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Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…

Soft Condensed Matter · Physics 2016-04-15 Jennifer J. McManus , Patrick Charbonneau , Emanuela Zaccarelli , Neer Asherie

We present systematic wetting experiments and numerical simulations of gravity driven liquid drops sliding on a plane substrate decorated with a linear chemical step. Surprisingly, the optimal direction to observe crossing is not the one…

Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein,…

Biomolecules · Quantitative Biology 2007-05-23 Richard P. Sear

Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…

Biomolecules · Quantitative Biology 2016-12-02 Himadri S. Samanta , Pavel I. Zhuravlev , Michael Hinczewski , Naoto Hori , Shaon Chakrabarti , D. Thirumalai

The contact line of a liquid drop on a solid exerts a nanometrically sharp surface traction. This provides an unprecedented tool to study highly localised and dynamic surface deformations of soft polymer networks. One of the outstanding…

Soft Condensed Matter · Physics 2018-11-21 Mathijs van Gorcum , Bruno Andreotti , Jacco H. Snoeijer , Stefan Karpitschka

Evaporation of water droplets deposited on metal and polymer substrates was studied. The evaporated droplet demonstrates different behaviors on low-pinning (polymer) and strong-pinning (metallic) surfaces. When deposited on polymer…

Chemical Physics · Physics 2011-02-23 Edward Bormashenko , Albina Musin , Michael Zinigrad

Previous experiments have shown that spherical colloidal particles relax to equilibrium slowly after they adsorb to a liquid-liquid interface, despite the large interfacial energy gradient driving the adsorption. The slow relaxation has…

Soft Condensed Matter · Physics 2016-11-08 Anna Wang , Ryan McGorty , David M. Kaz , Vinothan N. Manoharan

We analyze a bubble forming system composed of particles with competing long range repulsive and short range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a…

Soft Condensed Matter · Physics 2024-01-26 C. Reichhardt , C. J. O. Reichhardt

We use a free energy lattice Boltzmann approach to investigate numerically the dynamics of drops moving across superhydrophobic surfaces. The surfaces comprise a regular array of posts small compared to the drop size. For drops suspended on…

Soft Condensed Matter · Physics 2009-11-11 A. Dupuis , J. M. Yeomans

Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…

Biological Physics · Physics 2020-08-26 Warin Rangubpit , Sunan Kitjaruwankul , Pornthep Sompornpisut , R. B. Pandey

We report on new instabilities of the quasi-static equilibrium of water drops pinned by a hydrophobic inclined substrate. The contact line of a statically pinned drop exhibits three transitions of partial depinning: depinning of the…

Fluid Dynamics · Physics 2009-11-13 Viatcheslav V. Berejnov , Robert E. Thorne

We investigate contact angle hysteresis on chemically patterned and superhydrophobic surfaces, as the drop volume is quasi-statically increased and decreased. We consider both two, and three, dimensions using analytical and numerical…

Soft Condensed Matter · Physics 2008-03-12 H. Kusumaatmaja , J. M. Yeomans

We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…

Biomolecules · Quantitative Biology 2014-11-18 Yong-Yun Ji , You-Quan Li , Jun-Wen Mao , Xiao-Wei Tang

Cell adhesion proteins are transmembrane proteins that bind cells to their environment. These proteins typically cluster into disk-shaped or linear structures. Here we show that such clustering patterns spontaneously emerge when the protein…

Soft Condensed Matter · Physics 2023-07-10 Shao-Zhen Lin , Rishita Changede , Michael P. Sheetz , Jacques Prost , Jean-Francois Rupprecht

There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…

Subcellular Processes · Quantitative Biology 2019-12-19 William Bialek , Thomas Gregor , Gašper Tkačik

Liquid drops on soft solids generate strong deformations below the contact line, resulting from a balance of capillary and elastic forces. The movement of these drops may cause strong, potentially singular dissipation in the soft solid.…

Fluid Dynamics · Physics 2016-03-25 S. Karpitschka , S. Das , M. van Gorcum , H. Perrin , B. Andreotti , J. H. Snoeijer

The compression of soft elastic matter and biological tissue can lead to creasing, an instability where a surface folds sharply into periodic self-contacts. Intriguingly, the unfolding of the surface upon releasing the strain is usually not…

We discuss crystal formation in supersaturated suspensions of monodisperse hard spheres with a concentration of hard spheres randomly pinned in space and time. The pinning procedure introduces an external length scale and an external time…

Statistical Mechanics · Physics 2013-10-01 Sven Dorosz , Tanja Schilling

Liquid drops that are pinned to solid surfaces by contact-angle hysteresis can be dislodged by wind forcing. When this occurs at high Reynolds numbers, substantial drop-interface oscillations precede depinning. It has been hypothesized that…

Fluid Dynamics · Physics 2021-05-11 Roger L. Simon, , Edward B. White

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…

Statistical Mechanics · Physics 2009-11-10 Seung-Yeon Kim , Julian Lee , Jooyoung Lee