Related papers: The Most Severe Test for Hydrophobicity Scales: Tw…
Hydrophobic interactions have been studied in detail in the past based on hydrophobic polymers, such as polystyrene (PS). Because fluorinated materials have relatively low surface energy, they often show both oleophobicity and…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…
This work tests the statistical mechanical theory of hydrophobic interactions, isolates consequences of excluded volume interactions, and obtains B2 for those purposes. Cavity methods that are particularly appropriate for study of…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For…
In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of…
At low temperatures proteins exist in a glassy state, a state which has no conformational flexibility and shows no biological functions. In a hydrated protein, at and above 220 K, this flexibility is restored and the protein is able to…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
We review the development of thermodynamic protein hydropathic scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Darwinian evolution has organized each protein family…
The peculiar structuring of liquid water stems from a fine-tuned molecular principle embodying the two different interaction demands of the water molecule: The formation of hydrogen bonds or the compensation for coordination defects. Here…
Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules into surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations…