Various forms of the strain-displacement relations applied to experimental strain analysis

The purpose of this paper is to present the strain-displacement relations in a general way and to develop modified forms for three special cases which have application in experimental strain analysis:

1. 1.
   Small rotations—large strains     

Shedding light on biomolecule conformational dynamics using fluorescence measurements of trapped ions

Biomolecule conformational change has been widely investigated in solution using several methods; however, much less experimental data about structural changes are available for completely isolated, gas-phase biomolecules. Studies of conformational change in unsolvated biomolecules are required to complement the interpretation of mass spectrometry measurements and in addition, can provide a means to directly test theoretical simulations of biomolecule structure and dynamics independent of a simulated solvent. In this Feature Article, we review our recent introduction of a fluorescence-based method for probing local conformational dynamics in unsolvated biomolecules through interactions of an attached dye with tryptophan (Trp) residues and fields originating on charge sites. Dye-derivatized biomolecule ions are formed by electrospray ionization and are trapped in a variable-temperature quadrupole ion trap in which they are irradiated with either continuous or short pulse lasers to excite fluorescence. Fluorescence is measured as a function of temperature for different charge states. Optical measurements of the dye fluorescence include average intensity changes, changes in the emission spectrum, and time-resolved measurements of the fluorescence decay. These measurements have been applied to the miniprotein, Trp-cage, polyproline peptides and to a beta-hairpin-forming peptide, and the results are presented as examples of the broad applicability and utility of these methods. Model fits to Trp-cage fluorescence data measured as a function of temperature provide quantitative information on the thermodynamics of conformational changes, which are reproduced well by molecular dynamics. Time-resolved measurements of the fluorescence decays of Trp-cage and small polyproline peptides definitively demonstrate the occurrence of fluorescence quenching by the amino acid Trp in unsolvated biomolecules.     

Effect of IR laser radiation on the structure and optical properties of PC-PBT/Pd polymer nanocomposite films

ABSTRACT

Bayfol (PC-PBT blend ?lm) is a class of polymeric solid-state nuclear track detector which has a lot of applications in several radiation detection ?elds. It is a bisphenol-A polycarbonate PC blended with polybutylene terephthalate PBT. Bayfol/Palladium (PC-PBT/Pd) nanocomposite films have been deposited using the molding technique. It is worth mentioning that this report is almost the first one dealing with the topic of the changes of physical properties of Bayfol/Pd nanocomposite due to laser exposure. Samples from PC-PBT/Pd (5?wt%) nanocomposite were exposed to IR-pulsed laser of 5-W power, capable of producing 2000 pulses per second with pulse duration of 200?ns at 904?nm. The laser fluences were in the range 2–25?J/cm². The resultant modi?cations in the exposed nanocomposite samples have been studied as a function of fluence using different characterization techniques such as X-ray diffraction (XRD), UV spectroscopy and color difference studies. The results indicate the proper dispersion of Pd nanoparticles in the PC-PBT matrix that causes a strong intermolecular interaction between Pd and PC-PBT, resulted in an increase in refractive index and the amorphous phase. Also, it is found that the laser exposure reduces the optical energy gap that could be attributed to the increase in structural disorder of the exposed PC-PBT/Pd nanocomposites due to crosslinking. Further, the color intensity ΔE, which is the color difference between the exposed samples and the non-exposed one, was increased with increasing the laser fluence, convoyed by a significant increase in the green and yellow color components.     

Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding

The inter- and intramolecular interactions that determine the experimentally observed binding mode of the ligand (2Z)-2-(benzoylamino)-3-[4-(2-bromophenoxy)phenyl]-2-propenoate in complex with hepatitis C virus NS5B polymerase have been studied using QM/MM calculations. DFT-based QM/MM optimizations were performed on a number of ligand conformers in the protein-ligand complex. Using these initial poses, our aim is 2-fold. First, we identify the minimum energy pose. Second, we dissect the energetic contributions to this pose using QM/MM methods. The study reveals the critical importance of internal energy for the proper energy ranking of the docked poses. Using this protocol, we successfully identified three poses that have low RMSD with respect to the crystallographic structure from among the top 20 initially docked poses. We show that the most important energetic component contributing to binding for this particular protein-ligand system is the conformational (i.e., QM internal) energy.     

昆虫信息素研究III: 拟蚜虫警戒素的研究

合成了一系列碳数为十五和十四的倍半萜类蚜虫警戒素,并进行了生物活性测定,从中筛选有效化合物.     

Giant excitonic Zeeman splittings in colloidal Co2+ -doped ZnSe quantum dots

Colloidal Co(2+):ZnSe diluted magnetic semiconductor quantum dots (DMS-QDs) were prepared by the hot injection method and studied spectroscopically. Ligand-field electronic absorption and magnetic circular dichroism (MCD) spectra confirm homogeneous substitutional speciation of Co(2+) in the ZnSe QDs. Absorption spectra collected at various times throughout the syntheses reveal that dopants are absent from the central cores of the QDs but are incorporated at a constant concentration during nanocrystal growth. The undoped cores are associated with dopant exclusion from the ZnSe critical nuclei. Analysis of low-temperature electronic absorption and MCD spectra revealed excitonic Zeeman splitting energies (DeltaE(Zeeman)) of these Co(2+):ZnSe QDs that were substantially smaller than anticipated from bulk Co(2+):ZnSe data. This reduction in DeltaE(Zeeman) is explained quantitatively by the absence of dopants from the QD cores, where dopant-exciton overlap would be greatest. Since dopant exclusion from nucleation appears to be a general phenomenon for DMS-QDs grown by direct chemical methods, we propose that DeltaE(Zeeman) will always be smaller in colloidal DMS-QDs grown by such methods than in the corresponding bulk materials.     

Dual-core optofluidic chip for independent particle detection and tunable spectral filtering

We present the first integration of fluidically tunable filters with a separate particle detection channel on a single planar, optofluidic chip. Two optically connected, but fluidically isolated liquid-core antiresonant reflecting optical waveguide (ARROW) segments serve as analyte and spectral filter sections, respectively. Ultrasensitive detection of fluorescent nanobeads with high signal-to-noise ratio provided by a fluidically tuned excitation notch filter is demonstrated. In addition, reconfigurable filter response is demonstrated using both core index tuning and bulk liquid tuning. Notch filters with 43 dB rejection ratio and a record 90 nm tuning range are implemented by using different mixtures of ethylene glycol and water in the filter section. Moreover, absorber dyes and liquids with pH-dependent transmission in the filter channel provide additional spectral control independent of the waveguide response. Using both core index and pH control, independent filter tuning at multiple wavelengths is demonstrated for the first time. This extensive on-chip control over spectral filtering as one of the fundamental components of optical particle detection techniques offers significant advantages in terms of compactness, cost, and simplicity, and opens new opportunities for waveguide-based optofluidic analysis systems.     

Quantum chemical characterization of the reactions of guanine with the phenylnitrenium ion.

Density functional calculations at the B3LYP/6-311+G(2d,p)//pBP/DN level predict all cationic adducts combining guanine, at either its N2, O6, N7, or C8 positions, with phenylnitrenium ion, at either its N, 2, or 4 positions, to be lower in energy than the separated reactants. This relative stability of all adducts is preserved after addition of aqueous solvation free energies computed at the SM2 level, although some leveling of the adduct relative energies one to another is predicted. Cations having the lowest relative energies in solution correspond structurally to those adducts most commonly found when guanine reacts with larger, biologically relevant nitrenium ions in vitro and in vivo. One of these, the N-C8 adduct, is stabilized both by a rearomatized phenyl ring and by the operation of an anomeric effect not found in any of the others. On the basis of energetic analysis, direct conversion of an N-N7 cation to an N-C8 cation according to a previously proposed mechanism is unlikely; however, an alternative rearrangement converting a 2-N7 cation to an N-C8 cation via the intermediacy of a five-membered ring may be operative in nitrenium ions with aromatic frameworks better able than phenyl to stabilize endocyclic cationic charge.