bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphatidylinositol and phosphatidic acid transport between the ER and plasma membrane during PLC activation requires the Nir2 protein
Authors: Kim Yeun Ju , Guzman-Hernandez Maria Luisa , Wisniewski Eva , Echeverria Nicolas , Balla Tamas
Published: February 2016

Phospholipase C (PLC)-mediated hydrolysis of the limited pool of plasma membrane (PM) phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] requires replenishment from a larger pool of phosphatidylinositol (PtdIns) via sequential phosphorylation by PtdIns 4-kinases and phosphatidylinositol 4-phosphate (PtdIns4P) 5-kinases. Since PtdIns is synthesized in the endoplasmic reticulum (ER) and PtdIns(4,5)P2 is generated in the PM, it has been postulated that PtdIns transfer proteins (PITPs) provide the means for this lipid transfer function. Recent studies identified the large PITP protein, Nir2 as important for PtdIns transfer from the ER to the PM. It was also found that Nir2 was required for the transfer of phosphatidic acid (PtdOH) from the PM to the ER. In Nir2-depleted cells, activation of PLC leads to PtdOH accumulation in the PM and PtdIns synthesis becomes severely impaired. In quiescent cells, Nir2 is localized to the ER via interaction of its FFAT domain with ER-bound VAMP-associated proteins VAP-A and–B. After PLC activation, Nir2 also binds to the PM via interaction of its C-terminal domains with diacylglycerol (DAG) and PtdOH. Through these interactions, Nir2 functions in ER–PM contact zones. Mutations in VAP-B that have been identified in familial forms of amyotrophic lateral sclerosis (ALS or Lou-Gehrig's disease) cause aggregation of the VAP-B protein, which then impairs its binding to several proteins, including Nir2. These findings have shed new lights on the importance of non-vesicular lipid transfer of PtdIns and PtdOH in ER–PM contact zones with a possible link to a devastating human disease.
From endolysins to Artilysin®s: novel enzyme-based approaches to kill drug-resistant bacteria
Authors: Gerstmans Hans , Rodríguez-Rubio Lorena , Lavigne Rob , Briers Yves
Published: February 2016

One of the last untapped reservoirs in nature for the identification of new anti-microbials is bacteriophages, the natural killers of bacteria. Lytic bacteriophages encode peptidoglycan (PG) lytic enzymes able to degrade the PG layer in different steps of their infection cycle. Endolysins degrade the bacterial cell wall at the end of the infection cycle, causing lysis of the host to release the viral progeny. Recombinant endolysins have been successfully applied as anti-bacterial agent against antibiotic-resistant Gram-positive pathogens. This has boosted the study of these enzymes as new anti-microbials in different fields (e.g. medical, food technology). A key example is the recent development of endolysin-based anti-bacterials against Gram-negative pathogens in which the exogenous application of endolysins is hindered by the outer membrane (OM). These novel anti-microbials, termed Artilysin®s, are able to pass through the OM and reach the PG where they exert their action. In addition, mycobacteria whose cell wall is structurally different from both Gram-positive and Gram-negative bacteria have also been reported to be inhibited by mycobacteriophage-encoded endolysins. Endolysins and endolysin-based anti-microbials can be considered as ideal candidates for an alternative to antibiotics for several reasons: (1) their unique mode of action and activity against bacterial persisters (independent of an active host metabolism), (2) their selective activity against both Gram-positive and Gram-negative pathogens (including antibiotic resistant strains) and mycobacteria, (3) the limited resistance development reported so far. The present review summarizes and discusses the potential applications of endolysins as new anti-microbials.
Polyphosphate and acidocalcisomes
Authors: Lander Noelia , Cordeiro Ciro , Huang Guozhong , Docampo Roberto
Published: February 2016

Inorganic polyphosphate (polyP) accumulates in acidocalcisomes, acidic calcium stores that have been found from bacteria to human cells. Proton pumps, such as the vacuolar proton pyrophosphatase (V-H+-PPase or VP1), the vacuolar proton ATPase (V-H+-ATPase) or both, maintain their acidity. A vacuolar transporter chaperone (VTC) complex is involved in the synthesis and translocation of polyP to these organelles in several eukaryotes, such as yeast, trypanosomatids, Apicomplexan and algae. Studies in trypanosomatids have revealed the role of polyP and acidocalcisomes in osmoregulation and calcium signalling.
Discovery and industrial applications of lytic polysaccharide mono-oxygenases
Authors: Johansen Katja S.
Published: February 2016

The recent discovery of copper-dependent lytic polysaccharide mono-oxygenases (LPMOs) has opened up a vast area of research covering several fields of application. The biotech company Novozymes A/S holds patents on the use of these enzymes for the conversion of steam-pre-treated plant residues such as straw to free sugars. These patents predate the correct classification of LPMOs and the striking synergistic effect of fungal LPMOs when combined with canonical cellulases was discovered when fractions of fungal secretomes were evaluated in industrially relevant enzyme performance assays. Today, LPMOs are a central component in the Cellic CTec enzyme products which are used in several large-scale plants for the industrial production of lignocellulosic ethanol. LPMOs are characterized by an N-terminal histidine residue which, together with an internal histidine and a tyrosine residue, co-ordinates a single copper atom in a so-called histidine brace. The mechanism by which oxygen binds to the reduced copper atom has been reported and the general mechanism of copper–oxygen-mediated activation of carbon is being investigated in the light of these discoveries. LPMOs are widespread in both the fungal and the bacterial kingdoms, although the range of action of these enzymes remains to be elucidated. However, based on the high abundance of LPMOs expressed by microbes involved in the decomposition of organic matter, the importance of LPMOs in the natural carbon-cycle is predicted to be significant. In addition, it has been suggested that LPMOs play a role in the pathology of infectious diseases such as cholera and to thus be relevant in the field of medicine.
Polyphosphate as a haemostatic modulator
Authors: Mutch Nicola J.
Published: February 2016

Platelets are small anuclear cells that play a central role in haemostasis. Platelets become activated in response to various stimuli triggering release of their granular contents into the surrounding milieu. One of these types of granules, termed dense granules, have been found to contain polyphosphate (polyP) in addition to other inorganic biomolecules, such as serotonin, ADP, ATP, PPi. Individuals deficient in dense granules exhibit bleeding tendencies, emphasizing their importance in haemostasis. Platelet polyP is of a relatively defined size, approximately 60–100 phosphate monomers in length. These linear polymers act at various points in the coagulation and fibrinolytic systems thereby modulating the haemostatic response. Due to its highly anionic nature, polyP lends itself to being a natural activator of the contact system. The contact system functions in multiple pathways including coagulation, fibrinolysis, inflammation and complement. Activation of the contact system accelerates thrombin generation, the terminal enzyme in the coagulation cascade. PolyP also modulates factors further downstream in the coagulation cascade to augment thrombin generation. The net effect is increased fibrin formation and platelet activation resulting in faster clot formation. PolyP is incorporated into the forming clot thereby modifying the structure of the resulting fibrin network and its susceptibility to degradation by certain plasminogen activators. In conclusion, release of platelet polyP at the site of injury may facilitate clot formation and augment clot stability thereby promoting wound healing.
Specificity and disease in the ubiquitin system
Authors: Chaugule Viduth K. , Walden Helen
Published: February 2016

Post-translational modification (PTM) of proteins by ubiquitination is an essential cellular regulatory process. Such regulation drives the cell cycle and cell division, signalling and secretory pathways, DNA replication and repair processes and protein quality control and degradation pathways. A huge range of ubiquitin signals can be generated depending on the specificity and catalytic activity of the enzymes required for attachment of ubiquitin to a given target. As a consequence of its importance to eukaryotic life, dysfunction in the ubiquitin system leads to many disease states, including cancers and neurodegeneration. This review takes a retrospective look at our progress in understanding the molecular mechanisms that govern the specificity of ubiquitin conjugation.
The new world of inorganic polyphosphates
Authors: Azevedo Cristina , Saiardi Adolfo
Published: February 2016

Post-translational modifications (PTMs) add regulatory features to proteins that help establish the complex functional networks that make up higher organisms. Advances in analytical detection methods have led to the identification of more than 200 types of PTMs. However, some modifications are unstable under the present detection methods, anticipating the existence of further modifications and a much more complex map of PTMs. An example is the recently discovered protein modification polyphosphorylation. Polyphosphorylation is mediated by inorganic polyphosphate (polyP) and represents the covalent attachment of this linear polymer of orthophosphate to lysine residues in target proteins. This modification has eluded MS analysis as both polyP itself and the phosphoramidate bonds created upon its reaction with lysine residues are highly unstable in acidic conditions. Polyphosphorylation detection was only possible through extensive biochemical characterization. Two targets have been identified: nuclear signal recognition 1 (Nsr1) and its interacting partner, topoisomerase 1 (Top1). Polyphosphorylation occurs within a conserved N-terminal polyacidic serine (S) and lysine (K) rich (PASK) cluster. It negatively regulates Nsr1–Top1 interaction and impairs Top1 enzymatic activity, namely relaxing supercoiled DNA. Modulation of cellular levels of polyP regulates Top1 activity by modifying its polyphosphorylation status. Here we discuss the significance of the recently identified new role of inorganic polyP.
Inorganic polyphosphate in cardiac myocytes: from bioenergetics to the permeability transition pore and cell survival
Authors: Dedkova Elena N.
Published: February 2016

Inorganic polyphosphate (polyP) is a linear polymer of Pi residues linked together by high-energy phosphoanhydride bonds as in ATP. PolyP is present in all living organisms ranging from bacteria to human and possibly even predating life of this planet. The length of polyP chain can vary from just a few phosphates to several thousand phosphate units long, depending on the organism and the tissue in which it is synthesized. PolyP was extensively studied in prokaryotes and unicellular eukaryotes by Kulaev's group in the Russian Academy of Sciences and by the Nobel Prize Laureate Arthur Kornberg at Stanford University. Recently, we reported that mitochondria of cardiac ventricular myocytes contain significant amounts (280±60 pmol/mg of protein) of polyP with an average length of 25 Pi and that polyP is involved in Ca2+-dependent activation of the mitochondrial permeability transition pore (mPTP). Enzymatic polyP depletion prevented Ca2+-induced mPTP opening during ischaemia; however, it did not affect reactive oxygen species (ROS)-mediated mPTP opening during reperfusion and even enhanced cell death in cardiac myocytes. We found that ROS generation was actually enhanced in polyP-depleted cells demonstrating that polyP protects cardiac myocytes against enhanced ROS formation. Furthermore, polyP concentration was dynamically changed during activation of the mitochondrial respiratory chain and stress conditions such as ischaemia/reperfusion (I/R) and heart failure (HF) indicating that polyP is required for the normal heart metabolism. This review discusses the current literature on the roles of polyP in cardiovascular health and disease.
Inositol polyphosphate multikinase (IPMK) in transcriptional regulation and nuclear inositide metabolism
Authors: Malabanan M. Merced , Blind Raymond D.
Published: February 2016

Inositol polyphosphate multikinase (IPMK, ipk2, Arg82, ArgRIII) is an inositide kinase with unusually flexible substrate specificity and the capacity to partake in many functional protein–protein interactions (PPIs). By merging these two activities, IPMK is able to execute gene regulatory functions that are very unique and only now beginning to be recognized. In this short review, we present a brief history of IPMK, describe the structural biology of the enzyme and highlight a few recent discoveries that have shed more light on the role IPMK plays in inositide metabolism, nuclear signalling and transcriptional regulation.
Phosphoinositide signalling in type 2 diabetes: a β-cell perspective
Authors: Rameh Lucia E. , Deeney Jude T.
Published: February 2016

Type 2 diabetes is a complex disease. It results from a failure of the body to maintain energy homoeostasis. Multicellular organisms have evolved complex strategies to preserve a relatively stable internal nutrient environment, despite fluctuations in external nutrient availability. This complex strategy involves the co-ordinated responses of multiple organs to promote storage or mobilization of energy sources according to the availability of nutrients and cellular bioenergetics needs. The endocrine pancreas plays a central role in these processes by secreting insulin and glucagon. When this co-ordinated effort fails, hyperglycaemia and hyperlipidaemia develops, characterizing a state of metabolic imbalance and ultimately overt diabetes. Although diabetes is most likely a collection of diseases, scientists are starting to identify genetic components and environmental triggers. Genome-wide association studies revealed that by and large, gene variants associated with type 2 diabetes are implicated in pancreatic β-cell function, suggesting that the β-cell may be the weakest link in the chain of events that results in diabetes. Thus, it is critical to understand how environmental cues affect the β-cell. Phosphoinositides are important ‘decoders’ of environmental cues. As such, these lipids have been implicated in cellular responses to a wide range of growth factors, hormones, stress agents, nutrients and metabolites. Here we will review some of the well-established and potential new roles for phosphoinositides in β-cell function/dysfunction and discuss how our knowledge of phosphoinositide signalling could aid in the identification of potential strategies for treating or preventing type 2 diabetes.
A cautionary (spectral) tail: red-shifted fluorescence by DAPI–DAPI interactions
Authors: Omelon Sidney , Georgiou John , Habraken Wouter
Published: February 2016

The fluorescent dye DAPI is useful for its association with and consequent amplification of an ∼460 nm emission maximum upon binding to dsDNA. Labelling with higher DAPI concentrations is a technique used to reveal Pi polymers [polyphosphate (polyP)], with a red-shift to ∼520–550 nm fluorescence emission. DAPI–polyP emissions of ∼580 nm are also generated upon 415 nm excitation. Red-shifted DAPI emission has been associated with polyP and RNA and has more recently been reported with polyadenylic acid (polyA), specific inositol phosphates (IPs) and heparin. We find that amorphous calcium phosphate (ACP) also demonstrates red-shifted DAPI emission at high DAPI concentrations. This DAPI spectral shift has been attributed to DAPI–DAPI electrostatic interactions enabled by molecules with high negative charge density that increase the local DAPI concentration and favour DAPI molecular proximity, as observed by increasing the dye/phosphate ratio. Excitation of dry DAPI (∼360 nm) confirmed a red-shifted DAPI emission. Whereas enzymatic approaches to modify substrates can help define the nature of DAPI fluorescence signals, multiple approaches beyond red-shifted DAPI excitation/emission are advised before conclusions are drawn about DAPI substrate identification.
Phosphoinositides in the nucleus and myogenic differentiation: how a nuclear turtle with a PHD builds muscle
Authors: Divecha Nullin
Published: February 2016

Phosphoinositides are a family of phospholipid messenger molecules that control various aspects of cell biology in part by interacting with and regulating downstream protein partners. Importantly, phosphoinositides are present in the nucleus. They form part of the nuclear envelope and are present within the nucleus in nuclear speckles, intra nuclear chromatin domains, the nuclear matrix and in chromatin. What their exact role is within these compartments is not completely clear, but the identification of nuclear specific proteins that contain phosphoinositide interaction domains suggest that they are important regulators of DNA topology, chromatin conformation and RNA maturation and export. The plant homeo domain (PHD) finger is a phosphoinositide binding motif that is largely present in nuclear proteins that regulate chromatin conformation. In the present study I outline how changes in the levels of the nuclear phosphoinositide PtdIns5P impact on muscle cell differentiation through the PHD finger of TAF3 (TAF, TATA box binding protein (TBP)-associated factor), which is a core component of a number of different basal transcription complexes.
Emerging evidence of signalling roles for PI(3,4)P2 in Class I and II PI3K-regulated pathways
Authors: Hawkins Phillip T. , Stephens Len R.
Published: February 2016

There are eight members of the phosphoinositide family of phospholipids in eukaryotes; PI, PI3P, PI4P, PI5P, PI(4,5)P2, PI(3,4)P2, PI(3,5)P2 and PI(3,4,5)P3. Receptor activation of Class I PI3Ks stimulates the phosphorylation of PI(4,5)P2 to form PI(3,4,5)P3. PI(3,4,5)P3 is an important messenger molecule that is part of a complex signalling network controlling cell growth and division. PI(3,4,5)P3 can be dephosphorylated by both 3- and 5-phosphatases, producing PI(4,5)P2 and PI(3,4)P2, respectively. There is now strong evidence that PI(3,4)P2 generated by this route does not merely represent another pathway for removal of PI(3,4,5)P3, but can act as a signalling molecule in its own right, regulating macropinocytosis, fast endophilin-mediated endocytosis (FEME), membrane ruffling, lamellipodia and invadopodia. PI(3,4)P2 can also be synthesized directly from PI4P by Class II PI3Ks and this is important for the maturation of clathrin-coated pits [clathrin-mediated endocytosis (CME)] and signalling in early endosomes. Thus PI(3,4)P2 is emerging as an important signalling molecule involved in the coordination of several specific membrane and cytoskeletal responses. Further, its inappropriate accumulation contributes to pathology caused by mutations in genes encoding enzymes responsible for its degradation, e.g. Inpp4B.
Low‐complexity 0.55‐V 2.5‐μW bandgap reference and power‐on reset hybrid circuit
Authors: Zhou Bo , Liu Shuli , Chiang Patrick
Published: February 2016

A near‐threshold low‐complexity bandgap reference (BGR) and power‐on reset (POR) hybrid circuit is implemented in 65 nm CMOS, with an ultra‐low supply voltage of 0.55 V and power consumption of 2.5 μW. The BGR employing amplifier offset voltage and current matching, and the POR based on offset voltage matching and loop settling feature, are proposed. The circuit‐level simulation results verify that the presented implementation, not only generates a stable reference voltage with the typical temperature coefficient of 120 ppm/°C and line‐regulation feature of 3.3%/V, but provides a robust reset signal with power‐on and brown‐out detection function. The proposed near‐threshold circuit has ultra‐low power supply and design complexity, both for BGR and POR modules, when compared to the reported.
Signal‐to‐noise ratio mismatch in polar codes
Authors: Zhang Qingshuang , Liu Aijun , Zhang Yingxian
Published: February 2016

Theoretically, the accurate signal‐to‐noise ratio (SNR) is necessary when using a successive cancelation (SC) or belief propagation (BP) decoder for polar codes. However, the effect of an SNR mismatch on the bit error rate performance of polar codes has not been addressed yet. The sensitivity of polar decoding with SC and BP decoders to the mismatch of SNR is studied. Theoretical and simulation results show that an estimation of SNR is not necessary for polar codes from a practical point of view.
Secrecy performance of dual‐hop decode‐and‐forward relay system with diversity combining at the eavesdropper
Authors: Ghose Sarbani , Kundu Chinmoy , Bose Ranjan
Published: February 2016

We have considered a dual‐hop wireless network consisting of a decode‐and‐forward (DF) relay in presence of an eavesdropper. Relay can correctly decode and retransmit only if the received signal‐to‐noise ratio (SNR) meets a particular threshold. The eavesdropper can tap signals both from the relay and the source. The performance of the maximal ratio combining (MRC) and selection combining (SC) diversity at the eavesdropper is investigated. Whether knowledge of channel state information (CSI) at the transmitter is available or not is considered for the performance evaluation in secrecy outage probability and ergodic secrecy rate. Asymptotic analyses of performances are provided. We show that direct link has a significant impact on system secrecy. It is found that secrecy performances are the best if the relay is always able to decode correctly. We also found that knowledge of CSI helps to achieve better secrecy at lower rate. It is observed that unbalance created due to constraint on either of the source‐relay link average SNR or relay‐destination link average SNR does not yield similar secrecy outage performance but both can limit the secrecy outage performance. On the contrary, it is found that only source‐relay link quality can limit the ergodic secrecy rate performance.
Topology for cascaded multilevel inverter
Authors: Odeh Charles Ikechukwu , Obe Emeka S. , Ojo Olorunfemi
Published: February 2016

This study presents a topology for cascaded multilevel inverter (MLI). Each module is made up of H‐ and half‐bridges, two isolated equal dc sources and a bidirectional auxiliary circuit. One leg of the H‐bridge and the half‐bridge are cut and the corresponding terminals are connected to the both ends of an equal split dc source. The free ends of the half‐bridge are connected together to form a common output node of the inverter. The auxiliary circuit is inserted between the midpoint of the split dc sources and this very output node. The output point of the uncut leg of the H‐bridge forms the remaining output node. With this circuit arrangement, proper control of the switches in the bridges and the auxiliary circuit, in each cascaded cell, can produce nine output voltage levels. A comparison is made between the proposed inverter, classical CHB and some of the recent developed MLI topologies with respect to specified figure of merits, as well as the per unit power losses. For two cascaded modules, simulation and experimental verifications are carried out on the proposed inverter topology for an R‐L load; adequate results are presented.
Individual pitch controller based on fuzzy logic control for wind turbine load mitigation
Authors: Han Bing , Zhou Lawu , Yang Fan , Xiang Zeng
Published: February 2016

With the increasing size of modern large wind turbine (WT), the effects of dynamic loading on the structures become an important influence factor. There are mitigation measures for WT control systems to reduce these imbalance structural loads and regulate power. It has motivated the development of blade individual pitch control (IPC) methodologies. This study focuses on the design of fuzzy logic controller (FLC) for IPC. The controllers are designed in order to optimise a trade‐off among several control objectives such as blade root moment and generator torque. Three different FLC had been used in the controllers, the first one related to blade pitch angle and electromagnetic torque control variables to meet specified objectives for operation region, the second control model and the third model related to d‐q axis blade moment in non‐rotating frame of reference. Likewise, the optimisation criteria of FLC consider for each controller objective to mitigate fatigue loads and regulate output power. Finally, the effectiveness of proposed method is verified by simulation results for three‐bladed NREL 2 MW WT. The results proved that the fatigue loads in the turbine are reduced obviously.
Sub‐band classification of decomposed single event‐related potential co‐variants for multi‐class brain–computer interface: a qualitative and quantitative approach
Authors: Ahirwal Mitul Kumar , Kumar Anil , Singh Girish K. , Suri Jasjit S.
Published: February 2016

Subject dependent and co‐variant nature of electroencephalography (EEG)/event‐related potential (ERP) are still hurdles in the development of generalised EEG system such as clinical diagnoses and brain–computer interface (BCI) systems. Presently, classification of BCI classes is limited due to consideration of several trials of ERP as average case for generalisation or some time single‐trial ERP detection is preferred for subject specific schemes. Present study tries to develop a methodology for utilisation of co‐variant nature of ERP, based on the sub‐band decomposed ERPs. Proposed idea also explores a new dimension in BCI system design, as multi‐class classification for execution of multiple commands through single ERP. Sub‐band ERPs and their power spectrum‐based features are extracted and classified successfully with 70.64% accuracy using artificial neural network.
Biology, social science and history: interdisciplinarity in three directions
Authors: Renwick Chris
Published: February 2016

The relationship between biological and social science is a long-standing area of interest for researchers on both sides of the divide, as well as in the humanities, where historians, among others, have been fascinated by its wider social, political and cultural implications. Yet interdisciplinary work in this area has always been problematic, not least because researchers are understandably concerned about interdisciplinarity being a cover for importing ideas and methods wholesale from other fields. This article explores the lessons, both positive and negative, that can be drawn from an ongoing project focused on building links between biology, social science and history. The article argues that dialogue between different disciplines is a difficult process to get going but ultimately rewarding. However, the article also argues that interdisciplinary practice is a much more elusive goal. The key to developing such practices lies in identifying new spaces for cooperative work rather than areas that are already occupied by researchers. This article is published as part of a thematic collection on the concept of interdisciplinarity.
Dynamical error bounds for continuum discretisation via Gauss quadrature rules—A Lieb-Robinson bound approach
Authors: Woods M. P. , Plenio M. B.
Published: February 2016

Instances of discrete quantum systems coupled to a continuum of oscillators are ubiquitous in physics. Often the continua are approximated by a discrete set of modes. We derive error bounds on expectation values of system observables that have been time evolved under such discretised Hamiltonians. These bounds take on the form of a function of time and the number of discrete modes, where the discrete modes are chosen according to Gauss quadrature rules. The derivation makes use of tools from the field of Lieb-Robinson bounds and the theory of orthonormal polynomials.
Temperature-dependent recombination velocity analysis on artificial small angle grain boundaries using electron beam induced current method
Authors: Kojima Takuto , Tachibana Tomihisa , Ohshita Yoshio , Prakash Ronit R. , Sekiguchi Takashi , Yamaguchi Masafumi
Published: February 2016

The details of the process of carrier recombination via the Shockley-Read-Hall (SRH) defect level, at the grain boundaries of multicrystalline silicon, were investigated. For this, the temperature-dependent recombination velocities, as determined by experiments, were analyzed by the application of an electron beam induced current method. For the model, the misorientation angles at the grain boundaries were defined using a multi-seed casting-growth method. The results of our experiments indicated different temperature behaviors at low and high temperatures. These can be explained by controlling the process anticipated by the SRH model, that is, the process whereby minority carriers (electrons) are captured at lower temperatures, followed by the reemission of the carriers before recombination with Arrhenius behavior at higher temperatures. The minority capture process appeared to conform to the power law T−α temperature behavior. Thus, there are two candidate electron capture mechanisms, namely, cascade phonon emission capture for shallow centers and excitonic-Auger capture for deep centers. The activation energy for the reemission of carriers was around 0.1 eV. These findings regarding the temperature dependence are essentially independent of the misorientation angles, suggesting a common defect level and recombination mechanism. The difference in the recombination velocities can be regarded as being derived from the difference in the density at the defect level.
Study of infrared emission spectroscopy for the B1Δg–A1Πu and B′1Σg+–A1Πu systems of C2
Authors: Chen Wang , Kawaguchi Kentarou , Bernath Peter F. , Tang Jian
Published: February 2016

Thirteen bands for the B1Δg–A1Πu system and eleven bands for the B′1Σg+–A1Πu system of C2 were identified in the Fourier transform infrared emission spectra of hydrocarbon discharges. The B′1Σg+ v = 4 and the B1Δg v = 6, 7, and 8 vibrational levels involved in nine bands were studied for the first time. A direct global analysis with Dunham parameters was carried out satisfactorily for the B1Δg–A1Πu system except for a small perturbation in the B1Δg v = 6 level. The calculated rovibrational term energies up to B1Δg v = 12 showed that the level crossing between the B1Δg and d3Πg states is responsible for many of the prominent perturbations in the Swan system observed previously. Nineteen forbidden transitions of the B1Δg–a3Πu transition were identified and the off-diagonal spin-orbit interaction constant AdB between d3Πg and B1Δg was derived as 8.3(1) cm−1. For the B′1Σg+–A1Πu system, only individual band analyses for each vibrational level in the B′1Σg+ state could be done satisfactorily and Dunham parameters obtained from these effective parameters showed that the anharmonic vibrational constant ωexe is anomalously small (nearly zero). Inspection of the RKR (Rydberg-Klein-Rees) potential curves for the B′1Σg+ and X1Σg+ states revealed that an avoided crossing or nearly avoided crossing may occur around 30 000 cm−1, which is responsible for the anomalous molecular constants in these two states.
A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules
Authors: Bruetzel Linda K. , Fischer Stefan , Salditt Annalena , Sedlak Steffen M. , Nickel Bert , Lipfert Jan
Published: February 2016

We demonstrate the use of a molybdenum-anode-based in-house small-angle X-ray scattering (SAXS) setup to study biological macromolecules in solution. Our system consists of a microfocus X-ray tube delivering a highly collimated flux of 2.5 × 106 photons/s at a beam size of 1.2 × 1.2 mm2 at the collimation path exit and a maximum beam divergence of 0.16 mrad. The resulting observable scattering vectors q are in the range of 0.38 Å−1 down to 0.009 Å−1 in SAXS configuration and of 0.26 Å−1 up to 5.7 Å−1 in wide-angle X-ray scattering (WAXS) mode. To determine the capabilities of the instrument, we collected SAXS data on weakly scattering biological macromolecules including proteins and a nucleic acid sample with molecular weights varying from ∼12 to 69 kDa and concentrations of 1.5–24 mg/ml. The measured scattering data display a high signal-to-noise ratio up to q-values of ∼0.2 Å−1 allowing for an accurate structural characterization of the samples. Moreover, the in-house source data are of sufficient quality to perform ab initio 3D structure reconstructions that are in excellent agreement with the available crystallographic structures. In addition, measurements for the detergent decyl-maltoside show that the setup can be used to determine the size, shape, and interactions (as characterized by the second virial coefficient) of detergent micelles. This demonstrates that the use of a Mo-anode based in-house source is sufficient to determine basic geometric parameters and 3D shapes of biomolecules and presents a viable alternative to valuable beam time at third generation synchrotron sources.
Exceptional gettering response of epitaxially grown kerfless silicon
Authors: Powell D. M. , Markevich V. P. , Hofstetter J. , Jensen M. A. , Morishige A. E. , Castellanos S. , Lai B. , Peaker A. R. , Buonassisi T.
Published: February 2016

The bulk minority-carrier lifetime in p- and n-type kerfless epitaxial (epi) crystalline silicon wafers is shown to increase >500× during phosphorus gettering. We employ kinetic defect simulations and microstructural characterization techniques to elucidate the root cause of this exceptional gettering response. Simulations and deep-level transient spectroscopy (DLTS) indicate that a high concentration of point defects (likely Pt) is “locked in” during fast (60 °C/min) cooling during epi wafer growth. The fine dispersion of moderately fast-diffusing recombination-active point defects limits as-grown lifetime but can also be removed during gettering, confirmed by DLTS measurements. Synchrotron-based X-ray fluorescence microscopy indicates metal agglomerates at structural defects, yet the structural defect density is sufficiently low to enable high lifetimes. Consequently, after phosphorus diffusion gettering, epi silicon exhibits a higher lifetime than materials with similar bulk impurity contents but higher densities of structural defects, including multicrystalline ingot and ribbon silicon materials. Device simulations suggest a solar-cell efficiency potential of this material >23%.
Annular spherically focused ring transducers for improved single-beam acoustical tweezers
Authors: Mitri F. G.
Published: February 2016

The use of ultrasonic transducers with a central hollow is suggested for improved single-beam acoustical tweezers applications. Within the framework of the Fresnel-Kirchhoff parabolic approximation, a closed-form partial-wave series expansion (PWSE) for the incident velocity potential (or pressure) field is derived for an annular spherically focused ring (asfr) with uniform vibration across its surface in spherical coordinates. The Rayleigh-Sommerfeld diffraction integral and the addition theorems for the Legendre and spherical wave functions are used to obtain the PWSE assuming a weakly focused beam (with a focusing angle α ≤ 20°). The PWSE allows evaluating the incident field from the finite asfr in 3D. Moreover, the obtained solution allows computing efficiently the acoustic scattering and radiation force on a sphere centered on the beam's axis of wave propagation. The analytical solution is valid for wavelengths largely exceeding the radius of the asfr and when the viscosity of the surrounding fluid can be neglected. Numerical predictions for the beam-forming, scattering, and axial time-averaged radiation force are performed with particular emphasis on the asfr thickness, the axial distance separating the sphere from the center of the transducer, the (non-dimensional) size of the transducer, as well as the sphere's elastic properties without restriction to the long- (i.e., Rayleigh) or the short-wavelength (i.e., ray acoustics) regimes. Potential applications of the present solution are in beam-forming design, particle tweezing, and manipulation due to negative forces using ultrasonic asfr transducers.
Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone
Authors: Ravi Kumar Venkatraman , Verma Chandra , Umapathy Siva
Published: February 2016

Solvent plays a key role in diverse physico-chemical and biological processes. Therefore, understanding solute-solvent interactions at the molecular level of detail is of utmost importance. A comprehensive solvatochromic analysis of benzophenone (Bzp) was carried out in various solvents using Raman and electronic spectroscopy, in conjunction with Density Functional Theory (DFT) calculations of supramolecular solute-solvent clusters generated using classical Molecular Dynamics Simulations (c-MDSs). The >C=O stretching frequency undergoes a bathochromic shift with solvent polarity. Interestingly, in protic solvents this peak appears as a doublet: c-MDS and ad hoc explicit solvent ab initio calculations suggest that the lower and higher frequency peaks are associated with the hydrogen bonded and dangling carbonyl group of Bzp, respectively. Additionally, the dangling carbonyl in methanol (MeOH) solvent is 4 cm−1 blue-shifted relative to acetonitrile solvent, despite their similar dipolarity/polarizability. This suggests that the cybotactic region of the dangling carbonyl group in MeOH is very different from its bulk solvent structure. Therefore, we propose that this blue-shift of the dangling carbonyl originates in the hydrophobic solvation shell around it resulting from extended hydrogen bonding network of the protic solvents. Furthermore, the 11nπ∗ (band I) and 11ππ∗ (band II) electronic transitions show a hypsochromic and bathochromic shift, respectively. In particular, these shifts in protic solvents are due to differences in their excited state-hydrogen bonding mechanisms. Additionally, a linear relationship is obtained for band I and the >C=O stretching frequency (cm−1), which suggests that the different excitation wavelengths in band I correspond to different solvation states. Therefore, we hypothesize that the variation in excitation wavelengths in band I could arise from different solvation states leading to varying solvation dynamics. This will have implications for ultrafast processes associated with electron-transfer, charge transfer, and also the photophysical aspects of excited states.
A one-piece 3D printed flexure translation stage for open-source microscopy
Authors: Sharkey James P. , Foo Darryl C. W. , Kabla Alexandre , Baumberg Jeremy J. , Bowman Richard W.
Published: February 2016

Open source hardware has the potential to revolutionise the way we build scientific instruments; with the advent of readily available 3D printers, mechanical designs can now be shared, improved, and replicated faster and more easily than ever before. However, printed parts are typically plastic and often perform poorly compared to traditionally machined mechanisms. We have overcome many of the limitations of 3D printed mechanisms by exploiting the compliance of the plastic to produce a monolithic 3D printed flexure translation stage, capable of sub-micron-scale motion over a range of 8 × 8 × 4 mm. This requires minimal post-print clean-up and can be automated with readily available stepper motors. The resulting plastic composite structure is very stiff and exhibits remarkably low drift, moving less than 20 μm over the course of a week, without temperature stabilisation. This enables us to construct a miniature microscope with excellent mechanical stability, perfect for time-lapse measurements in situ in an incubator or fume hood. The ease of manufacture lends itself to use in containment facilities where disposability is advantageous and to experiments requiring many microscopes in parallel. High performance mechanisms based on printed flexures need not be limited to microscopy, and we anticipate their use in other devices both within the laboratory and beyond.
Recurrence relations of the multi-indexed orthogonal polynomials. III
Authors: Odake Satoru
Published: February 2016

In Paper II, we presented conjectures of the recurrence relations with constant coefficients for the multi-indexed orthogonal polynomials of Laguerre, Jacobi, Wilson, and Askey-Wilson types. In this paper we present a proof for the Laguerre and Jacobi cases. Their bispectral properties are also discussed, which gives a method to obtain the coefficients of the recurrence relations explicitly. This paper extends to the Laguerre and Jacobi cases the bispectral techniques recently introduced by Gómez-Ullate et al. [J. Approx. Theory 204, 1 (2016); e-print arXiv:1506.03651 [math.CA]] to derive explicit expressions for the coefficients of the recurrence relations satisfied by exceptional polynomials of Hermite type.
Multiple product pathways in photodissociation of nitromethane at 213 nm
Authors: Sumida Masataka , Kohge Yasunori , Yamasaki Katsuyoshi , Kohguchi Hiroshi
Published: February 2016

In this paper, we present a photodissociation dynamics study of nitromethane at 213 nm in the π → π* transition. Resonantly enhanced multiphoton ionization spectroscopy and ion-imaging were applied to measure the internal state distributions and state-resolved scattering distributions of the CH3, NO(X 2Π, A 2Σ+), and O(3PJ) photofragments. The rotationally state-resolved scattering distribution of the CH3 fragment showed two velocity components, of which the slower one decreased the relative intensity as the rotational and vibrational excitations. The translational energy distribution of the faster CH3 fragment indicated the production of the NO2 counter-product in the electronic excited state, wherein 1 2B2 was the most probable. The NO(v = 0) fragment exhibited a bimodal translational energy distribution, whereas the NO(v = 1 and 2) fragment exhibited a single translational energy component with a relatively larger internal energy. The translational energy of a portion of the O(3PJ) photofragment was found to be higher than the one-photon dissociation threshold, indicating the two-photon process involved. The NO(A 2Σ+) fragment, which was detected by ionization spectroscopy via the Rydberg ←A 2Σ+ transition, also required two-photon energy. These experimental data corroborate the existence of competing photodissociation product pathways, CH3 + NO2,CH3 + NO + O,CH3O + NO, and CH3NO + O, following the π → π* transition. The origins of the observed photofragments are discussed in this report along with recent theoretical studies and previous dynamics experiments performed at 193 nm.
Computational study of the shock driven instability of a multiphase particle-gas system
Authors: McFarland Jacob A. , Black Wolfgang J. , Dahal Jeevan , Morgan Brandon E.
Published: February 2016

This paper considers the interaction of a shock wave with a multiphase particle-gas system which creates an instability similar in some ways to the Richtmyer-Meshkov instability but with a larger parameter space. As this parameter space is large, we only present an introductory survey of the effects of many of these parameters. We highlight the effects of particle-gas coupling, incident shock strength, particle size, effective system density differences, and multiple particle relaxation time effects. We focus on dilute flows with mass loading up to 40% and do not attempt to cover all parametric combinations. Instead, we vary one parameter at a time leaving additional parametric combinations for future work. The simulations are run with the Ares code, developed at Lawrence Livermore National Laboratory, which uses a multiphase particulate transport method to model two-way momentum and energy coupling. A brief validation of these models is presented and coupling effects are explored. It is shown that even for small particles, on the order of 1 μm, multi-phase coupling effects are important and diminish the circulation deposition on the interface by up to 25%. These coupling effects are shown to create large temperature deviations from the dusty gas approximation, up to 20% greater, especially at higher shock strengths. It is also found that for a multiphase instability, the vortex sheet deposited at the interface separates into two sheets. Depending on the particle and particle-gas Atwood numbers, the instability may be suppressed or enhanced by the interactions of these two vortex sheets.
Entropy production of doubly stochastic quantum channels
Authors: Müller-Hermes Alexander , Stilck França Daniel , Wolf Michael M.
Published: February 2016

We study the entropy increase of quantum systems evolving under primitive, doubly stochastic Markovian noise and thus converging to the maximally mixed state. This entropy increase can be quantified by a logarithmic-Sobolev constant of the Liouvillian generating the noise. We prove a universal lower bound on this constant that stays invariant under taking tensor-powers. Our methods involve a new comparison method to relate logarithmic-Sobolev constants of different Liouvillians and a technique to compute logarithmic-Sobolev inequalities of Liouvillians with eigenvectors forming a projective representation of a finite abelian group. Our bounds improve upon similar results established before and as an application we prove an upper bound on continuous-time quantum capacities. In the last part of this work we study entropy production estimates of discrete-time doubly stochastic quantum channels by extending the framework of discrete-time logarithmic-Sobolev inequalities to the quantum case.
Research Update: Structural and transport properties of (Ca,La)FeAs2 single crystal
Authors: Caglieris F. , Sala A. , Fujioka M. , Hummel F. , Pallecchi I. , Lamura G. , Johrendt D. , Takano Y. , Ishida S. , Iyo A. , Eisaki H. , Ogino H. , Yakita H. , Shimoyama J. , Putti M.
Published: February 2016

Structural and transport properties in the normal and superconducting states are investigated in a Ca0.8La0.2FeAs2 single crystal with Tc = 27 K, belonging to the newly discovered 112 family of iron based superconductors. The transport critical current density Jc for both field directions measured in a focused ion beam patterned microbridge reveals a weakly field dependent and low anisotropic behaviour with a low temperature value as high as Jc(B = 0) ∼ 105 A/cm2. This demonstrates not only bulk superconductivity but also the potential of 112 superconductors towards applications. Interestingly, this superconducting compound undergoes a structural transition below 100 K which is evidenced by temperature-dependent X-ray diffraction measurements. Data analysis of Hall resistance and magnetoresistivity indicate that magnetotransport properties are largely dominated by an electron band, with a change of regime observed in correspondence of the onset of a structural transition. In the low temperature regime, the contribution of a hole band to transport is suggested, possibly playing a role in determining the superconducting state.