Role of the Residue Q1919 in Increasing Kinase Activity of G2019S LRRK2 Kinase: A Computational Study

Mutations in multi-domain leucine-rich repeat kinase 2 (LRRK2) have been an interest to researchers as these mutations are associated with Parkinson's disease. G2019S mutation in LRRK2 kinase domain leads to the formation of additional hydrogen bonds by S2019 which results in stabilization of the active state of the kinase, thereby increasing kinase activity. Two additional hydrogen bonds of S2019 are reported separately. Here, a mechanistic picture of the formation of additional hydrogen bonds of S2019 with Q1919 (also with E1920) is presented using ‘active’ Roco4 kinase as a homology model and its relationship with the stabilization of the ‘active’ G2019S LRRK2 kinase. A conformational flipping of residue Q1919 was found which helped to form stable hydrogen bond with S2019 and made ‘active’ state more stable in G2019S LRRK2. Two different states were found within the ‘active’ kinase with respect to the conformational change (flipping) in Q1919. Two doubly-mutated systems, G2019S/Q1919A and G2019S/E1920 K, were studied separately to check the effect of Q1919 and E1920. For both cases, the stable S2 state was not formed, leading to a decrease in kinase activity. These results indicate that both the additional hydrogen bonds of S2019 (with Q1919 and E1920) are necessary to stabilize the active G2019S LRRK2.     

Frequency encoded optical four-bit adder/subtractor with control input using semiconductor optical amplifiers

Optical adder/subtractor for two four-bit frequency encoded binary numbers are proposed and designed based on four wave mixing, add drop multiplexing and frequency conversion in semiconductor optical amplifier. The input bits and the control input are intensity-modulated signal of two specific frequencies suitable for optical communication in the C band of wavelength. The device can distinguish negative and positive results and controlled operation are most promising in this proposal. The use of semiconductor optical amplifiers along with frequency encoding makes the system very fast and useful for future optical communication and computation systems.     

Alternative method of implementation of frequency encoded N bit comparator exploiting four wave mixing in semiconductor optical amplifiers

A frequency encoded all optical N bit comparator is proposed. The implementation is ultrafast one and the frequency encoding makes it intensity loss dependent problem free. The use of polarization insensitive four wave mixing makes the design polarization independent and the hardware simple. The frequency conversion by the RSOA makes the design faster compared to other SOA based design. The required gates, i.e. X-OR and AND gates for the implementation of the comparator in frequency encoded format are also discussed.     

Using recurrence plot analysis to distinguish between endogenous and exogenous stock market crashes

Recurrence Plots are graphical tools based on Phase Space Reconstruction. Recurrence Quantification Analysis (RQA) is a statistical quantification of RPs. RP and RQA are good at working with non-stationarity and noisy data, in detecting changes in data behavior, in particular in detecting breaks, like a phase transition and in informing about other dynamic properties of a time series. Endogenous Stock Market Crashes have been modeled as phase changes in recent times. Motivated by this, we have used RP and RQA techniques for detecting critical regimes preceding an endogenous crash seen as a phase transition and hence give an estimation of the initial bubble time. We have used a new method for computing RQA measures with confidence intervals. We have also used the techniques on a known exogenous crash to see if the RP reveals a different story or not. The analysis is made on Nifty, Hong Kong AOI and Dow Jones Industrial Average, taken over a time span of about 3 years for the endogenous crashes. Then the RPs of all time series have been observed, compared and discussed. All the time series have been first transformed into the classical momentum divided by the maximum Xmax of the time series over the time window which is considered in the specific analysis. RPs have been plotted for each time series, and RQA variables have been computed on different epochs. Our studies reveal that, in the case of an endogenous crash, we have been able to identify the bubble, while in the case of exogenous crashes the plots do not show any such pattern, thus helping us in identifying such crashes.     

Influence of reagent rotation on (H-, D2) and (D-, H2) collisions: a quantum mechanical study

Time-independent quantum mechanical (TIQM) approach (helicity basis truncated at k = 2) has been used for computing differential and integral cross sections for the exchange reaction H- + D2 (v = 0, j = 0-4) --> HD + D- and D- + H2 (v = 0, j = 0-3) --> HD + H- in three dimensions on an accurate ab initio potential energy surface. It is shown that the j-weighted differential reaction cross section values are in good agreement with the experimental results reported by Zimmer and Linder at four different relative translational energies (Etrans = 0.55, 0.93, 1.16 and 1.48 eV) for (H-, D2) and at one relative translational energy (Etrans = 0.6 eV) by Haufler et al. for both (H-, D2) and (D-, H2) collisions. The j-weighted integral reaction cross section values are in good agreement with the crossed beam measurements by Zimmer and Linder in the Etrans range 0.5-1.5 eV and close to the guided ion beam results by Haufler et al. for (H-, D2) in the range 0.8-1.2 eV. Time-dependent quantum mechanical (TDQM) results obtained using centrifugal sudden approximation are reported in the form of integral reaction cross section values as a function of Etrans in the range 0.3-3.0 eV for both reactions in three dimensions on the same potential energy surface. The TDQM reaction cross section values decline more sharply than the TIQM results with increase in the initial rotational quantum number (j) for the D2 molecules in their ground vibrational state (v = 0) for (H-, D2) collisions. The computed j-weighted reaction cross section values are in good agreement with the experimental results reported by Zimmer and Linder for (H-, D2) collisions and guided ion beam results by Haufler et al. for both (H-, D2) and (D-, H2) collisions for energies below the threshold for electron detachment channel.     

Electrical conductivity and dielectric properties of SiO<Subscript>2</Subscript> nanoparticles dispersed in conducting polymer matrix

Electrical and dielectric properties of conducting polypyrrole–wide band gap silica (PPY–SiO₂) nanocomposites have been investigated as a function of temperature and frequency for different concentrations of polypyrrole. The average grain size of the nanocomposites is in the range of 40–80 nm. Impedance spectra reveal two distorted semicircles corresponding to grain and grain boundary effects. The magnitude of conductivity and its temperature variation are significantly different from polypyrrole and silica. A very large dielectric constant of about 4800 at 30 kHz and at room temperature has been observed for the highest concentration of silica. Inhomogeneous behavior of nanocomposites gives rise to high dielectric constant.     

An all optical method of implementing a wavelength encoded simultaneous binary full adder-full subtractor unit exploiting nonlinear polarization rotation in semiconductor optical amplifier

Full adders and full subtractors are the basic circuit elements of any digital data processor in electronics as well as in the all optical domain. Again the wavelength dependent encoding/decoding techniques have established itself as a very promising and efficient tool having some inherent and unique advantages relative to the other well known intensity or polarization or phase dependent optical data encoding mechanisms. In this communication, the authors therefore propose a new scheme of implementing a wavelength encoded complete binary full adder-full subtractor unit in the all optical domain using the wavelength conversion by the nonlinear polarization rotation in a single semiconductor optical amplifier. The interacting signals are counter propagating in the semiconductor optical amplifier and hence can be set at the same wavelength. To realize the binary logic wavelength dependent encoding/decoding mechanism is exploited in our proposed scheme of full adder-full subtractor unit. Also the optical add/drop multiplexing employing the special filtering property of the semiconductor optical amplifier is utilized for the designing of the all optical system.     

A method of implementation of frequency encoded all optical logic gates based on non-linear total reflectional switch at the interface

A novel method of implementation of frequency encoded logic gates NOT, OR, AND, NOR, NAND, X-OR, X-NOR is discussed. The frequency sources and physical requirements for the implementation are also discussed. The non-linear material (liquid) suitable for these operations to be performed should be of large non-linear coefficient, high reverse saturation absorption, large thermo-optic coefficient and low viscosity. The input controlling beams used to induce non-linearity in the switch are either of frequency υ₁ or υ₂ and the probe beam is a mixed signal of frequencies υ₁ and υ₂. Depending on the nature of the controlling inputs the output conditions of the probe can be adjusted to get different logic gates.