Phase ordering of hard needles on a quasicrystalline substrate

Quasicrystals possess long-range positional and orientational order. However, they cannot be periodic in space due to their non-crystallographic symmetries such as a 10-fold rotational axis. We perform Monte Carlo simulations of two-dimensional hard-needle systems subject to a quasiperiodic substrate potential. We determine phase diagrams as a function of density and potential strength for two needle lengths. With increasing potential strength short needles tend to form isolated clusters that display directional order along the decagonal directions. Long needles create interacting clusters that stabilize the nematic phase. At large potential strengths the clusters position themselves on two interwoven Fibonacci sequences perpendicular to the cluster orientation. Alternatively, one obtains extended domains of needle clusters which are aligned along all decagonal symmetry directions.     

Low voltage tunable liquid crystal Fibonacci grating

ABSTRACT

In this article, we disclose low voltage tunable liquid crystal Fibonacci gratings (FbG). Photoalignment technique has been used to create two domains of Fibonacci structure using a photomask. Switchable properties of LC are used to tune the diffraction efficiency of different orders by modulating the phase using the electric field. Position of split first orders shows good agreement with the golden ratio characteristic of the FbG. An increase in first-order diffraction efficiency from 3.7% to 6.7% has been achieved with a response time of 5.1 ms. The diffraction almost diminishes at 15 V with a very fast response time of 100 µs, the relaxation time is relatively slower ~26 ms, which is primarily due to higher viscosity. Variation and switching of the intensity of different orders in FbG, by the application of the electric field, can be utilised for selective far-field super-resolution imaging and different photonic applications.     

Tensile behavior of quasi-unidirectional glass fiber/polypropylene composites at room and elevated temperatures

In the present study, the tensile behavior of quasi-unidirectional glass fiber/polypropylene composites at room and elevated temperatures were investigated by both micro- and macromechanical test methods. In the micromechanical studies, a single fiber fragmentation test was employed for measuring the interfacial shear strength at fiber-polypropylene interface in the temperature range from 23 °C to 90 °C. The results show that interfacial shear strength decreases with increasing testing temperature. In the macromechanical studies, experimental results show that the elastic modulus of polypropylene and transverse elastic modulus of composites are sensitive to the testing temperature. The weakened fiber-polypropylene interface due to elevated temperatures led to the vanishing of “knee” in transverse tensile stress-strain curves. A function was proposed to evaluate the dependence of the elastic modulus of quasi-unidirectional glass fiber/polypropylene composites on the testing temperatures and tested against experimental data. Tensile failure mechanisms of composites were demonstrated to evolve with the testing temperature.     

Pattern formation and spatial self-entrainment in bistable chemical systems

We describe the formation of spatial structures generated by diffusive instabilities in bistable systems. The coupling between the different spatial modes emanating from the two homogeneous steady states can then give rise to self-parametric instabilities favoring the occurrence of resonant rhombic or quasiperiodic structures such as superlattices or quasicrystalline patterns.     

Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry

We present the first global computer-aided sequencing algorithm for the de novo determination of short nucleic acid sequences. The method compares the fragment ion spectra generated by collision-induced dissociation of multiply charged oligodeoxynucleotide-ions to the m/z values predicted employing established fragmentation pathways from a known reference sequence. The closeness of matching between the measured spectrum and the predicted set of fragment ions is characterized by the fitness, which takes into account the difference between measured and predicted m/z values, the intensity of the fragment ions, the number of fragments assigned, and the number of nucleotide positions not covered by fragment ions in the experimental spectrum. Smaller values for the fitness indicate a closer match between the measured spectrum and predicted m/z values. In order to find the sequence most closely matching the experimental spectrum, starting from a given nucleotide composition all possible oligonucleotide sequences are assembled followed by identification of the correct sequence by the lowest fitness value. Using this concept, sequences of 5- to 12-mer oligodeoxynucleotides were successfully de novo determined. High sequence coverage with fragment ions was essential for obtaining unequivocal sequencing results. Moreover, the collision energy was shown to have an impact on the interpretability of tandem mass spectra by the de novo sequencing algorithm. Experiments revealed that the optimal collision energy should be set to a value just sufficient for complete fragmentation of the precursor ion.     

Ultrasonic properties of PVC (S-27/R63) in the glassy region

The ultrasonic properties of PVC (S-27/R63) in the glassy region have been investigated as a function of temperature. The propagation velocities and absorption of the longitudinal and transverse ultrasonic waves have been measured at constant frequency of 2 MHz and at temperatures varying between ?5°C and 75°C, using the ultrasonic immersion technique. The variation of the elastic moduli with temperature has been derived from these measurements. The results thus obtained have been compared to those previously published in the literature for different PVC and other polymer samples. ©1995 John Wiley & Sons, Inc.     

Photodissociation spectroscopy of trapped protonated tryptophan

We have coupled a quadrupole ion trap with a frequency doubled optical parametric oscillator laser. The photodissociation spectrum of the protonated tryptophan ion from 215 to 320 nm is reported. The yields of fragmentation on each mass channel as a function of the laser wavelength were obtained. We also report experiments involving multiple stages of laser induced dissociation and discuss possible structures for the fragmentation products.     

Heuristic-based tabu search algorithm for folding two-dimensional AB off-lattice model proteins

The protein structure prediction problem is a classical NP hard problem in bioinformatics. The lack of an effective global optimization method is the key obstacle in solving this problem. As one of the global optimization algorithms, tabu search (TS) algorithm has been successfully applied in many optimization problems. We define the new neighborhood conformation, tabu object and acceptance criteria of current conformation based on the original TS algorithm and put forward an improved TS algorithm. By integrating the heuristic initialization mechanism, the heuristic conformation updating mechanism, and the gradient method into the improved TS algorithm, a heuristic-based tabu search (HTS) algorithm is presented for predicting the two-dimensional (2D) protein folding structure in AB off-lattice model which consists of hydrophobic (A) and hydrophilic (B) monomers. The tabu search minimization leads to the basins of local minima, near which a local search mechanism is then proposed to further search for lower-energy conformations. To test the performance of the proposed algorithm, experiments are performed on four Fibonacci sequences and two real protein sequences. The experimental results show that the proposed algorithm has found the lowest-energy conformations so far for three shorter Fibonacci sequences and renewed the results for the longest one, as well as two real protein sequences, demonstrating that the HTS algorithm is quite promising in finding the ground states for AB off-lattice model proteins.     

Mechanical anisotropy in biaxially oriented polyvinyl chloride

The mechanical anisotropy of polyvinyl chloride oriented in two perpendicular directions with different draw ratios has been studied. The results are compared with the anisotropy of uniaxial samples oriented at a common draw ratio. The propagation velocities of ultrasonic pulses have been measured by an immersion technique. Longitudinal wave velocities have been measured in three principal planes over a wide range of propagation directions. The limitations of measuring velocities in the planes containing the draw axes were mitigated by use of a special slicing technique. Measurements were performed at 2 MH_z and 25°C. Velocities of the transverse waves were measured for incident wave angles greater than the critical angle. From these measurements, five elastic moduli were calculated for the uniaxially oriented samples, and nine elastic moduli were obtained for the biaxially oriented samples. In biaxially oriented samples, the moduli along the draw axes are directly proportional to the draw ratio in the same direction.     

Two-wave mixing on the cubic non-linearity in the smectic A liquid crystals

We present a theoretical study of two-wave mixing in smectic A liquid crystals (S_ALC) due to the resonant interaction of the electromagnetic (EM) waves through the second sound (SS), which is a new type of the cubic non-linearity. It is shown that a parametric amplification of one EM wave by the other occurs. Explicit expressions for the EM and SS wave amplitudes are obtained, which appear to be of the kink and transverse spatial soliton form, respectively. It is also shown that the SS wave creates flexoelectric polarization and space charge. The estimated gain is one or two orders of magnitude greater than the gain for the stimulated Brillouin scattering in isotropic organic liquids. The theoretical results obtained may be used as a basis for an experimental investigation of SS high frequency behaviour.     

Interpretation of ESI(+)-MS-MS spectra—Towards the identification of “unknowns”

We report a systematic empirical investigation of ESI(+)-MS-MS dissociation pathways of over 1000 spectra of small organic compounds, containing more than 30 chemical functional groups. The dissociation processes of the protonated molecular ions were explored and interpretated. We derived typical basic fragmentation channels for individual functional groups and established a unified set of fragmentation rules. Multiple bond cleavages of molecules containing single and multiple functional groups were explored as well and the corresponding fragmentation rules were derived. Applying these rules enabled to match between proposed chemical structures and an ESI(+)-MS-MS spectrum of an “unknown”. Comparison to EI fragmentation routes was also carried out. Despite the general dissimilarity between ESI(+)-MS-MS and EI-MS spectra, we exploit the minor similarities between the spectra, and utilizing NIST-EI database and search option, can be successfully reduced the number of proposed structures. The two step methodology developed here is demonstrated and evaluated in the identification of various “unknowns”.     

The use of MS classifiers and structure generation to assist in the identification of unknowns in effect-directed analysis

Structure generation and mass spectral classifiers have been incorporated into a new method to gain further information from low-resolution GC-MS spectra and subsequently assist in the identification of toxic compounds isolated using effect-directed fractionation. The method has been developed for the case where little analytical information other than the mass spectrum is available, common, for example, in effect-directed analysis (EDA), where further interpretation of the mass spectra is necessary to gain additional information about unknown peaks in the chromatogram. Structure generation from a molecular formula alone rapidly leads to enormous numbers of structures; hence reduction of these numbers is necessary to focus identification or confirmation efforts. The mass spectral classifiers and structure generation procedure in the program MOLGEN-MS was enhanced by including additional classifier information available from the NIST05 database and incorporation of post-generation ‘filtering criteria’. The presented method can reduce the number of possible structures matching a spectrum by several orders of magnitude, creating much more manageable data sets and increasing the chance of identification. Examples are presented to show how the method can be used to provide ‘lines of evidence’ for the identity of an unknown compound. This method is an alternative to library search of mass spectra and is especially valuable for unknowns where no clear library match is available.     

Elastic excitations in polycarbonate membranes

Brillouin light scattering was used to probe acoustic waves propagating with both longitudinal and transverse polarizations in the surface and the bulk of self‐supported particle track‐etched polycarbonate membranes with 15‐ and 80‐nm nanopores. The recorded scattering line shape at gigahertz frequencies reveals changes in the surface waves of the membranes which are more pronounced for the 80‐nm nanopores despite the low porosity (0.7 and 0.05%). Because the measured elastic constants (1.2 and 6.2 GPa) were found to compare very well with the values for thick polycarbonate film, modifications of the elasto‐optical coefficients and/or the transparency might be the reason for the different scattering line shapes. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3311–3317, 2004     

Negative-ion fragmentation pathways in 2,4,6-trinitrotoluene

The mass spectrum of 2,4,6-trinitrotoluene vapour in air was recorded and the negative-ion fragmentation pathways of the molecular anion were investigated down to the fourth generation. The dissociation of the parent anion led to the production of three fragment anions with masses 46, 197 and 210 u where the last two daughter ions initiated two entirely separate fragmentation pathways. These pathways were studied and the fragmentation mechanisms identified. The background negative-ion mass spectrum, generated by the glow discharge ion source in the airstream which carries the sample vapour into the source, was examined in detail and an assignment of this mass spectrum is included.     

Elastic properties and mechanical relaxation behaviors of PVDF (poly (vinylidene fluoride)) at temperatures between −20 and 100 °C and at 2 MHz ultrasonic frequency

The elastic properties of PVDF have been investigated as a function of temperature. The propagation velocity and absorption of longitudinal and transverse ultrasonic waves have been measured at a constant frequency of 2 MHz and temperatures between –20 and 100 °C. Hence, the temperature dependences of storage and loss elastic constants have been obtained for temperatures between –20 and 100 °C. It has been seen that the relaxation behavior is affected from the form of mechanical disturbance. For the longitudinal mode, only one relaxation peak at 42 °C, but for transverse mode three relaxation peaks at 28 °C, 60 °C, and 94 °C have been observed. The results have been compared with the literature values obtained previously for PVDF. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2862–2873, 2005     

Mass spectral fragmentation reactions of a therapeutic 4-azasteroid and related compounds

Mass spectra were acquired for a therapeutic 4-azasteroid (dutasteride), and some related compounds, using various ionization conditions (EI, CI, APCI and ESI) in both positive and negative ion modes. The ionization and fragmentation behavior of the compound dutasteride, its precursors and several analogs is reported. Positive atmospheric pressure chemical ionization (APCI+) and positive electrospray ionization (ESI+) produced distinctive collision-induced dissociation (CID) spectra for the respective [MH]+ ions of dutasteride. The spectral differences are attributed to ion populations having either different structures or different internal energy distributions (as a consequence of the method of ionization). Irrespective of their origin, the protonated molecules undergo interesting fragmentation reactions when collisionally activated. The identity of the major fragmentation products was confirmed by accurate mass measurement. The negative APCI mass spectrum of dutasteride displays extensive dehydrohalogenation, apparently due to the thermal component of the APCI process. Some of the resulting radical anions display remarkable stability toward collisional decomposition. Details of the fragmentation behavior for the negative ion species and their relationship to the positive ion results are discussed.     

Probing alpha-helical and beta-sheet structures of peptides at solid/liquid interfaces with SFG

We demonstrated that sum frequency generation (SFG) vibrational spectroscopy can distinguish different secondary structures of proteins or peptides adsorbed at solid/liquid interfaces. The SFG spectrum for tachyplesin I at the polystyrene (PS)/solution interface has a fingerprint peak corresponding to the B1/B3 mode of the antiparallel beta-sheet. This peak disappeared upon the addition of dithiothreitol, which can disrupt the beta-sheet structure. The SFG spectrum indicative of the MSI594 alpha-helical structure was observed at the PS/MSI594 solution interface. This research validates SFG as a powerful technique for revealing detailed secondary structures of interfacial proteins and peptides.     

Mass spectrometric and quantum mechanical analysis of gas-phase formation, structure, and decomposition of various b2 ions and their specifically deuterated analogs

B ions represent an important type of fragment ions derived from protonated peptides by cleavage of an amide bond with N-terminal charge retention. Such species have also been discussed as key intermediates during cyclic peptide fragmentation. Detailed structural information on such ion types can facilitate the interpretation of multiple step fragmentations such as the formation of inner chain fragments from linear peptides or the fragmentation of cyclic peptides. The structure of different b₂ ion isomers was investigated with collision-induced dissociations (CID) in combination with hydrogen/deuterium (H/D) exchange of the acidic protons. Special care was taken to investigate fragment ions derived from pure gas-phase processes. Structures deduced from the results of the CID analysis were compared with structures predicted on the basis of quantum chemical density functional theory (DFT) calculations to be most stable. The results pointed to different types of structures for b₂ ion isomers of complementary amino acid sequences. Either the protonated oxazolone structure or the N-terminally protonated immonium ion structure were proposed on the basis of the CID results and the DFT calculations. In addition, the analysis of different selectively N-alkylated peptide analogs revealed mechanistic details of the processes generating b ions.     

Structural characterization of sialylated glycoforms of H. influenzae by electrospray mass spectrometry: fragmentation of protonated and sodiated O-deacylated lipopolysaccharides

Sialylated lipopolysaccharide (LPS) glycoforms from Haemophilus influenzae were characterized by tandem mass spectrometry using a new generation hyphenated mass spectrometer which combines a triple quadrupole and a linear ion trap (Q-Trap). The fragmentation of both protonated and sodiated molecular ions from O-deacylated LPS (LPS-OH) obtained in MS(2) experiments in the positive mode was studied. The MS(2) spectra of protonated ions provided unambiguous evidence for the presence and sequence of sialylated lactosamine present in lacto-N-neotetraose oligosaccharide extensions but not for sialyl-lactose structures whilst fragmentation of sodiated adducts, [M+Na](+), afforded information diagnostic of mono- and disialylated lactose extensions. To study this we used a highly sialylated LPS from a H. influenzae strain capable of sialyl-lactose expression only. We then applied the method to the H. influenzae genome strain, Rd, in which glycoforms containing both sialyl-lactose and sialyl-lacto-N-neotetraose were detected from diagnostic B-ions at m/z 638.2 ([Neu5Ac(1) Hex(2)+Na](+)) and 657.2 ([Neu5Ac(1) Hex(1) HexNAc(1)+H](+)). Unique fragmentation patterns provided the locations and sequences of these oligosaccharide extensions. This is the first time both sialylated lactose and sialylated lacto-N-neotetraose units have been detected and characterized by tandem mass spectrometry in the same molecule. This methodology is of general applicability for determination of common sialylated oligosaccharide extension in bacterial LPS.     

Synthesis, self-assembly, and characterization of supramolecular polymers from electroactive dendron rodcoil molecules

We report here the synthesis and self-assembly of a series of three molecules with dendron rodcoil architecture that contain conjugated segments of oligo(thiophene), oligo(phenylene-vinylene), and oligo(phenylene). Despite their structural differences, all three molecules yield similar self-assembled structures. Electron and atomic force microscopy reveals the self-assembly of the molecules into high aspect ratio ribbon-like nanostructures which at low concentrations induce gelation in nonpolar solvent. Self-assembly results in a blue-shifted absorption spectrum and a red-shifted, quenched fluorescence spectrum, indicating aggregation of the conjugated segments within the ribbon-like structures. The assembly of these molecules into one-dimensional nanostructures is a route to pi-pi stacked supramolecular polymers for organic electronic functions. In the oligo(thiophene) derivative, self-assembly leads to a 3 orders of magnitude increase in the conductivity of iodine-doped films due to self-assembly. We also found that electric field alignment of these supramolecular assemblies can be used to create arrays of self-assembled nanowires on a device substrate.