Bulk Majorana mass terms and Dirac neutrinos in the Randall-Sundrum model

We present a novel scheme where Dirac neutrinos are realized even if lepton number violating Majorana mass terms are present. The setup is the Randall-Sundrum framework with bulk right-handed neutrinos. Bulk mass terms of both Majorana and Dirac type are considered. It is shown that massless zero mode solutions exist when the bulk Dirac mass term is set to zero. In this limit, it is found that the effective 4D small neutrino mass is primarily of Dirac nature, with the Majorana-type contributions being negligible. Interestingly, this scenario is very similar to the one known with flat extra dimensions. Neutrino phenomenology is discussed by fitting both charged lepton masses and neutrino masses simultaneously. A single Higgs localized on the IR brane is highly constrained, as unnaturally large Yukawa couplings are required to fit charged lepton masses. A simple extension with two Higgs doublets is presented, which facilitates a proper fit for the lepton masses.

Physical layer network coding for two-way relaying with QAM and latin squares

In the design of modulation schemes for the physical layer network-coded two way relaying scenario with two phases (Multiple access (MA) Phase and Broadcast (BC) Phase), it was observed by Koike-Akino et al. that adaptively changing the network coding map used at the relay according to the channel conditions greatly reduces the impact of multiple access interference and all these network coding maps should satisfy a requirement called the exclusive law. In [11] the case in which the end nodes use M-PSK signal sets is extensively studied using Latin Squares. This paper deals with the case in which the end nodes use square M-QAM signal sets. In a fading scenario, for certain channel conditions, termed singular fade states, the MA phase performance is greatly reduced. We show that the square QAM signal sets lead to lesser number of singular fade states compared to PSK signal sets. Because of this, the complexity at the relay is enormously reduced. Moreover lesser number of overhead bits are required in the BC phase. We find the number of singular fade states for PAM and QAM signal sets used at the end nodes. The fade state γejθ = 1 is a singular fade state for M-QAM for all values of M and it is shown that certain block circulant Latin Squares remove this singular fade state. Simulation results are presented to show that QAM signal set perform better than PSK.

LHC constraints on light neutralino dark matter in the MSSM

Light neutralino dark matter can be achieved in the Minimal Supersymmetric Standard Model if staus are rather light, with mass around 100 GeV. We perform a detailed analysis of the relevant supersymmetric parameter space, including also the possibility of light selectons and smuons, and of light higgsino- or wino-like charginos. In addition to the latest limits from direct and indirect detection of dark matter, ATLAS and CMS constraints on electroweak-inos and on sleptons are taken into account using a ``simplified models'' framework. Measurements of the properties of the Higgs boson at 125 GeV, which constrain amongst others the invisible decay of the Higgs boson into a pair of neutralinos, are also implemented in the analysis. We show that viable neutralino dark matter can be achieved for masses as low as 15 GeV. In this case, light charginos close to the LEP bound are required in addition to light right-chiral staus. Significant deviations are observed in the couplings of the 125 GeV Higgs boson. These constitute a promising way to probe the light neutralino dark matter scenario in the next run of the LHC. (C) 2013 Elsevier B.V. All rights reserved.

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

Background: The set of indispensable genes that are required by an organism to grow and sustain life are termed as essential genes. There is a strong interest in identification of the set of essential genes, particularly in pathogens, not only for a better understanding of the pathogen biology, but also for identifying drug targets and the minimal gene set for the organism. Essentiality is inherently a systems property and requires consideration of the system as a whole for their identification. The available experimental approaches capture some aspects but each method comes with its own limitations. Moreover, they do not explain the basis for essentiality in most cases. A powerful prediction method to recognize this gene pool including rationalization of the known essential genes in a given organism would be very useful. Here we describe a multi-level multi-scale approach to identify the essential gene pool in a deadly pathogen, Mycobacterium tuberculosis. Results: The multi-level workflow analyses the bacterial cell by studying (a) genome-wide gene expression profiles to identify the set of genes which show consistent and significant levels of expression in multiple samples of the same condition, (b) indispensability for growth by using gene expression integrated flux balance analysis of a genome-scale metabolic model, (c) importance for maintaining the integrity and flow in a protein-protein interaction network and (d) evolutionary conservation in a set of genomes of the same ecological niche. In the gene pool identified, the functional basis for essentiality has been addressed by studying residue level conservation and the sub-structure at the ligand binding pockets, from which essential amino acid residues in that pocket have also been identified. 283 genes were identified as essential genes with high-confidence. An agreement of about 73.5% is observed with that obtained from the experimental transposon mutagenesis technique. A large proportion of the identified genes belong to the class of intermediary metabolism and respiration. Conclusions: The multi-scale, multi-level approach described can be generally applied to other pathogens as well. The essential gene pool identified form a basis for designing experiments to probe their finer functional roles and also serve as a ready shortlist for identifying drug targets.

Average Modelling of a Voltage Source Inverter with Dead-Time in a Synchronous Reference Frame

Voltage source inverters are an integral part of renewable power sources and smart grid systems. Computationally efficient and fairly accurate models for the voltage source inverter are required to carry out extensive simulation studies on complex power networks. Accuracy requires that the effect of dead-time be incorporated in the inverter model. The dead-time is essentially a short delay introduced between the gating pulses to the complementary switches in an inverter leg for the safety of power devices. As the modern voltage source inverters switch at fairly high frequencies, the dead-time significantly influences the output fundamental voltage. Dead-time also causes low-frequency harmonic distortion and is hence important from a power quality perspective. This paper studies the dead-time effect in a synchronous dq reference frame, since dynamic studies and controller design are typically carried out in this frame of reference. For the sake of computational efficiency, average models are derived, incorporating the dead-time effect, in both RYB and dq reference frames. The average models are shown to consume less computation time than their corresponding switching models, the accuracies of the models being comparable. The proposed average synchronous reference frame model, including effect of dead-time, is validated through experimental results.

Desingularization of the Milne Universe

Resolution of cosmological singularities is an important problem in any full theory of quantum gravity. The Milne orbifold is a cosmology with a big-bang/big-crunch singularity, but being a quotient of flat space it holds potential for resolution in string theory. It is known, however, that some perturbative string amplitudes diverge in the Milne geometry. Here we show that flat space higher spin theories can effect a simple resolution of the Milne singularity when one embeds the latter in 2 + 1 dimensions. We explain how to reconcile this with the expectation that non-perturbative string effects are required for resolving Milne. Along the way, we introduce a Grassmann realization of the inonfi-Wigner contraction to export much of the AdS technology to -our flat space computation. (C) 2014 The Authors. Published by Elsevier BAT.

Current kinematics and dynamics of Africa and the East African Rift System

Although the East African Rift System (EARS) is an archetype continental rift, the forces driving its evolution remain debated. Some contend buoyancy forces arising from gravitational potential energy (GPE) gradients within the lithosphere drive rifting. Others argue for a major role of the diverging mantle flow associated with the African Superplume. Here we quantify the forces driving present-day continental rifting in East Africa by (1) solving the depth averaged 3-D force balance equations for 3-D deviatoric stress associated with GPE, (2) inverting for a stress field boundary condition that we interpret as originating from large-scale mantle tractions, (3) calculating dynamic velocities due to lithospheric buoyancy forces, lateral viscosity variations, and velocity boundary conditions, and (4) calculating dynamic velocities that result from the stress response of horizontal mantle tractions acting on a viscous lithosphere in Africa and surroundings. We find deviatoric stress associated with lithospheric GPE gradients are similar to 8-20 MPa in EARS, and the minimum deviatoric stress resulting from basal shear is similar to 1.6 MPa along the EARS. Our dynamic velocity calculations confirm that a force contribution from GPE gradients alone is sufficient to drive Nubia-Somalia divergence and that additional forcing from horizontal mantle tractions overestimates surface kinematics. Stresses from GPE gradients appear sufficient to sustain present-day rifting in East Africa; however, they are lower than the vertically integrated strength of the lithosphere along most of the EARS. This indicates additional processes are required to initiate rupture of continental lithosphere, but once it is initiated, lithospheric buoyancy forces are enough to maintain rifting.

Multimodal therapy for complete regression of malignant melanoma using constrained nonlinear optimal dynamic inversion

Using a realistic nonlinear mathematical model for melanoma dynamics and the technique of optimal dynamic inversion (exact feedback linearization with static optimization), a multimodal automatic drug dosage strategy is proposed in this paper for complete regression of melanoma cancer in humans. The proposed strategy computes different drug dosages and gives a nonlinear state feedback solution for driving the number of cancer cells to zero. However, it is observed that when tumor is regressed to certain value, then there is no need of external drug dosages as immune system and other therapeutic states are able to regress tumor at a sufficiently fast rate which is more than exponential rate. As model has three different drug dosages, after applying dynamic inversion philosophy, drug dosages can be selected in optimized manner without crossing their toxicity limits. The combination of drug dosages is decided by appropriately selecting the control design parameter values based on physical constraints. The process is automated for all possible combinations of the chemotherapy and immunotherapy drug dosages with preferential emphasis of having maximum possible variety of drug inputs at any given point of time. Simulation study with a standard patient model shows that tumor cells are regressed from 2 x 107 to order of 105 cells because of external drug dosages in 36.93 days. After this no external drug dosages are required as immune system and other therapeutic states are able to regress tumor at greater than exponential rate and hence, tumor goes to zero (less than 0.01) in 48.77 days and healthy immune system of the patient is restored. Study with different chemotherapy drug resistance value is also carried out. (C) 2014 Elsevier Ltd. All rights reserved.

In situ formation of silver nanowire networks on paper

Simple, universally adaptable techniques for fabricating conductive patterns are required to translate laboratory-scale innovations into low-cost solutions for the developing world. Silver nanostructures have emerged as attractive candidates for forming such conductive patterns. We report here the in situ formation of conductive silver-nanowire networks on paper, thereby eliminating the need for either cost-intensive ink formulation or substrate preparation or complex post-deposition sintering steps. Reminiscent of the photographic process of `salt printing', a desktop office printer was used to deposit desired patterns of silver bromide on paper, which were subsequently exposed to light and then immersed in a photographic developer. Percolating silver nanowire networks that conformally coated the paper fibres were formed after 10 min of exposure to light from a commercial halogen lamp. Thus, conductive and patterned films with sheet resistances of the order of 4 Omega/rectangle can be easily formed by combining two widely used processes - inkjet printing and photographic development.

Organic passivation layer on flexible Surlyn substrate for encapsulating organic photovoltaics

Barrier materials are required for encapsulating organic devices. A simple methodology based on organic passivation layer on a flexible substrate has been developed in this work. Stearyl stearate ( SS) was directly coated over the flexible Surlyn film. The barrier films with SS passivation layer exhibited much lower water vapor transmission rates compared to the neat Surlyn films. Moreover, the effect of the process of deposition of organic passivation layer on the resultant water vapor properties of the barrier films was evaluated. The accelerated lifetime studies conducted on encapsulated organic photovoltaics showed that the passivation layer improved the device performance by several fold compared to the non-passivated barrier films. (C) 2014 AIP Publishing LLC.

Roles of the troponin isoforms during indirect flight muscle development in Drosophila

Troponin proteins in cooperative interaction with tropomyosin are responsible for controlling the contraction of the striated muscles in response to changes in the intracellular calcium concentration. Contractility of the muscle is determined by the constituent protein isoforms, and the isoforms can switch over from one form to another depending on physiological demands and pathological conditions. In Drosophila, a majority of the myofibrillar proteins in the indirect flight muscles (IFMs) undergo post-transcriptional and post-translational isoform changes during pupal to adult metamorphosis to meet the high energy and mechanical demands of flight. Using a newly generated Gal4 strain (UH3-Gal4) which is expressed exclusively in the IFMs, during later stages of development, we have looked at the developmental and functional importance of each of the troponin subunits (troponin-I, troponin-T and troponin-C) and their isoforms. We show that all the troponin subunits are required for normal myofibril assembly and flight, except for the troponin-C isoform 1 (TnC1). Moreover, rescue experiments conducted with troponin-I embryonic isoform in the IFMs, where flies were rendered flightless, show developmental and functional differences of TnI isoforms and importance of maintaining the right isoform.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

Selective Review of Proton Magnetic Resonance Spectroscopy in Schizophrenia

Magnetic Resonance Spectroscopy (MRS) offers a unique opportunity to measure brain metabolites in-vivo, and in doing so enables one to understand the brain function and cellular processes implicated in the pathophysiology of psychiatric disorders. MRS, in addition to being non-invasive, is devoid of radioactive tracers and ionizing radiation, a distinct advantage over other imaging modalities like positron emission tomography and single photon emission computed tomography. With advances in MRS technique it is now possible to quantify concentrations of relevant compounds like neurotransmitters, neuronal viability markers and pharmacological compounds. Majority of the MRS studies have examined the neurometabolites in schizophrenia, a common and debilitating psychiatric disorder. Abnormalities in N Acetyl aspartate and Glutamate are consistently reported while the reports regarding the myoinsoitol and choline are inconsistent. These abnormalities are not changed across the illness stages and despite treatment. However, multiple technical challenges have limited the widespread use of MRS in psychiatric disorders. Guidelines for uniform acquisition and preprocessing are need of the hour, which. would increase the replicability and validity of MRS measures in psychiatry. Finally long term, prospective, longitudinal studies are required in different psychiatric disorders for potential clinical applications.

A model for the classification and survey of clock synchronization protocols in WSNs

Clock synchronization in wireless sensor networks (WSNs) assures that sensor nodes have the same reference clock time. This is necessary not only for various WSN applications but also for many system level protocols for WSNs such as MAC protocols, and protocols for sleep scheduling of sensor nodes. Clock value of a node at a particular instant of time depends on its initial value and the frequency of the crystal oscillator used in the sensor node. The frequency of the crystal oscillator varies from node to node, and may also change over time depending upon many factors like temperature, humidity, etc. As a result, clock values of different sensor nodes diverge from each other and also from the real time clock, and hence, there is a requirement for clock synchronization in WSNs. Consequently, many clock synchronization protocols for WSNs have been proposed in the recent past. These protocols differ from each other considerably, and so, there is a need to understand them using a common platform. Towards this goal, this survey paper categorizes the features of clock synchronization protocols for WSNs into three types, viz, structural features, technical features, and global objective features. Each of these categories has different options to further segregate the features for better understanding. The features of clock synchronization protocols that have been used in this survey include all the features which have been used in existing surveys as well as new features such as how the clock value is propagated, when the clock value is propagated, and when the physical clock is updated, which are required for better understanding of the clock synchronization protocols in WSNs in a systematic way. This paper also gives a brief description of a few basic clock synchronization protocols for WSNs, and shows how these protocols fit into the above classification criteria. In addition, the recent clock synchronization protocols for WSNs, which are based on the above basic clock synchronization protocols, are also given alongside the corresponding basic clock synchronization protocols. Indeed, the proposed model for characterizing the clock synchronization protocols in WSNs can be used not only for analyzing the existing protocols but also for designing new clock synchronization protocols. (C) 2014 Elsevier B.V. All rights reserved.

CHEXVIS: a tool for molecular channel extraction and visualization

Background: Understanding channel structures that lead to active sites or traverse the molecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Efficient methods for extracting, storing, and analyzing protein channels are required to support such studies. Further, there is a need for an integrated framework that supports computation of the channels, interactive exploration of their structure, and detailed visual analysis of their properties. Results: We describe a method for molecular channel extraction based on the alpha complex representation. The method computes geometrically feasible channels, stores both the volume occupied by the channel and its centerline in a unified representation, and reports significant channels. The representation also supports efficient computation of channel profiles that help understand channel properties. We describe methods for effective visualization of the channels and their profiles. These methods and the visual analysis framework are implemented in a software tool, CHEXVIS. We apply the method on a number of known channel containing proteins to extract pore features. Results from these experiments on several proteins show that CHEXVIS performance is comparable to, and in some cases, better than existing channel extraction techniques. Using several case studies, we demonstrate how CHEXVIS can be used to study channels, extract their properties and gain insights into molecular function. Conclusion: CHEXVIS supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels. The CHEXVIS web-server is freely available at http://vgl.serc.iisc.ernet.in/chexvis/. The web-server is supported on all modern browsers with latest Java plug-in.