Amplifiers and Lasers in PCF Configurations

In this paper we will present an overview of the use of photonic crystal fibers as fiber amplifiers. We will describe the basic concepts of optical amplification, and how to do numerical modelling of such components. We will then identify advantages and disadvantages of amplifiers based on PCF technology compared to conventional fibers, and then go into greater detail on some of these specific applications, such as low pump power amplifiers, and high-power double-clad amplifiers and lasers.     

Microelectromagnet for magnetic manipulation in lab-on-a-chip systems

We demonstrate a simple scheme for fabrication of microelectromagnets consisting of planar spiral coils semi-encapsulated in soft magnetic yokes using conventional microfabrication techniques. The microelectromagnets are suitable for applications operating at frequencies below 250 kHz. Conventional fabrication schemes for planar microelectromagnets typically rely on five mask steps. We allow the current to flow in the soft magnetic yoke and thereby two mask steps are eliminated. We have characterized the electromagnets electrically, the results agree well with theory, and the implications arising from current flowing in the magnetic yoke are discussed. We have integrated the microelectromagnets with microfluidic channels, and demonstrated separation of commercially available magnetic beads from a fluid in a microfluidic system, i.e. a lab-on-a-chip system.     

Dynamic stability of weakly damped oscillators with elastic impacts and wear

The dynamics of non-linear oscillators comprising of a single-degree-of-freedom system and beams with elastic two-sided amplitude constraints subject to harmonic loads is analyzed. The beams are clamped at one end, and constrained against unilateral contact sites near the other end. The structures are modelled by a Bernoulli-type beam supported by springs using the finite element method. Rayleigh damping is assumed. Symmetric and elastic double-impact motions, both harmonic and sub-harmonic, are studied by way of a Poincaré mapping that relates the states at subsequent impacts. Stability and bifurcation analyses are performed for these motions, and domains of instability are delineated. Impact work rate, which is the rate of energy dissipation to the impacting surfaces, is evaluated and discussed. In addition, an experiment conducted by Moon and Shaw on the vibration of a cantilevered beam with one-sided amplitude constraining stop is modelled. Bifurcation observed in the experiment could be captured.     

Membrane ion-exchange chromatography for process-scale antibody purification

Microemulsion electrokinetic chromatography (MEEKC) was evaluated as a screening tool for the indirect measurement of octanol–water partition coefficients (log P_o/w) of pesticide compounds. Over 80 pesticide compounds representing a variety of structural characteristics were studied, and good correlation of log P_o/w with the logarithm of the retention factor was found. The microemulsion system studied allowed the separation of compounds in the log P_o/w range of −1 to 7. In addition, a smaller set of simple organic molecules that vary in structural features was evaluated and compared to the pesticide log P_o/w calibration. The pesticide and simple organic molecule log P_o/w calibration lines were statistically similar. This suggests that a universal set of standard compounds may be employed for the log P_o/w calibration to provide measurements for a variety of compounds with good accuracy.     

Evolutionary rate variation and RNA secondary structure prediction

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.     

Configuration and E/Z interconversion mechanism of O(S)-allyl-S(O)-methyl-N-(acridin-9-yl) iminothiocarbonate

The configuration and dynamic behavior of O-allyl-S-methyl-N-(acridin-9-yl)iminothiocarbonate (1) and its S-allyl-O-methyl regioisomer (2) were studied using quantum chemical calculations and by applying a novel graphical method to scatter maps obtained from MD simulations for evaluation of an NOE-weighted internuclear distance (r(NOE)). Energy calculations indicated that the Z configuration was predominant for each compound and, further, this was supported both by the calculated chemical shifts and the r(NOE). Both N-inversion- and rotation-type transition-state structures were also calculated for the E/Z isomerization process, the results indicating that the preferred interconversion mechanism for 1 is N-inversion, but contrastingly, interconversion via rotation is equally as probable as N-inversion for 2. This supports the notion that one or the other or both pathways can be active and each system needs to be assessed on a case-by-case basis.