also how cell wall polymers are assembled, packed, and dynamically organised within the intact wall. More broadly, our findings establish molecular mobility as a sensitive signature of cell wall architecture that reveals structural consequences of biosynthetic perturbation not apparent from composition alone. Mobility-resolved solid-state NMR therefore provides a powerful framework for linking genetic perturbations to molecular dynamics and supramolecular organisation in intact fungal cell walls.
]]></description>
<dc:creator><![CDATA[ Singh, A., Massam-Wu, T., Balasubramanian, M., Chow, W. Y. ]]></dc:creator>
<dc:date>2026-07-21</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739653</dc:identifier>
<dc:title><![CDATA[Solid-state NMR Reveals Mobility-Based Organisation of the Schizosaccharomyces pombe Cell Wall]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-21</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739477v1?rss=1">
<title>
<![CDATA[
Chaotic internal dynamics coexist with a stable temporal scaffold in a mesoscale sarcomere model informed by high-resolution recordings 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739477v1?rss=1
</link>
<description><![CDATA[
Cardiomyocytes maintain a coherent mechanical rhythm despite fluctuations in myosin motors and local contractile units. To examine the intervening mesoscale, we used a reversible state in neonatal rat cardiomyocytes: local warming evokes slow Ca2+-associated sarcomere-length changes together with faster oscillations near the neonatal beat rate, termed hyperthermal sarcomeric oscillations (HSOs). High-speed sarcomere-length nanometry followed five consecutive sarcomeres simultaneously in seven cells. Local amplitudes varied much more than fast-cycle periods, and adjacent sarcomeres displayed both co-directed and opposed motion. These observations motivated a compact chain model with interacting local amplitude--phase states and a common fast phase. The prescribed common phase allowed the model to focus on internal organization under stable timing. A parameter set selected in an exploratory screen was used throughout the subsequent dynamical analyses. Complete ten-dimensional Lyapunov spectra from 360 runs identified a reproducible positive-largest-exponent regime at intermediate coupling. In the same regime, an identical perturbation accessed more independent response directions across initial states, and a simple linear rule transferred less well between trajectories. Small harmonic terms in the observation map improved HSO-like waveform asymmetry in held-out cells while leaving the internal dynamics unchanged. The model also reproduced the experimentally observed predominance of one-link phase updates (95.4% versus 93.9%), although its length redistribution remained more local. Thus, stable beat-like timing can coexist with sensitive, nonrepeating redistribution among coupled local contractile elements, providing a concrete mesoscale representation of robust temporal order with flexible internal organization.
]]></description>
<dc:creator><![CDATA[ Shintani, S. A. ]]></dc:creator>
<dc:date>2026-07-20</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739477</dc:identifier>
<dc:title><![CDATA[Chaotic internal dynamics coexist with a stable temporal scaffold in a mesoscale sarcomere model informed by high-resolution recordings]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-20</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.20.739429v1?rss=1">
<title>
<![CDATA[
Chromosome topology gates productive RecA homology search 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.20.739429v1?rss=1
</link>
<description><![CDATA[
In homologous recombination, DNA repair depends on recombinase filaments finding homologous templates on chromosomes whose topology is continually remodeled by replication and transcription. How dynamic chromosome topology affects homology search and DNA repair remains unknown. By combining live-cell imaging of RecA-mediated homology search with single-molecule assays on topologically-defined DNA substrates, we show that DNA supercoiling acts as a selectivity filter for productive homology search. In Caulobacter crescentus cells, supercoiling is dispensable for the filament movement required for homology search, but required for homology target capture and repair. In vitro, filaments transiently sample both relaxed and supercoiled DNA, yet selectively commit to capture only on negatively supercoiled targets. Mechanistically, we find an extreme kinetic preference (~100-fold) of filaments towards negatively supercoiled DNA targets; this topological preference is independent of DNA compaction, pins plectonemes at the capture site, and is conserved across diverse bacterial RecA homologs. Our findings establish that chromosome topology physically regulates homology search and DNA repair.
]]></description>
<dc:creator><![CDATA[ Tisma, M., Bhattacharyya, S., Chang, S., Ha, T., Badrinarayanan, A., Loparo, J. ]]></dc:creator>
<dc:date>2026-07-20</dc:date>
<dc:identifier>doi:10.64898/2026.07.20.739429</dc:identifier>
<dc:title><![CDATA[Chromosome topology gates productive RecA homology search]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-20</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.18.739361v1?rss=1">
<title>
<![CDATA[
Psi RNA-specific Binding Promotes HIV-1 Gag Conformational Change Critical for Immature Viral Particle Assembly 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.18.739361v1?rss=1
</link>
<description><![CDATA[
The immature HIV-1 virion is assembled by the Gag polyprotein using inositol hexakisphosphate (IP6) as an essential assembly co-factor. Gag binds the genomic RNA Psi packaging signal via the nucleocapsid (NC) domain and associates with the plasma membrane via the matrix (MA) domain. Previous studies revealed that Gag exists in both compact (C) and extended (E) conformational states in solution. Only E-Gag formed virus-like particles with the correct size and IP6 shifted the equilibrium of DNA-bound Gag to the E state. The influence of specific RNA elements on this conformational change is unknown. In this work, a dual dye-labeled Gag was prepared for probing the effect of RNA binding on Gag conformation using Forster resonance energy transfer (FRET). In low salt and in the absence of other factors, Gag was primarily in the C state. Psi RNA binding induced a more significant FRET decrease than binding to non-Psi RNAs, consistent with a shift to E-Gag. IP6 alone also promoted the E-Gag state in the absence and presence of RNA. Atomistic molecular dynamics simulations are consistent with and provide detail into the role of NC-Psi RNA binding in the conformational switch of C-Gag to assembly-competent E-Gag. Simulations also showed that this switch is driven by capsid (CA) linker domain orientational flexibility and MA-CA unbinding dynamics. Thus, the highly flexible multi-domain Gag polyprotein leverages both viral and host cell factors to sample and stabilize distinct conformations, thereby orchestrating the viral assembly process.
]]></description>
<dc:creator><![CDATA[ Qiu, Y., Banerjee, P., Grabarkewitz, K., Wysocki, V. H., Rouzina, I., Voth, G. A., Musier-Forsyth, K. ]]></dc:creator>
<dc:date>2026-07-20</dc:date>
<dc:identifier>doi:10.64898/2026.07.18.739361</dc:identifier>
<dc:title><![CDATA[Psi RNA-specific Binding Promotes HIV-1 Gag Conformational Change Critical for Immature Viral Particle Assembly]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-20</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.16.739021v1?rss=1">
<title>
<![CDATA[
Temporal ordering of migration increments carries directional memory under MYO10 depletion and collagen exposure 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.16.739021v1?rss=1
</link>
<description><![CDATA[
Cell migration is commonly summarized by speed, mean-squared displacement, or a single persistence time, although these descriptors discard the order of successive displacement increments. We reanalyzed 48,134 trajectories from 117 fields of view in a public two-by-two factorial experiment combining MYO10 depletion and collagen exposure, using equal-field and equal-repeat inference. Both perturbations suppressed motility, but their combination produced a positive buffering interaction in directional persistence. An analytical order-null that preserves each trajectory's increments, length, net displacement, and static polarity showed that most of the reproducible interaction depended on serial order. Exact decompositions localized the signal to directional organization and to both shared-field and cell-relative motion; leave-one-cell-out estimation excluded focal-cell self-inclusion as its source. We then froze the framework and evaluated 65 public movies from MDA-MB-231, HUVEC, and MDCK systems. HUVEC retained positive sequence excess through 120 min, MDA-MB-231 showed a shorter positive horizon, and MDCK regions transitioned from positive to negative sequence excess. A stationary linear active-memory model and a stationary angular hidden-state model failed to reproduce the complete lag-resolved hierarchy. Serial ordering therefore provides a transferable coordinate for distinguishing migration-memory regimes, whereas the specific MYO10-collagen interaction remains limited to the discovery dataset.
]]></description>
<dc:creator><![CDATA[ Dutta, S. ]]></dc:creator>
<dc:date>2026-07-20</dc:date>
<dc:identifier>doi:10.64898/2026.07.16.739021</dc:identifier>
<dc:title><![CDATA[Temporal ordering of migration increments carries directional memory under MYO10 depletion and collagen exposure]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-20</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739201v1?rss=1">
<title>
<![CDATA[
Emergent, cost-free surplus of core biosynthesis governs bacterial fitness 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739201v1?rss=1
</link>
<description><![CDATA[
Cells often express essential components in excess of the levels required to sustain steady-state growth. The concept of protein reserve or surplus has recently emerged as a strategy for long-term cell fitness in bacteria, typically assumed to reduce steady-state growth as a trade-off for faster adaptation to a new environment. However, the origin and physiological consequences of such surplus remain unclear, particularly for core cellular processes including transcription, translation, and central metabolism. Here, we establish a unified operational definition of surplus and quantify it for selected key components of transcription, translation, and central metabolism machinery in Escherichia coli at the single-cell level. By combining microfluidics, quantitative fluorescence imaging, and CRISPR interference-based gene knockdown, we demonstrate that substantial fractions of core biosynthetic components can be removed without affecting steady-state growth under nutrient-limited conditions. Unexpectedly, this surplus imposes no cost on steady-state growth, in contrast to prevailing trade-off models. Instead, we show that surplus emerges as a passive consequence of substrate limitation using a simple theoretical model, which is based on the universal autocatalytic-network structure of bacterial cells. Perturbation experiments confirm model predictions that surplus of transcription and translation machinery accelerates growth adaptation to nutrient-rich conditions, without affecting steady-state growth. Moreover, under slow-growth conditions, surplus suppresses cell death by reducing the risk of stochastic collapse of biosynthetic cycles, also in accord with our theoretical model prediction. Altogether, our results identify surplus as an intrinsic property of core biosynthesis and a key determinant of long-term bacterial fitness in fluctuating environments.
]]></description>
<dc:creator><![CDATA[ Wang, H., Goberman, D., Aldrich, C., Pugatch, R., Si, F. ]]></dc:creator>
<dc:date>2026-07-19</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739201</dc:identifier>
<dc:title><![CDATA[Emergent, cost-free surplus of core biosynthesis governs bacterial fitness]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-19</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739215v1?rss=1">
<title>
<![CDATA[
Motor Occupancy Defines Emergent Mechanical States in Cardiac Myosin Ensembles 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739215v1?rss=1
</link>
<description><![CDATA[
Myosin II generates force through the collective action of mechanically coupled motor ensembles, yet the mechanisms by which these ensembles sense changes in motor occupancy and coordinate force generation remain poorly understood. Ensemble force production may be governed by an optimal balance between effective motor occupancy and mechanical coordination rather than by motor number alone. We reconstituted cardiac myosin ensembles and systematically perturbed effective motor occupancy using the small-molecule drugs omecamtiv mecarbil (OM), which prolongs actomyosin interactions, and mavacamten (MAVA), which reduces the number of available force-generating myosin heads. Optical trapping measurements of full-length and S1 cardiac myosin ensembles revealed that force generation depended on both myosin concentration and pharmacological perturbation. Reducing myosin concentration increased force generation in the absence of drug, while OM and MAVA produced responses that varied with the initial occupancy state of the ensemble. Low concentrations of MAVA enhanced force generation under high motor occupancy but reduced force under low motor occupancy, whereas OM produced occupancy-dependent changes in both endpoint force and force dynamics. Force traces further revealed changes in the persistence and temporal coordination of force generation. These findings support a model in which cardiac myosin ensembles operate along an occupancy-coordination landscape, where maximal force generation is achieved at an intermediate level of effective motor occupancy. Our results illuminate how changes in motor occupancy are translated into coordinated ensemble mechanics and suggest that emergent mechanical feedback through the shared actin filament may enable ensembles to collectively sense and adapt to their mechanical state.
]]></description>
<dc:creator><![CDATA[ Alazzam, O. Y., Chowdhury, M. A. H., Stevens, H. M., Reinemann, D. N. ]]></dc:creator>
<dc:date>2026-07-19</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739215</dc:identifier>
<dc:title><![CDATA[Motor Occupancy Defines Emergent Mechanical States in Cardiac Myosin Ensembles]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-19</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.18.739347v1?rss=1">
<title>
<![CDATA[
Rho ({rho}) Analysis to Dissect RNA Folding and Assembly Pathways 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.18.739347v1?rss=1
</link>
<description><![CDATA[
The modular structure and energetics of RNA simplifies its folding. Leveraging this modularity, we introduce Rho ({rho}) analysis to systematically dissect RNA conformational pathways. {rho} analysis uses isolated RNA secondary or tertiary contacts as external standards to provide insights not possible via the internal comparisons of traditional {varphi} analysis. Equivalent effects of a mutation on the folding rate constant of the RNA of interest and the thermodynamic stability of the isolated contact indicate that the mutated interaction is fully formed prior to the rate-limiting transition state; the absence of a kinetic effect indicates that the interaction is formed after this transition state. Comparisons with properties of the isolated contact provide additional insights about conformational pathways. We demonstrate {rho} analysis by dissecting Tetrahymena group I intron folding pathways, using a split intron in which the P5abc subdomain assembles with the intron core through three tertiary contacts. We uncover multiple folding pathways and modulation in pathway flux that are readily understood from the energetic properties of the constituent RNA motifs. Extending these concepts to RNA-guided DNA recognition by CRISPR-Cas12a, crRNA-DNA mismatches give substantial {varphi} values across much of the target, indicating a late transition state in binding. Thermodynamic penalties from mismatches support modular base-pairing energetics and define an upper bound on DNA target specificity. Our results establish {rho} analysis as a general framework to probe RNA conformational pathways and function. It is straightforward to implement and can be readily applied in vitro and in cells.
]]></description>
<dc:creator><![CDATA[ Gracia, B., Nielson, S. E., Herschlag, D., Russell, R. ]]></dc:creator>
<dc:date>2026-07-19</dc:date>
<dc:identifier>doi:10.64898/2026.07.18.739347</dc:identifier>
<dc:title><![CDATA[Rho ({rho}) Analysis to Dissect RNA Folding and Assembly Pathways]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-19</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739187v1?rss=1">
<title>
<![CDATA[
Cooperativity and Conformational Rearrangements in Protein-Protein and Protein-Ligand Interactions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739187v1?rss=1
</link>
<description><![CDATA[
Streptavidin-biotin, avidin-biotin interactions are classical models for protein-ligand binding, yet the energetic changes accompanying biotin binding remain poorly resolved. Using fluorescent dyes as energy sensors, we show that biotin binding produces two distinct regimes occurring in parallel as concentration of biotin increases cooperativity and conformational rearrangements, wherein cooperativity is observed via exchange broadening of fluorescence linewidth and conformational rearrangements exclusively observed in emission energy. Where the first biotin binding creates the highest contribution to the emission energy. Further analysis of tetramer-tetramer only interactions revealed extremely long ranged intermolecular interactions extending to hundreds of nm. The intermolecular interactions become negligible only at concentrations of approximately 10 nM for both streptavidin and avidin. Affinity values estimated for these diluted samples were below 1 nM.
]]></description>
<dc:creator><![CDATA[ Thiyagaraj, D., Del Re, A., Pham, Q. D., Gomez Garrote, I., Saudi, A., Fedorych, O. ]]></dc:creator>
<dc:date>2026-07-18</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739187</dc:identifier>
<dc:title><![CDATA[Cooperativity and Conformational Rearrangements in Protein-Protein and Protein-Ligand Interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-18</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.16.738902v1?rss=1">
<title>
<![CDATA[
Fluorescence cross-correlation spectroscopy quantifies affinity, cooperativity, and kinetic stability in ternary protein complexes 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.16.738902v1?rss=1
</link>
<description><![CDATA[
Many biological processes and emerging therapeutic modalities rely on higher-order protein complexes whose properties cannot be predicted from their constituent binary interactions. However, methods for directly quantifying affinity, cooperativity, and kinetic stability within such assemblies remain limited. Here, we establish fluorescence cross-correlation spectroscopy (FCCS) as a solution-phase approach for characterizing multicomponent protein interactions and apply it to the clinically important HER2-targeting antibodies trastuzumab and pertuzumab.

Using fluorescently labelled HER2, trastuzumab, and pertuzumab, we quantified binary binding affinities, directly measured ternary complex formation, and characterized the dissociation kinetics of binary and ternary complexes. FCCS measurements revealed positive cooperativity in the formation of the HER2-trastuzumab-pertuzumab ternary complex, while dissociation experiments demonstrated that the ternary complex is kinetically more stable than the corresponding binary interactions. Together, these findings provide direct solution-phase evidence that cooperative interactions stabilize the HER2-trastuzumab-pertuzumab complex, offering a molecular explanation for the enhanced efficacy of dual HER2 targeting in cancer therapy. More broadly, this work demonstrates that FCCS can robustly quantify affinity, cooperativity, and kinetic stability of multicomponent protein complexes using a commercially available platform. We provide a broadly accessible framework for studying higher-order protein interactions and supporting the development of next-generation multispecific and combination therapeutics.

Significance StatementMany proteins function as part of multicomponent complexes, yet most experimental methods characterize interactions only one pair at a time, or indirectly through secondary reporters, or necessitating saturation of binary interactions first. We show that fluorescence cross-correlation spectroscopy can directly quantify how multiple binding partners interact simultaneously by measuring affinity, cooperativity, and kinetic stability in solution. Applying this approach to the clinically important HER2-targeting antibodies trastuzumab and pertuzumab reveals cooperative stabilization of their ternary complex. Because the measurements are performed on a commercially available instrument and require no surface immobilization, this broadly accessible method should facilitate mechanistic studies of complex biomolecular interactions and aid the development of multispecific and combination therapeutics.
]]></description>
<dc:creator><![CDATA[ Mueller, S. H., Mohanan, G., Abdelhamid, M. A. S., Toseland, C. P., Craggs, T. D. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.16.738902</dc:identifier>
<dc:title><![CDATA[Fluorescence cross-correlation spectroscopy quantifies affinity, cooperativity, and kinetic stability in ternary protein complexes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739185v1?rss=1">
<title>
<![CDATA[
Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739185v1?rss=1
</link>
<description><![CDATA[
Martini 3 is a force field ideally suited to simulating long intrinsically disordered proteins (IDPs) in cell-like surroundings. So far, most Martini 3 variations intended for IDPs have only been benchmarked on shorter IDPs of up to 140 amino acids. In this paper, we present a comprehensive benchmark including IDPs up to 809 amino acids in length and compare the behavior of four well-known Martini 3 variations for IDPs. Modifications to only the bonded parameters result in excessively compact conformations, thereby failing to reproduce the experimental radius of gyration observed for large IDPs. In contrast, general rescaling of interaction parameters, including tuning electrostatic interactions in the case of highly-charged long IDPs, yields acceptable levels of compaction at all tested length scales.
]]></description>
<dc:creator><![CDATA[ Goss, C., Aponte-Santamaria, C., Gräter, F. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739185</dc:identifier>
<dc:title><![CDATA[Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739057v1?rss=1">
<title>
<![CDATA[
Excited state Relaxation Activation Energy (ESRAct) of Di-4-ANEPPDHQ Maps Nanoscale Molecular Organization in Biomembranes 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739057v1?rss=1
</link>
<description><![CDATA[
Live cell plasma membranes show spatially heterogeneous liquid-ordered (Lo)-like and liquid-disordered (Ld)-like regions similar to the co-existing Lo/Ld phases observed in lipid vesicles. The Lo-like regions are relatively less hydrated and less polar due to tight packing of the membrane components compared to the Ld-like regions. The steady-state fluorescence spectra of Di-4-ANEPPDHQ (Di-4), a widely used polarity-sensitive probe, is blue or red shifted when solvated in less polar (Ld-like) or more polar (Lo-like) regions respectively. However, quantification of Di-4 fluorescence in blue and red channels for the evaluation of membrane phase state suffers from the lack of specific wavelength choice for these two channels and relatively higher concentration of Di-4 in Ld phase (red channel) due to its partitioning preference. To address these issues, we employed fluorescence lifetime of Di-4, a concentration independent photophysical parameter, to understand membrane biophysical properties. The fluorescence lifetime of Di-4 in lipid vesicles exhibits Arrhenius-like temperature dependence. Centred around this energetic feature of Di-4 photophysics, we developed a novel analytical module, namely excited state relaxation activation energy (ESRAct), that serves as an intrinsic descriptor of the membrane nano-environment sensed by this probe. We show that the ESRAact value scales with increasing disorder in nanoscale phase separation (i.e., ESRAct of pure Ld > mixed Ld/Lo > pure Lo phase). We then extended its applications to giant plasma membrane vesicles (GPMVs) isolated from MCF-7 cells and found that these vesicles exhibit nanoscale Lo/Ld co-existing phase within 16-37C. We envisage wide applications of ESRAct to delineate plasma membrane phase behavior as well as general photophysical studies on other newly designed polarity-sensitive probes.
]]></description>
<dc:creator><![CDATA[ Medda, D., Tripathy, A., Bag, N. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739057</dc:identifier>
<dc:title><![CDATA[Excited state Relaxation Activation Energy (ESRAct) of Di-4-ANEPPDHQ Maps Nanoscale Molecular Organization in Biomembranes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739191v1?rss=1">
<title>
<![CDATA[
Mechanosensation, habituation, and behavioural plasticity in tintinnid ciliates 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739191v1?rss=1
</link>
<description><![CDATA[
Unicellular organisms sense, integrate and respond to environmental cues despite lacking neurons or a nervous system. Several species, notably ciliates, are capable of adaptive behaviours normally associated with multicellular animals. Integral to marine ecosystems are planktonic ciliates called tintinnids, which feed on microbes and serve as prey for larger predators. In nature, they swim, feed, hunt, and build ornate loricas, while experiencing varied mechanical and flow perturbations from encounters with other organisms and their environment. Here, we investigated mechanosensory responses in tintinnids at single-cell resolution using temporally controlled touch and vibrational stimuli. Localised touch stimulation of the ciliary band triggered stereotyped ciliary reversals and beat frequency elevation, but strong vibrational stimuli elicited rapid whole-cell contractions. Repeated stimulation produced a progressive decline in response probability that depends on stimulus frequency, with spontaneous recovery if stimulation is withheld. Our work identifies a novel form of cilia-associated habituation response to mechanical stimulation in tintinnids that is distinct from contractile whole-body responses previously reported in other protists. The results show how motility and sensory feedback are tightly coupled to coordinate cellular information processing and a hierarchy of mechanosensory responses in a single-celled organism.
]]></description>
<dc:creator><![CDATA[ Laeverenz-Schlogelhofer, H., Wan, K. Y. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739191</dc:identifier>
<dc:title><![CDATA[Mechanosensation, habituation, and behavioural plasticity in tintinnid ciliates]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739178v1?rss=1">
<title>
<![CDATA[
Mapping absolute membrane voltage using dynamic photocycle control 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739178v1?rss=1
</link>
<description><![CDATA[
Fluorescent voltage indicators are widely used to report relative changes in membrane potential, but mapping absolute voltages remains difficult. Here we present Voltage Measurement by Activated Photocycles (VMAP), a simple method for absolute voltage imaging based on a photophysical switch between voltage-insensitive and sensitive indicator states. VMAP requires no specialized hardware or additional labeling, and is applicable across species, sample preparations, and microscope configurations. Using VMAP, we quantified drug-induced shifts in neuronal resting potential, revealed the emergence of bioelectric patterns during multi-day recordings of human iPSC populations, and created 3D membrane-potential maps across whole live zebrafish embryos. By making absolute voltage imaging accessible from cellular to organismal scales and from milliseconds to days, VMAP opens a route to mapping bioelectrical organization in complex living systems.
]]></description>
<dc:creator><![CDATA[ Gong, D., Zhang, J., Howell, M. R., Wu, X., Jia, B. Z., Cohen, A. E. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739178</dc:identifier>
<dc:title><![CDATA[Mapping absolute membrane voltage using dynamic photocycle control]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739107v1?rss=1">
<title>
<![CDATA[
Multi-modal MRI characterisation of vascular remodelling, muscle fibre integrity, and inflammatory recovery in a hindlimb ischaemia mouse model 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739107v1?rss=1
</link>
<description><![CDATA[
The hindlimb ischaemia (HLI) mouse model is a widely used preclinical model of chronic limb-threatening ischaemia (CLTI). While CLTI involves complex interactions between impaired perfusion, inflammation and muscle wasting, the standard imaging approach, laser Doppler imaging (LDI), only assesses perfusion. MRI is used clinically to assess neural tracts, inflammation, and perfusion in the brain. We therefore evaluated whether a multimodal MRI approach could longitudinally monitor recovery in the HLI mouse model. Mice underwent MRI three days pre-HLI surgery, and on Days +3 and +7 post-surgery, with histology on Day +7. The MRI detected significant increases in muscle volume and inflammation after HLI surgery, with significant decreases in perfusion, vascular length, and muscle fibre integrity. Overall, MRI can monitor inflammation, muscle fibre integrity, and vascular recovery post-HLI and should be applied in future studies to identify mechanisms of therapeutic recovery in a sequential in vivo analysis without requiring animal sacrifice.



O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/739107v1_ufig1.gif" ALT="Figure 1">
View larger version (45K):
org.highwire.dtl.DTLVardef@150a245org.highwire.dtl.DTLVardef@cd64caorg.highwire.dtl.DTLVardef@941057org.highwire.dtl.DTLVardef@bcc00c_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG
]]></description>
<dc:creator><![CDATA[ Lyons, C. J., Doulgkeroglou, M. N., Sanz-Nogues, C., Lagonda, C. A., Chen, X., Colgan, N., O'Brien, T. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739107</dc:identifier>
<dc:title><![CDATA[Multi-modal MRI characterisation of vascular remodelling, muscle fibre integrity, and inflammatory recovery in a hindlimb ischaemia mouse model]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.17.739112v1?rss=1">
<title>
<![CDATA[
How specific structural differences of Bcl2 proteins modulate the interaction with BH3 domains and apoptotic function 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.17.739112v1?rss=1
</link>
<description><![CDATA[
Intrinsic apoptosis is mainly regulated through a network of conserved interactions between Bcl-2 proteins involving hydrophobic binding grooves and BH3 domains. Despite these conserved interfaces, family members exhibit distinct binding affinities and play opposing roles in apoptosis. While static structural differences partially account for this divergence, it remains unclear how opposing apoptotic function reflects in BH3 helix engagement of individual members. Here, we investigate how a BidBH3 peptide engages with the hydrophobic groove of full-length membrane-anchored Bcl-xL and Bax to identify shared and unique features of binding that may relate to distinct apoptotic functions. Using state-of-the-art enhanced-sampling simulations, we mapped the complete binding and folding landscapes of these critical cell-death regulators in membranes. Our simulations align with experimental measurements in terms of predicted absolute binding affinities, and also capture the dynamic, atomistic details of the conformational changes induced by BH3 helices. Together, these details highlight the structural principles of BH3 in-groove engagement that determine apoptotic function, paving the way towards the modulation of the interactions among the Bcl-2 family members.
]]></description>
<dc:creator><![CDATA[ Hanke, A., Elsner, C., Aureli, S., Bordignon, E., Gervasio, F. L. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.17.739112</dc:identifier>
<dc:title><![CDATA[How specific structural differences of Bcl2 proteins modulate the interaction with BH3 domains and apoptotic function]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.12.738114v1?rss=1">
<title>
<![CDATA[
Quantitative Comparison of 3D-1D Vascular Coupling Models: Lateral Average versus Sphere of Influence Methods 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.12.738114v1?rss=1
</link>
<description><![CDATA[
Computational models coupling one-dimensional vascular networks with three-dimensional tissue domains are widely used for predicting blood flow distribution in tumor perfusion, drug delivery, and therapeutic planning. Two prominent coupling paradigms have emerged: the Lateral Average Model (LAM) which implements distributed transmural exchange via a vessel wall conductivity parameter{gamma} (m Pa-1 s-1), and the Sphere of Influence (SOI) model, which employs localized terminal coupling via a source sphere radius{varepsilon} (m). Despite their broad application, systematic quantitative comparisons of their parametric behavior and predictive equivalence remain lacking.

We compare LAM and SOI in 3D-1D simulations on a benchmark vascular network and a porcine liver study with a hepatic arterial network reconstructed from CT arteriography.

Across a benchmark vascular network under three sink configurations, the LAM net flow rate rose smoothly with{gamma} and saturated at a plateau, while the SOI net flow rate increased with{varepsilon} without saturating; as a result, global-flow equivalence between the two formulations exists only for particular boundary geometries, and not at all within the tested parameter range for one of the three configurations examined. Despite this partial agreement in total flow, the two models diverged substantially in regional perfusion: in a porcine hepatic arterial network reconstructed from CT arteriography, SOI predicted stable perfusion fractions to two regions of interest across its full tested parameter range, whereas LAM predictions for the same regions varied several-fold with vessel wall permeability and, at low permeability, could invert which region received more flow. These results indicate that the choice of coupling model has limited consequence for predicted total organ flow but substantial consequence for predicted local drug delivery, and we provide guidance for selecting between the two formulations depending on the clinical or research question being asked.

Author SummaryWhen doctors plan treatments for liver cancer, they often rely on computer simulations to predict how blood flows through the liver and how well a drug will reach the tumor. These simulations depend on mathematical models that describe how blood moves from vessels into surrounding tissue. Two commonly used approaches exist for building these models, but researchers have generally chosen between them based on habit or convenience rather than on a principled understanding of how their predictions differ.

In this work, we directly compared these two approaches, one that spreads blood exchange continuously along the vessel wall, and one that delivers blood from the vessel tips into a surrounding spherical zone, using both a simple test network and a realistic pig liver reconstructed from medical imaging. We found that the two approaches can agree on the total amount of blood reaching the liver, but disagree substantially on where that blood goes within the tissue. This distinction matters enormously for treatment planning: a model that predicts the right total blood flow but delivers it to the wrong region of the liver could lead to an inaccurate forecast of drug concentration at the tumor site. Our results provide practical guidance for researchers on which approach to use depending on what information is available and what question is being asked.
]]></description>
<dc:creator><![CDATA[ Amare, R., Vargun, D., Zhang, P., Parrish, S., Stolley, D., Santos, C., Jacobsen, M., Cressman, E., Riviere, B., Fuentes, D. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.12.738114</dc:identifier>
<dc:title><![CDATA[Quantitative Comparison of 3D-1D Vascular Coupling Models: Lateral Average versus Sphere of Influence Methods]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.14.738422v1?rss=1">
<title>
<![CDATA[
Telomeric G-Quadruplexes Formed by Six G-overhang Permutation Repeats 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.14.738422v1?rss=1
</link>
<description><![CDATA[
The single-stranded G-overhangs of vertebrate telomeres, composed of guanine (G)-rich hexanucleotide repeats, can adopt six register-dependent permutations: GGTTAG, GTTAGG, TTAGGG, TAGGGT, AGGGTA, and GGGTTA. Telomeric G-quadruplexes (G4s) formed by the first two repeat permutations, which are the most prevalent at human chromosome ends, have been largely overlooked. Here, G4 formation across all six permutations, each containing 4 to 9 repeats, are systematically investigated under varying cation conditions and molecular crowding environments. Our findings reveal that distinct repeat permutations yield markedly different G4 stabilities and folding topologies, which in turn modulate DNA polymerase activity. This expanded perspective on telomeric structural diversity provides new insights into telomere biology and suggests that multiple repeat patterns may cooperatively influence chromosome end protection and targeting.
]]></description>
<dc:creator><![CDATA[ Guan, Z., Luo, T., Shen, J., Zhang, S., Chu, C., Zhou, J., Mergny, J.-L., Cheng, M. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.14.738422</dc:identifier>
<dc:title><![CDATA[Telomeric G-Quadruplexes Formed by Six G-overhang Permutation Repeats]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.15.738578v1?rss=1">
<title>
<![CDATA[
DNA-Programmed Condensate-Membrane Wetting and Cellular Internalization 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.15.738578v1?rss=1
</link>
<description><![CDATA[
Deformable condensates offer dynamic interfaces for biomolecule delivery, yet membrane adhesion does not necessarily lead to cellular internalization. The physical transition that determines whether a membrane-bound soft material remains surface-anchored or proceeds through wetting towards productive uptake remains poorly understood, particularly at active living-cell membranes. Here, we engineer sequence-defined DNA condensates through liquid-liquid phase separation (LLPS) and program their interfacial behavior by tuning sticky-end valency and cholesterol organization. These molecular designs precisely regulate condensate fluidity, fusion dynamics and internal organization, generating distinct states of weak contact, persistent anchoring and rapid wetting. Increasing cholesterol-mediated affinity does not enhance uptake. Instead, productive internalization emerges from a balance between membrane adhesion and condensate fluidity and deformability. Native membrane composition further modulates condensate interfacial fate across mammalian cells and plant protoplasts. DNA condensates enrich and deliver CpG ODNs, mRNA ([~]2000 nt) and proteins, while cargo loading experiments reveal that preserving condensate architecture is essential for functional delivery. Our findings identify wetting competence as a design parameter for controlling soft material engagement and cellular entry.
]]></description>
<dc:creator><![CDATA[ Chen, Z., Chen, W., Ye, J., Lu, D., Landry, M. P., Zhang, H., Fan, C., Zhang, H. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.15.738578</dc:identifier>
<dc:title><![CDATA[DNA-Programmed Condensate-Membrane Wetting and Cellular Internalization]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.16.738946v1?rss=1">
<title>
<![CDATA[
Stress-Induced Mechanical Memory in Respiratory Mucus: Anisotropy, Network Reorganization, and Directional Transport 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.16.738946v1?rss=1
</link>
<description><![CDATA[
Mucus transport is essential for lung health, as ciliated cells constantly propel mucus outward to clear bacteria, viruses, and particles. This defense relies on a material that must be elastic enough to maintain ciliary traction, but capable of reorganizing under sustained directional loading. How the mucin network reconciles these demands, and whether it retains a memory of the stresses it experiences, remains poorly understood. Here we show that lung mucus develops a persistent, direction-dependent mechanical asymmetry under physiologically relevant stress--a mechanical memory encoded in the slow scaffold of the network. Using bulk rheology, we find that directional pre-stress produces a residual anisotropy that grows with stress magnitude and persists long after the load is removed. A transient network model attributes this memory to a separation of timescales between transient bonds and a long-lived crosslink scaffold, and particle-tracking microrheology confirms that the memory reorganizes the network geometry at the scale of biological particles, biasing tracer diffusion along the axis of applied stress. The stresses required to induce memory are within the range generated by ciliary beating and remain below the mucus yield threshold, suggesting that mucociliary clearance operates in a regime where directional alignment accumulates without compromising the coherence of the mucus layer. This proximity to yield may not be coincidental, it allows mucus to accumulate mechanical memory under physiological forcing while remaining poised to flow during clearance events such as coughing.
]]></description>
<dc:creator><![CDATA[ Prabhune, A. G., Rezaei, B., Garcia-Gordillo, A. S., Das, M., Vernerey, F. J., Figueroa-Morales, N. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.16.738946</dc:identifier>
<dc:title><![CDATA[Stress-Induced Mechanical Memory in Respiratory Mucus: Anisotropy, Network Reorganization, and Directional Transport]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.15.738743v1?rss=1">
<title>
<![CDATA[
Many-body quantum percolation sustains ohmic proton flux through the nanoconfined Fo motor 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.15.738743v1?rss=1
</link>
<description><![CDATA[
The FoF1-ATP synthase drives cellular bioenergetics by translocating protons across the inner mitochondrial membrane. We recently demonstrated that the lipid cardiolipin acts as a 2D antenna, actively funnelling protons into the nanoconfined Fo motor and enforcing severe "dimensional squeezing". This 1D nanoconfinement forces protons into such close proximity that their hydration shells physically overlap, theoretically generating an infinite classical steric gridlock. Yet, empirical measurements show the Fo motor operates at ~90% efficiency and exhibits barrierless, Ohmic conductance, presenting a biophysical paradox. To resolve this contradiction between classical physics and biological reality, we employed a differentiable inverse-physics framework to blindly deduce the proton wires geometry based solely on macroscopic physiological constraints: ohmic linearity and a 1.7 Deuterium Kinetic Isotope Effect. By substituting classical diffusion frameworks with a Many-Body Overdamped Quantum Langevin Equation (QLE), the optimiser successfully converged. It deduced that physiological flux dictates a steric boundary of 0.137 nm (aligning with the effective crystal radius of oxygen) and a structural confinement scale of 0.974 nm. We demonstrate that when these discovered biological parameters are evaluated under classical, independent-particle assumptions, the 1/r12 steric repulsive forces diverge to infinity, causing a simulation collapse. In contrast, the quantum mechanical nature of the QLE allows protons to exist as spatially spread-out clouds rather than fixed point particles. This enables them to traverse tight steric boundaries via a coordinated chain reaction similar to a frictionless nanoscale Newtons cradle. These findings prove that classical, independent-particle models are incompatible with the spatial confinement of respiratory complexes. We conclude that physiological proton transport through the Fo motor mandates a continuous quantum percolation channel, redefining our theoretical understanding of biological energy transduction.

Statement of significanceThe FoF1-ATP synthase sustains cellular life by translocating protons across membranes, driven by its membrane-bound Fo motor. Within this motor, protons navigate a 1-2 nm water wire. Under this extreme biological nanoconfinement, classical physics predicts a structural "traffic jam", i.e., protons should gridlock due to the repulsive overlap of their hydration shells. Yet, the motor operates with highly efficient, ohmic conductance. Using a differentiable inverse-physics framework and the Many-Body Quantum Langevin Equation, we prove classical physics cannot resolve this steric gridlock. Instead, we demonstrate that physiological proton transport inherently mandates many-body quantum percolation. Protons navigate extreme nanoconfinement via spatial quantum delocalisation, establishing that biological energy transduction operates as a nanoscale quantum percolation channel.
]]></description>
<dc:creator><![CDATA[ Adeniran, I., Lightfoot, A. P. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.15.738743</dc:identifier>
<dc:title><![CDATA[Many-body quantum percolation sustains ohmic proton flux through the nanoconfined Fo motor]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.16.738899v1?rss=1">
<title>
<![CDATA[
Rocking Without a Tune: Ex vivo and in vivo Responses to Sound in the Basilar Papilla of the Tokay Gecko 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.16.738899v1?rss=1
</link>
<description><![CDATA[
Like mammals, some reptiles possess sensitive and frequency-selective hearing at high frequencies. Both groups employ a place-frequency map within the inner ear to encode sound stimuli, but the mechanisms by which they achieve tuned nerve activation along the cochlea are believed to be distinct. To investigate the mechanical origins of auditory sensation in the reptiles, we measured sound-evoked displacement responses in the hearing organ of the tokay gecko (Gekko gecko), known as the basilar papilla. Using optical coherence tomography, we were able to resolve sub-nanometer-scale vibrations throughout the organ both in vivo and ex vivo. We found that tuning was not present in the tissue-scale mechanics at any position within the organ; it instead exhibits an untuned rotational motion. We developed a mathematical model which predicted that this motion induces hair-bundle-stimulating fluid velocity, and is due to an anatomical asymmetry seen in many reptile and bird species. These results suggest that hair-bundle-level mechanics are primarily responsible for tuning in the tokay gecko cochlea, and we argue that our proposed mechanisms generalize to many other species across the Reptilia class.

SIGNIFICANCEWe present the most comprehensive picture of tissue-scale mechanics in a reptile hearing organ to-date: sound-evoked displacement responses within the basilar papilla of the tokay gecko (Gekko gecko) both ex vivo and in vivo, across the animals auditory frequency range, and along all three spatial dimensions. We find that place-frequency tuning is not present in the mechanics of the tissue as it is in mammals. Instead, this organ relies on an untuned rocking mechanism to stimulate hair bundles. A mathematical model shows that this may be at play in other reptile and bird species, indicating a unifying mechanism of hearing in the class Reptilia in which hair bundle mechanics play the leading role in frequency tuning.
]]></description>
<dc:creator><![CDATA[ Frost, B. L., Vazquez, Y., Horii, K., Fabella, B. A., Hudspeth, A. J. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.16.738899</dc:identifier>
<dc:title><![CDATA[Rocking Without a Tune: Ex vivo and in vivo Responses to Sound in the Basilar Papilla of the Tokay Gecko]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.16.739031v1?rss=1">
<title>
<![CDATA[
Geometry derived Hamiltonian organization distinguishes recurrent biological Fe S architectures 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.16.739031v1?rss=1
</link>
<description><![CDATA[
Iron-sulfur (Fe-S) clusters are among the most ancient biological cofactors, yet the physical properties associated with the recurrent biological utilization of specific Fe-S architectures remain unclear.

Here, we analyzed 2,404 experimentally resolved Fe-S clusters using an integrated framework combining structural geometry, geometry-derived effective-coupling network robustness, and coarse-grained open-system quantum transport simulations.

We show that 4Fe-4S clusters occupy a compact and partially distinct region of structural-descriptor space characterized by low geometric distortion, elevated geometry-derived network robustness, and broad taxonomic representation within the available structural dataset.

Geometry-derived coarse-grained effective Hamiltonian reconstruction and Lindblad simulations further showed architecture-dependent differences in Hamiltonian organization and simulated transport behavior under a common set of model assumptions.

Together, these findings establish a hierarchical comparative framework linking Fe-S geometry, effective Hamiltonian organization, simulated open-system transport, and broad taxonomic recurrence, and suggest that geometry-derived transport organization may represent one physical property contributing to the recurrent biological utilization of Fe-S architectures.
]]></description>
<dc:creator><![CDATA[ Sung, J.-Y., Cheong, J.-H. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.16.739031</dc:identifier>
<dc:title><![CDATA[Geometry derived Hamiltonian organization distinguishes recurrent biological Fe S architectures]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.15.738683v1?rss=1">
<title>
<![CDATA[
Quantitative Susceptibility Mapping for Differentiating Hydroxyapatite and Calcium Oxalate Breast Calcifications at 3T: A Phantom Study 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.15.738683v1?rss=1
</link>
<description><![CDATA[
PurposeBreast microcalcifications trigger 70-80% of unnecessary biopsies because current imaging cannot distinguish malignancy-associated hydroxyapatite (HA) from benign-associated calcium oxalate (CaOx). Quantitative susceptibility mapping (QSM) could exploit the susceptibility contrast between these minerals (HA: {Delta}{chi} {approx} -7 ppm; CaOx: {Delta}{chi} {approx} -1 ppm relative to water), but no study has demonstrated compositional differentiation at clinical field strength. This work assessed susceptibility and R2* relaxation rate maps for microcalcification differentiation at 3 T using tissue-mimicking phantoms.

MethodsA phantom comprising 12 tubes, each containing co-embedded HA and CaOx particles in BaCl2-crosslinked alginate gels (pure alginate, adipose-mimicking, and fibroglandular tissue-mimicking relaxation properties; n = 4 per type), were scanned at 0.70 mm and 0.86 mm isotropic resolution using a multi-echo gradient echo sequence. A consensus-aligned QSM pipeline and mono-exponential R2* fitting was developed. A digital twin phantom simulation quantified the contributions of partial volume effects and Total Variation (TV) regularisation to susceptibility underestimation.

ResultsQSM detected HA in 18/24 measurements ({Delta}{chi}peak = -0.37 {+/-} 0.07 ppm in alginate at 0.70 mm) and CaOx in 0/24. R2* mapping detected HA in 23/24 and CaOx in 22/24. The digital twin identified TV regularisation as the dominant signal loss mechanism (57.5% loss), exceeding partial volume effects (24.3% loss). Combined parameters yielded three classification categories: QSM-positive with elevated R2* (HA), QSM-negative with moderate R2* (CaOx), and neither elevated (no calcification).

ConclusionQSM at 3 T enables categorical HA detection while R2* provides complementary CaOx sensitivity, together enabling two-parameter microcalcification classification from a single multi-echo acquisition.
]]></description>
<dc:creator><![CDATA[ Misak, K., De Vita, E., Clark, C. A., Cashmore, M. T., Walker-Samuel, S. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.15.738683</dc:identifier>
<dc:title><![CDATA[Quantitative Susceptibility Mapping for Differentiating Hydroxyapatite and Calcium Oxalate Breast Calcifications at 3T: A Phantom Study]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.15.738799v1?rss=1">
<title>
<![CDATA[
A shear lag model of the podocyte foot process network predicts a mechanical feedback loop driving progressive effacement 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.15.738799v1?rss=1
</link>
<description><![CDATA[
The podocyte foot process network forms the final barrier of the kidneys glomerular filtration system. Under mechanical stress this network is prone to injury in which podocytes lose connectivity to their neighbors and begin the progression toward effacement, but what governs its mechanical resilience is unknown. We show that the network is built like a lap joint: two major processes coupled through interdigitating foot processes, a configuration that behaves as a classical shear lag system, with force concentrating at the joint ends and decaying over a characteristic transfer length set by geometry and stiffness. A discrete network model reproduces the continuum shear lag solution and identifies a hierarchy among governing parameters, with cytoskeletal stiffening of the major process amplifying foot process force more potently than basement membrane stiffness. Applying the model to morphometric data from puromycin aminonucleoside nephrosis, a model of human minimal change disease and early focal segmental glomerulosclerosis, reveals a mechanical positive feedback loop: force concentration drives foot process loss, which raises force on surviving segments and accelerates further loss. This nonlinear amplification implies a threshold beyond which failure becomes self-sustaining, analogous to the critical crack length in fracture mechanics.
]]></description>
<dc:creator><![CDATA[ Bi, M., Jin, H., Puapatanakul, P., Huang, Y., Qu, C., Miner, J. E., Suleiman, H., Genin, G. M. M. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.15.738799</dc:identifier>
<dc:title><![CDATA[A shear lag model of the podocyte foot process network predicts a mechanical feedback loop driving progressive effacement]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.16.738963v1?rss=1">
<title>
<![CDATA[
GW182 silencing domain engages the tristetraprolin-binding pocket of CNOT1 to recruit CNOT1 into multiprotein condensates 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.16.738963v1?rss=1
</link>
<description><![CDATA[
GW182 recruits the CCR4-NOT deadenylase complex through its CIM1 region, yet the CNOT1 surface mediating this interaction has remained unknown. Using hydrogen- deuterium exchange mass spectrometry, we map CIM1 binding to a hydrophobic groove within CNOT1 residues 800-999. Unexpectedly, this groove coincides with the tristetraprolin (TTP)-binding pocket. CIM1 and the C-terminal TTP peptide engage this surface through a shared RL(P/{zeta})X{Omega} sequence pattern despite lacking overall homology, suggesting a convergently evolved short linear motif (SLiM). We further show that the GW182 silencing domain (GW182 SD) and TTP compete for CNOT1 binding using orthogonal in vitro assays, including a reconstituted liquid-liquid phase separation system in which GW182 SD acts as a scaffold and recruits CNOT1 as a client through specific binding. These findings define a shared CNOT1 recognition site and reveal SLiM-mediated competition as a molecular principle governing CCR4-NOT engagement, with consequences for GW182-driven silencing condensate assembly in vitro.

SignificanceGW182 silencing domain binds the tristetraprolin pocket of CNOT1 and recruits it into multiprotein condensates, providing a biophysical framework for coordinated miRNA- and ARE-mediated gene expression regulation.
]]></description>
<dc:creator><![CDATA[ Bialobrzewski, M. K., Cieplak-Rotowska, M. K., Michas, A., Staszalek, Z., Sonenberg, N., Dadlez, M., Niedzwiecka, A. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.16.738963</dc:identifier>
<dc:title><![CDATA[GW182 silencing domain engages the tristetraprolin-binding pocket of CNOT1 to recruit CNOT1 into multiprotein condensates]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.16.738959v1?rss=1">
<title>
<![CDATA[
A Glycan-Aware Diffusion Model for Carbohydrate and Glycoprotein Structure Prediction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.16.738959v1?rss=1
</link>
<description><![CDATA[
Biomolecular diffusion models can now predict proteins and heterogeneous complexes, but glycans remain difficult because their branched topology, conformational flexibility, and strict stereochemical rules must be captured simultaneously. We developed SweetFold, a glycan-aware adaptation of Boltz-1x for the structure prediction of free glycans, glycoproteins, and protein-glycan complexes. SweetFold represents glycans as pseudo-polymers rather than generic ligands, preserving monosaccharide identity, anomeric state, glycosidic connectivity, and atom-level stereochemistry. We pair this representation with glycan-specific architecture, stereochemical supervision, and a sugar-centric training curriculum. Across monosaccharide, oligosaccharide, lectin, and glycoprotein benchmarks, SweetFold improves structural metrics relative to baseline all-atom diffusion models while retaining protein-only benchmark performance. These results show that chemically localized representation and supervision can extend biomolecular diffusion models to carbohydrate chemistry.
]]></description>
<dc:creator><![CDATA[ Sundar, K., Yang, H. ]]></dc:creator>
<dc:date>2026-07-17</dc:date>
<dc:identifier>doi:10.64898/2026.07.16.738959</dc:identifier>
<dc:title><![CDATA[A Glycan-Aware Diffusion Model for Carbohydrate and Glycoprotein Structure Prediction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-17</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
