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We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…

Condensed Matter · Physics 2009-11-07 Audun Bakk , Johan S. Hoye , Alex Hansen

The preference of water self-ions (hydronium and hydroxide) towards air/oil-water interfaces is one of the hottest topics in water research due to its importance for understanding properties, phenomena, and reactions of interfaces. In this…

Chemical Physics · Physics 2025-02-04 Pengchao Zhang , Xuefei Xu

Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…

Soft Condensed Matter · Physics 2021-03-16 Debdas Dhabal , Zhitong Jiang , Amish J. Patel

The adhesion of flowing particles and biological cells over fixed collecting surfaces is vitally important in diverse situations and potentially controlled by small-scale surface heterogeneity on the particle. Differences in the behavior of…

Soft Condensed Matter · Physics 2015-06-19 Marina Bendersky , Maria M. Santore , Jeffrey M. Davis

We theoretically study in detail the hydrodynamic coupling of two equal-sized colloidal spheres at low Reynolds numbers assuming the particles to be harmonically trapped with respect to both their positions and orientations. By taking into…

Soft Condensed Matter · Physics 2007-05-23 Michael Reichert , Holger Stark

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems unveil microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block…

The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide…

The molecular dynamics in the ambient-pressure solid phase of (1,1,2)-trichloroethane is studied by means of broadband dielectric spectroscopy and molecular dynamics simulations. The dielectric spectra of polycrystalline samples obtained by…

The dynamics of ideally polarizable spherical particles in concentrated suspensions under the effects of nonlinear electrokinetic phenomena is analysed using large-scale numerical simulations. Particles are assumed to carry no net charge…

Soft Condensed Matter · Physics 2019-07-23 Siamak Mirfendereski , Jae Sung Park

We present an experimentally guided, multi-phase, multi-species polyelectrolyte gel model to make quantitative predictions on the electro-chemical properties of articular cartilage. The mixture theory consists of two different types of…

Tissues and Organs · Quantitative Biology 2013-08-22 Sarthok Sircar , Elizabeth Aisenbrey , Stephanie J. Bryant , David M. Bortz

Understanding concentrated electrolytes requires a theory that spans local hydration and mesoscale interfacial assembly. We present an integrated workflow-SCOPE-that combines (i) enhanced sampling focused on a single Li+ ion, (ii)…

Soft Condensed Matter · Physics 2026-01-27 Xiaoxu Ruan , Fabrice Roncoroni , David Prendergast , Tod A Pascal

Hard-sphere model systems are well-suited in both experiment and simulations to investigate fundamental aspects of the crystallization of fluids. In experiments on colloidal models of hard-sphere fluids, the uid is unavoidably at contact…

Soft Condensed Matter · Physics 2021-04-28 Jorge R. Espinosa , Carlos Vega , Chantal Valeriani , Daan Frenkel , Eduardo Sanz

Salt water is ubiquitous, playing crucial roles in geological and physiological processes. Despite centuries of investigations, whether or not water's structure is drastically changed by dissolved ions is still debated. Based on density…

Chemical Physics · Physics 2022-02-14 Chunyi Zhang , Shuwen Yue , Athanassios Z. Panagiotopoulos , Michael L. Klein , Xifan Wu

Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…

Biological Physics · Physics 2018-11-06 Farzad Mohajerani , Xi Zhao , Ambika Somasundar , Darrell Velegol , Ayusman Sen

A mixture of hard-sphere particles and model emulsion droplets is studied with a Brownian dynamics simulation. We find that the addition of nonwetting emulsion droplets to a suspension of pure hard spheres can lead to both gas-liquid and…

Soft Condensed Matter · Physics 2015-03-13 Andrea Fortini

A major goal of many spectroscopic techniques is to provide comprehensive information on the local chemical environment. Electron transfer mediated decay (ETMD) is a sensitive probe of the environment since it is actively involved in this…

The study of competitive and cooperative adsorption of functionalized molecules such as polymers, rheology modifiers and surfactant molecules on colloidal particles immersed in a solvent is undertaken using coarse grained, dissipative…

Soft Condensed Matter · Physics 2014-06-13 A. Gama Goicochea

Hydrogen incorporation in native surface oxides of metal alloys often controls the onset of metal hydriding, with implications for materials corrosion and hydrogen storage. A key representative example is titania, which forms as a…

The electric double layer is an important structure that appears at charged liquid interfaces, and it determines the performance of various electrochemical devices such as supercapacitors and electrokinetic energy converters. Here the…

Soft Condensed Matter · Physics 2023-08-15 Haruto Iwasaki , Yasuyuki Kimura , Yuki Uematsu

In solution, electrically like-charged particles can experience a strong and long-ranged attraction that leads to the formation of stable, slowly reorganizing clusters. The attractive force underpinning this spontaneous organization process…

Soft Condensed Matter · Physics 2026-01-14 Sida Wang , Angela Le , Rowan Walker-Gibbons , Madhavi Krishnan
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