in the present paper, resonant frequencies and modes of a three-atom photonic molecule and a photonic crystal placed within a cavity are numerically calculated. first, governing formulation in transverse electric field mode (te) is obtained using maxwell equations. then, an algorithm based on a finite difference scheme and matrix algebra is presented. the algorithm is then implemented in a comp...

Congo red has been used to identify amyloid fibrils in tissues for more than 80 years and is also a weak inhibitor to both amyloid-beta fibril formation and toxicity. However, the specificity of the binding and its inhibition mechanism remain unclear. Using all-atom molecular dynamics simulations with the explicit solvent model, we have identified and characterized two specific binding modes of...

Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid...

Acetylcholine-based neurotransmission is regulated by cationic, ligand-gated ion channels called nicotinic acetylcholine receptors (nAChRs). These receptors have been linked to numerous neurological diseases and disorders such as Alzheimer's disease, Parkinson's disease, and nicotine addiction. Recently, a class of compounds has been discovered that antagonize nAChR function in an allosteric fa...

The ribonuclease P (RNase P) in the hyperthermophilic archaeon Pyrococcus horikoshii comprises RNA (PhopRNA) and five proteins. We analyzed the RNA binding mode of the protein, using a pair of complementary fluorescence-labeled oligoribonucleotides. Fluorescence resonance energy transfer (FRET)-based assays suggested that the RNase P proteins assist PhopRNA in attaining a functionally active co...