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Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
Porous asphalt (PA) is an open-graded porous material with a porosity of 20%, allowing fast drainage of rain and improving driving and acoustic conditions. However, the high porosity leads to significant contact with water resulting in a…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
A tethered vesicle, which consists of a cylindrical membrane tube and a spherical vesicle, is produced by a mechanical force that is experimentally imposed by optical tweezers and a micropipette. This tethered vesicle is employed for…
The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Accurate quantification of protein-nanoparticle interactions is essential for applications in nanobiotechnology, nanomedicine, and drug delivery. Motivated by recent computational and experimental work, we combine coarse-grained united-atom…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language…
The structure of liquid water in the proximity of an interface can deviate significantly from that of bulk water, with surface-induced structural perturbations typically converging to bulk values at about ~1 nm from the interface. While…
We study the pore-scale transport of a conservative scalar forming an advancing mixing front, which can be re-interpreted to predict instantaneous mixing-limited bimolecular reactions. We investigate this using a set of two-dimensional,…
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer.…
The main idea of the interstitial-ice model is that liquid water consists of an intact hexagonal lattice with both vacant lattice positions and interstitial water molecules. Narten, Danford and Levy derived the model parameters from the…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
We consider a model of bilayer lipid membrane with bola-lipids. The bola-lipid is modeled by linking tails of the hydrophobic chains in the opposite monolayers within bilayer as a first approximation. A number of thermodynamical…
We investigate rearrangements of a single hairy particle at a liquid-liquid interface using coarse-grained molecular dynamics simulations. We consider the particles with the same (symmetrical interactions) and different (asymmetrical…
We study theoretically the thermodynamics, over a broad temperature range (5 C to 125 C), related to hydrated water upon protein unfolding. The hydration effect is modeled as interacting dipoles in an external field, mimicking the influence…
Using an interface displacement model derived from a microscopic density functional theory we investigate thin liquidlike wetting layers adsorbed on flat substrates with an embedded chemical heterogeneity forming a stripe. For a wide range…
We consider a two-dimensional model of a porous medium where circular grains are uniformly distributed in a squared container. We assume that such medium is partially filled with water and that the stationary interface separating the water…