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Pattern formation in drying protein droplets continues to attract considerable research attention because it can be linked to specific protein-protein interactions. An extensive study of the drying evolution and the final crack patterns are…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
We study the mixing in the presence of convective flow in a porous medium. Convection is characterized by the formation of vortices and stagnation points, where the fluid interface is stretched and compressed enhancing mixing. We analyze…
Biological membranes are dynamic surfaces whose shape and function are critically influenced by protein inclusions (PIs). While membrane deformations induced by PIs have been extensively studied in the small-deformation regime, a variety of…
Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a \b{eta}-sheet protein stacked onto graphene. We found that the stacking assembly of the model protein on graphene could be controlled by…
Large pretrained language models have transformed natural language processing, and their adaptation to protein sequences -- viewed as strings of amino acid characters -- has advanced protein analysis. However, the distinct properties of…
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…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium…
We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound…
We review the theoretical analyses and simulations of the interactions between curvature-inducing proteins and biomembranes. Laterally isotropic proteins induce spherical budding, whereas anisotropic proteins, such as Bin/Amphiphysin/Rvs…
Most organic and inorganic surfaces (e.g., glass, nucleic acids or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces. Stacks of like-charged…
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…
We present a coarse-grained model for ionic surfactants in explicit aqueous solutions, and study by computer simulation both the impact of water content on the morphology of the system, and the consequent effect of the formed interfaces on…
Bacteria at fluid interfaces endure physical and chemical stresses unique to these highly asymmetric environments. The responses of Pseudomonas aeruginosa PAO1 and PA14 to a hexadecane-water interface are compared. PAO1 cells form elastic…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
We study an elasticity model for compressed protein monolayers or particle rafts at a liquid interface. Based on the microscopic view of hard-core particles with soft shells, a bead-spring model is formulated and analyzed in terms of…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter…