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Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein-protein interaction…

Genomics · Quantitative Biology 2024-05-21 Jiayu Shang , Cheng Peng , Yongxin Ji , Jiaojiao Guan , Dehan Cai , Xubo Tang , Yanni Sun

Soft colloids are increasingly used as model systems to address fundamental issues such as crystallisation and the glass and jamming transitions. Among the available classes of soft colloids, microgels are emerging as the gold standard.…

We measure the elastic and dissipative responses of a multicontact interface, formed between the rough surfaces of two contacting macroscopic solids, submitted to a biased oscillating shear force. We evidence that beyond a linear…

Soft Condensed Matter · Physics 2007-05-23 L. Bureau , C. Caroli , T. Baumberger

Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using $\beta$-lactoglobulin fibrils as a model, that semiflexible…

Biomolecules · Quantitative Biology 2015-05-20 Sophia Jordens , Emily E. Riley , Ivan Usov , Lucio Isa , Peter D. Olmsted , Raffaele Mezzenga

The dynamics of active colloids is very sensitive to the presence of boundaries and interfaces which therefore can be used to control their motion. Here we analyze the dynamics of active colloids adsorbed at a fluid-fluid interface. By…

Soft Condensed Matter · Physics 2019-11-18 T. Peter , P. Malgaretti , N. Rivas , A. Scagliarini , J. Harting , S. Dietrich

We present a new methodology for efficient and high-quality patterning of biological reagents for surface-based biological assays. The method relies on hydrodynamically confined nanoliter volumes of reagents to interact with the substrate…

Biomolecules · Quantitative Biology 2016-04-27 J. Autebert , J. F. Cors , David P. Taylor , G. V. Kaigala

When a binary liquid is confined by a strongly repulsive wall, the local density is depleted near the wall and an interface similar to that between the liquid and its vapor is formed. This analogy suggests that the composition of the binary…

Soft Condensed Matter · Physics 2015-11-04 Shibu Saw , S. M. Kamil , Chandan Dasgupta

Negative activation volumes for dielectric relaxation are rarely reported in solid state physics and are limited to atomic scale processes. Broadband Dielectric Spectroscopy on heterogeneous systems, such as polycrystalline calcite and…

Geophysics · Physics 2025-05-23 Anthony N. Papathanassiou

Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures…

Biomolecules · Quantitative Biology 2022-12-08 Siddharth Bhadra-Lobo , Georgy Derevyanko , Guillaume Lamoureux

Chain-like macromolecules (polymers) show characteristic adsorption properties due to their flexibility and internal degrees of freedom, when attracted to surfaces and interfaces. In this review we discuss concepts and features that are…

Soft Condensed Matter · Physics 2009-11-07 Roland Netz , David Andelman

The biophysical analysis of dynamically formed multi-protein complexes in solution presents a formidable technical challenge. Sedimentation velocity (SV) analytical ultracentrifugation achieves strongly size-dependent hydrodynamic…

Quantitative Methods · Quantitative Biology 2017-04-12 Peter Schuck , Sumit K. Chaturvedi

This article presents a multi-physics methodology for the numerical simulation of physical systems that involve the non-linear interaction of multi-phase reactive fluids and elastoplastic solids, inducing high strain-rates and high…

Computational Physics · Physics 2021-06-04 Tim Wallis , Philip T. Barton , Nikolaos Nikiforakis

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…

Biomolecules · Quantitative Biology 2021-03-16 Charlotte W. van Noort , Rodrigo V. Honorato , Alexandre M. J. J. Bonvin

Low temperature covalent direct wafer-wafer bonding allows for the fusion of multiple semiconductor wafers without any additional material at the bonding interface. In the context of particle pixel detectors this might provide an…

Instrumentation and Detectors · Physics 2022-10-18 Johannes Wüthrich , André Rubbia

Living cells are capable of interacting with their environments in a variety of ways, including cell signalling, adhesion, and directed motion. These behaviours are often mediated by receptor molecules embedded in the cell membrane, which…

Biological Physics · Physics 2023-10-17 Hannah Sleath , Bortolo Mognetti , Yuval Elani , Lorenzo Di Michele

We demonstrate that the driving forces for ion adsorption to the air-water interface for point charge models results from both cavitation and a term that is of the form of a negative electrochemical surface potential. We carefully…

Soft Condensed Matter · Physics 2013-07-08 Marcel D. Baer , Abraham C. Stern , Yan Levin , Douglas J. Tobias , Christopher J. Mundy

Membrane-induced interactions have been predicted to be important for the organization of membrane proteins. Measurements of the interactions between two and three membrane deforming objects have revealed their non-additive nature. They are…

Soft Condensed Matter · Physics 2024-03-11 Ali Azadbakht , Thomas R. Weikl , Daniela J. Kraft

We compute ionic free energy adsorption profiles at aqueous graphene interface by developing a self-consistent approach. To do so, we design a microscopic model for water and put the liquid on an equal footing with the graphene described by…

Soft Condensed Matter · Physics 2023-03-01 Anton Robert , Hélène Berthoumieux , Marie-Laure Bocquet

Understanding the phase behaviour of pheromones and other messaging molecules remains a significant and largely unexplored challenge, even though it plays a central role in chemical communication. Here, we present all-atom molecular…

Soft Condensed Matter · Physics 2025-12-05 Ludovic Jami , Bertrand Siboulet , Thomas Zemb , Jérôme Casas , Jean-François Dufrêche

At the molecular level, most biological processes entail protein associations which in turn rely on a small fraction of interfacial residues called hot spots. Here we show that hot spots share a unifying molecular attribute: they provide a…