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The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
We study a coarse-grained model for a water monolayer that cannot crystallize due to the presence of confining interfaces, such as protein powders or inorganic surfaces. Using both Monte Carlo simulations and mean field calculations, we…
Using a combination of dielectric spectroscopy and solid-state deuteron NMR, the hydration water dynamics of connective tissue proteins is studied at sub-ambient temperatures. In this range, the water dynamics follows an Arrhenius law. A…
A computer simulation model is proposed to study film growth and surface roughness in aqueous ($A$) solution of hydrophobic ($H$) and hydrophilic ($P$) groups on a simple three dimensional lattice of size $L_x \times L_y \times L_z$ with an…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
While nucleic-acids can be readily amplified for single-marker detection, a comparable method for proteins assay is currently unavailable. Proteins potentiometric detections at 10-20 molar have been demonstrated, but the mechanism remains…
We provide experimental evidence for confinement of water molecules in the pores of hexagonal structure of YPO4 at elevated temperatures upto 600 K using powder neutron diffraction. In order to avoid the large incoherent scattering from the…
We report on the frozen-spin polarized hydrogen--deuteride (HD) targets for photoproduction experiments at SPring-8/LEPS. Pure HD gas with a small amount of ortho-H2 (~0.1%) was liquefied and solidified by liquid helium. The temperature of…
Here we report the polarization dependent non-resonant second harmonic generation (SHG) measurement of the interfacial water molecules at the aqueous solution of the following salts: NaF, NaCl, NaBr, KF, KCl, and KBr. Through quantitative…
The supramolecular organization of wheat gluten proteins is largely unknown due to the intrinsic complexity of this family of proteins and their insolubility in water. We fractionate gluten in a water/ethanol (50/50 v/v) and obtain a…
As valuable digital assets, deep neural networks necessitate robust ownership protection, positioning neural network watermarking (NNW) as a promising solution. Among various NNW approaches, weight-based methods are favored for their…
The increase of aqueous solubility of nonpolar compounds upon cooling and the cold denaturation of proteins are established experimental facts. Both phenomena have been hypothesized to be related to restructuring of the hydrogen bond…
Water is an associated liquid in which the main intermolecular interaction is the hydrogen bond (HB) which is limited to four per atom, independently of the number of neighbours. We have considered a hydrogen bond net superposed on Bernal's…
Proteins involved in signaling pathways represent an interesting target for experimental analysis by ODNP (Overhauser Dynamic Nuclear Polarization), which determines the translational mobility at the surface of proteins. They also represent…
Interfacial interactions significantly alter the fundamental properties of water confined in mesoporous structures, with crucial implications for geological, physicochemical, and biological processes. Herein, we focused on the effect of…
The formation of a spanning hydrogen-bonded network of hydration water is found to occur via a 2D percolation transition in various systems: smooth hydrophilic surfaces, the surface of a single protein molecule, protein powder and diluted…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
Simulating water accurately has been a challenge due to the complexity of describing polarization and intermolecular charge transfer. Quantum mechanical (QM) electronic structures provide an accurate description of polarization in response…