Lehigh University

About: Lehigh University is a education organization based out in Bethlehem, Pennsylvania, United States. It is known for research contribution in the topics: Catalysis & Fracture mechanics. The organization has 12684 authors who have published 26550 publications receiving 770061 citations.

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Abstract: Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental methods. Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. In our previous study, we developed Glycan Reader, a web-based tool for detecting carbohydrate molecules from a PDB structure and generation of simulation system and input files. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/fragment-db). Our benchmark tests demonstrate the universal applicability of Glycan Reader & Modeler to various glycan sequences and target proteins. We also investigated the structural properties of modeled glycan structures by running 2-μs molecular dynamics simulations of HIV envelope protein. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler. Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan.

The organized nature of flow impingement upon a corner

Abstract: Oscillations of impinging flows, which date back to the jet-edge phenomenon (Sondhaus 1854), have been observed for a wide variety of impingement configurations. However, alteration of the structure of the shear layer due to insertion of an impingement edge (or surface) and the mechanics of impingement of vortical structures upon an edge have remained largely uninvestigated. In this study, the impingement of a shear layer upon a cavity edge (or corner) is examined in detail. Water is used as a working fluid and laser anemometry and hydrogen bubble flow visualization are used to characterize the flow dynamics. Reynolds numbers (based on momentum thickness at separation) of 106 and 324 are employed. Without the edge, the shear layer produces the same sort of non-stationary (variable) velocity autocorrelations observed by Dimotakis & Brown (1976). When the edge is inserted, the organization of the flow is dramatically enhanced as evidenced by a decrease in variability of autocorrelations and appearance of well-defined peaks in the corresponding spectra. This enhanced organization is not locally confined to the region of the edge but extends along the entire length of the shear layer, thereby reinforcing the concept of disturbance feedback. Comparison of spectra with and without insertion of the edge reveals a remarkable similarity to those of a non-impinging shear layer with and without application of sound at a discrete frequency (Browand 1966; Miksad 1972); with enhanced organization at the fundamental frequency, simultaneous enhancement occurs also at the sub- and higher-harmonics.

Incoherently coupled soliton pairs in biased photorefractive crystals

Abstract: Summary form only given. Recently it was demonstrated that spatial optical solitons at /spl mu/W power levels can be supported in photorefractive (PR) media. We show that a new type of incoherently coupled soliton pairs is possible under steady-state conditions provided that their carrier beams share the same polarization and wavelength and are mutually incoherent. They can be readily realized in a simple experimental setup where the optical beams co-propagate collinearly in a biased PR crystal in which case they experience equal electrooptic coefficients.