相关论文: Ligand Discrimination in Myoglobin from Linear-Sca…
We study tight-binding models in the crossover from hyperbolic to Euclidean lattices, realized through the successive insertion of Euclidean defects into hyperbolic lattices. We analyze how the holographic two-point boundary correlation…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Predicting the compositional phase stability of strongly correlated electron materials is an outstanding challenge in condensed matter physics, requiring precise computations of total energies. In this work, we employ the density functional…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…
Many experimental techniques such as tagging photodissociation and helium nanodroplet isolation spectroscopy operate at very low temperatures in order to investigate hydrogen bonding. To elucidate the differences between such ultra-cold and…
We study entanglement in states of holographic CFTs defined by Euclidean path integrals over geometries with slowly varying metrics. In particular, our CFT spacetimes have $S^1$ fibers whose size $b$ varies along one direction ($x$) of an…
The chemistry (composition and bonding information) of metallic glasses (MGs) is at least as important as structural topology for understanding their properties and production/processing peculiarities. This article reports a machine…
The effect of orbital magnetism on the chemical bonding of lateral, two-dimensional artificial molecules is studied in the case of a 2e double quantum dot (artificial molecular hydrogen). It is found that a perpendicular magnetic field…
We propose a model of mass-conserving heterogeneous nucleation to describe the dynamics of ligand-receptor binding in closed cellular compartments. When the ligand dissociation rate is small, competition among receptors for free ligands…
Predicting the 3D conformation of small molecules within protein binding sites is a key challenge in drug design. When a crystallized reference ligand (template) is available, it provides geometric priors that can guide 3D pose prediction.…
In all theoretical treatments of electron transport through single molecules between two metal electrodes, a clear distinction has to be made between a coherent transport regime with a strong coupling throughout the junction and a Coulomb…
Predicting protein-ligand binding affinity remains intractable for multi-domain proteins, where inter-domain dynamics govern molecular recognition. Existing geometric deep learning methods typically treat proteins as monolithic static…
Fibrinogen, the monomeric unit of fibrin, the main constituent of blood clot, has a very complex structure. The fibrinogen builds the fibrin fiber and network through the half-staggered packing via knob-hole interaction and the $\alpha$C…
Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Prior work focused on supervised learning methods using a large set of binding affinity data for small molecules, but it is hard to apply the same…
The dissociation of a hydrogen molecule on MgO(001) films deposited on Mo(001) surface is investigated systematically using periodic density-functional theory method. The unusual adsorption behavior of heterolytic dissociative hydrogen…
Analysis of the electron density distribution in clusters composed of hydrogen fluoride, water, and ammonia molecules, especially within the hydrogen-bond domains, reveals the existence of both \sigma- and \pi-binding between molecules. The…
This article presents the results of several magnetic phases of doped La$_{2-x}$Sr$_x$CuO$_4$ using density-functional theory with an added Hubbard term (DFT+U). Doping factors from $x=0$ to 0.25 were examined. We found that a bond centered…
Hydrogen bonding plays a role in the microphase separation behavior of many block copolymers, such as those used in lithography, where the stronger interactions due to H-bonding can lead to a smaller period for the self-assembled…
Light absorption of myoglobin triggers diatomic ligand photolysis and spin crossover transition of iron(II) that initiate protein conformational change. The photolysis and spin crossover reactions happen concurrently on a femtosecond…
An approach has been proposed to characterize the competitive association of D2O and to study the heterogeneity of hydration water adsorbed by the protein, immunoglobulin G, using methodology for determining of non-freezing water in mixed…