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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…
Scaling law for geometrical and dynamical quantities of biological molecules is an interesting topic. According to Flory's theory, a power law between radius of gyration and the length of homopolymer chain is found, with exponent 3/5 for…
We perform numerical simulations to study the dynamics of the entry of hydrophobic spheres in a pool of water using ANSYS. To track the air-water interface during the translation of the sphere in the pool of water, we use the volume of…
The objective of this project is to develop an automated device used to spot protein samples on a hydrophobic membrane to be used for the patented electrophoresis method developed by Chang and Yonan in 2008 [1]. This novel method performs…
The study of protein interactions has generated great interest in the food industry. Therefore, research on new supramolecular structures shows promise. Supramolecular structures of the whey proteins {\alpha}-lactalbumin and…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…
Rigidity analysis using the "pebble game" can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not…
Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Water plays a crucial role in geological, biological, and technological processes. Nanoscale water confinement occurs in many of these settings, including sedimentary rocks, water channel proteins, and applications like desalination and…
We perform systematic molecular dynamics simulations of water confined between two nanoscale plates at T=300 K. We investigate the effect of pressure (-0.15 GPa <= P <= 0.2 GPa) and plate separation (0.4 nm <= d <= 1.6 nm) on the phase…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
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…
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…
Protein structure is key to understanding protein function and is essential for progress in bioengineering, drug discovery, and molecular biology. Recently, with the incorporation of generative AI, the power and accuracy of computational…
An accurate description of the structure and dynamics of interfacial water is essential for phospholipid membranes, since it determines their function and their interaction with other molecules. Here we consider water confined in stacked…