Ion pairs in non-redundant protein structures

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 angstrom and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.

Kinetics of photocatalytic reduction of NO by CO with Pd2+-Ion-Substituted Nano-TiO2

The objective of the present study is to develop the reaction mechanism and kinetics of photoreduction of NO by CO. For this purpose, the reactions were conducted in the presence of Pd-ion-substituted nano-TiO2, Ti1-xPdxO2-delta, which was synthesized via a solution combustion method. The photocatalytic activity was investigated with unsubstituted TiO2, 1% Pd/TiO2(imp), and Ti1-xPdxO2-delta (where x = 0.05-0.3). No appreciable NO conversion was observed over unsubstituted TiO2, although, despite competitive adsorption of NO and CO on the Pd2+ sites, there was a significant reduction of NO over Ti1-xPdxO2-delta. The kinetic model showed that the enhanced catalytic activity is due to the NO photodissociation at the oxide-ion vacancy.

Ion channel gene variants predisposing to severe human ventricular arrhythmias

Congenital long QT syndrome (LQTS) with an estimated prevalence of 1:2000-1:10 000 manifests with prolonged QT interval on electrocardiogram and risk for ventricular arrhythmias and sudden death. Several ion channel genes and hundreds of mutations in these genes have been identified to underlie the disorder. In Finland, four LQTS founder mutations of potassium channel genes account for up to 40-70% of genetic spectrum of LQTS. Acquired LQTS has similar clinical manifestations, but often arises from usage of QT-prolonging medication or electrolyte disturbances. A prolonged QT interval is associated with increased morbidity and mortality not only in clinical LQTS but also in patients with ischemic heart disease and in the general population. The principal aim of this study was to estimate the actual prevalence of LQTS founder mutations in Finland and to calculate their effect on QT interval in the Finnish background population. Using a large population-based sample of over 6000 Finnish individuals from the Health 2000 Survey, we identified LQTS founder mutations KCNQ1 G589D (n=8), KCNQ1 IVS7-2A>G (n=1), KCNH2 L552S (n=2), and KCNH2 R176W (n=16) in 27 study participants. This resulted in a weighted prevalence estimate of 0.4% for LQTS in Finland. Using a linear regression model, the founder mutations resulted in a 22- to 50-ms prolongation of the age-, sex-, and heart rate-adjusted QT interval. Collectively, these data suggest that one of 250 individuals in Finland may be genetically predisposed to ventricular arrhythmias arising from the four LQTS founder mutations. A KCNE1 D85N minor allele with a frequency of 1.4% was associated with a 10-ms prolongation in adjusted QT interval and could thus identify individuals at increased risk of ventricular arrhythmias at the population level. In addition, the previously reported associations of KCNH2 K897T, KCNH2 rs3807375, and NOS1AP rs2880058 with QT interval duration were confirmed in the present study. In a separate study, LQTS founder mutations were identified in a subgroup of acquired LQTS, providing further evidence that congenital LQTS gene mutations may underlie acquired LQTS. Catecholaminergic polymorphic ventricular tachycardia (CPVT) is characterized by exercise-induced ventricular arrhythmias in a structurally normal heart and results from defects in the cardiac Ca2+ signaling proteins, mainly ryanodine receptor type 2 (RyR2). In a patient population of typical CPVT, RyR2 mutations were identifiable in 25% (4/16) of patients, implying that noncoding variants or other genes are involved in CPVT pathogenesis. A 1.1 kb RyR2 exon 3 deletion was identified in two patients independently, suggesting that this region may provide a new target for RyR2-related molecular genetic studies. Two novel RyR2 mutations showing a gain-of-function defect in vitro were identified in three victims of sudden cardiac death. Extended pedigree analyses revealed some surviving mutation carriers with mild structural abnormalities of the heart and resting ventricular arrhythmias suggesting that not all RyR2 mutations lead to a typical CPVT phenotype, underscoring the relevance of tailored risk stratification of a RyR2 mutation carrier.

Chemically Programmed Ultrahigh Density Two-Dimensional Semiconductor Superlattice Array

Designing an ultrahigh density linear superlattice array consisting of periodic blocks of different semiconductors in the strong confinement regime via a direct synthetic route remains an unachieved challenge in nanotechnology. We report a general synthesis route for the formulation of a large-area ultrahigh density superlattice array that involves adjoining multiple units of ZnS rods by prolate US particles at the tips. A single one-dimensional wire is 300-500 nm long and consists of periodic quantum wells with a barrier width of 5 nm provided by ZnS and a well width of 1-2 nm provided by CdS, defining a superlattice structure. The synthesis route allows for tailoring of ultranarrow laserlike emissions (fwhm approximate to 125 meV) originating from strong interwell energy dispersion along with control of the width, pitch, and registry of the superlattice assembly. Such an exceptional high-density superlattice array could form the basis of ultrahigh density memories in addition to offering opportunities for technological advancement in conventional heterojunction-based device applications.

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials. (C) 2009 Elsevier B.V. All rights reserved.

Magneto-transport and optical properties of diluted magnetic semiconductor Ga1-xMnxSb

We have studied magneto-transport and optical properties of Ga1-xMnxSb crystals (x = 0.01, 0.02, 0.03 and 0.04) grown by horizontal Bridgman method. Negative magnetoresistance and anomalous Hall effect have been observed below 10K. Temperature dependence of magnetization measurement shows a magnetic ordering below 10K which could arise from Ga1-xMnxSb alloy formation. Also, saturation in magnetization observed even at room temperature suggests the existence of ferromagnetic MnSb clusters. Reduction in band gap is observed with increasing Mn concentration in the crystals. Temperature dependence of band gap follows Bose-Einstein's model.

Dynamics of free-running, pump-modulated and coupled semiconductor and solid-state lasers

The output of a laser is a high frequency propagating electromagnetic field with superior coherence and brightness compared to that emitted by thermal sources. A multitude of different types of lasers exist, which also translates into large differences in the properties of their output. Moreover, the characteristics of the electromagnetic field emitted by a laser can be influenced from the outside, e.g., by injecting an external optical field or by optical feedback. In the case of free-running solitary class-B lasers, such as semiconductor and Nd:YVO4 solid-state lasers, the phase space is two-dimensional, the dynamical variables being the population inversion and the amplitude of the electromagnetic field. The two-dimensional structure of the phase space means that no complex dynamics can be found. If a class-B laser is perturbed from its steady state, then the steady state is restored after a short transient. However, as discussed in part (i) of this Thesis, the static properties of class-B lasers, as well as their artificially or noise induced dynamics around the steady state, can be experimentally studied in order to gain insight on laser behaviour, and to determine model parameters that are not known ab initio. In this Thesis particular attention is given to the linewidth enhancement factor, which describes the coupling between the gain and the refractive index in the active material. A highly desirable attribute of an oscillator is stability, both in frequency and amplitude. Nowadays, however, instabilities in coupled lasers have become an active area of research motivated not only by the interesting complex nonlinear dynamics but also by potential applications. In part (ii) of this Thesis the complex dynamics of unidirectionally coupled, i.e., optically injected, class-B lasers is investigated. An injected optical field increases the dimensionality of the phase space to three by turning the phase of the electromagnetic field into an important variable. This has a radical effect on laser behaviour, since very complex dynamics, including chaos, can be found in a nonlinear system with three degrees of freedom. The output of the injected laser can be controlled in experiments by varying the injection rate and the frequency of the injected light. In this Thesis the dynamics of unidirectionally coupled semiconductor and Nd:YVO4 solid-state lasers is studied numerically and experimentally.

Irradiation-mediated tailoring of carbon nanotubes

The ever-increasing demand for faster computers in various areas, ranging from entertaining electronics to computational science, is pushing the semiconductor industry towards its limits on decreasing the sizes of electronic devices based on conventional materials. According to the famous law by Gordon E. Moore, a co-founder of the world s largest semiconductor company Intel, the transistor sizes should decrease to the atomic level during the next few decades to maintain the present rate of increase in the computational power. As leakage currents become a problem for traditional silicon-based devices already at sizes in the nanometer scale, an approach other than further miniaturization is needed to accomplish the needs of the future electronics. A relatively recently proposed possibility for further progress in electronics is to replace silicon with carbon, another element from the same group in the periodic table. Carbon is an especially interesting material for nanometer-sized devices because it forms naturally different nanostructures. Furthermore, some of these structures have unique properties. The most widely suggested allotrope of carbon to be used for electronics is a tubular molecule having an atomic structure resembling that of graphite. These carbon nanotubes are popular both among scientists and in industry because of a wide list of exciting properties. For example, carbon nanotubes are electronically unique and have uncommonly high strength versus mass ratio, which have resulted in a multitude of proposed applications in several fields. In fact, due to some remaining difficulties regarding large-scale production of nanotube-based electronic devices, fields other than electronics have been faster to develop profitable nanotube applications. In this thesis, the possibility of using low-energy ion irradiation to ease the route towards nanotube applications is studied through atomistic simulations on different levels of theory. Specifically, molecular dynamic simulations with analytical interaction models are used to follow the irradiation process of nanotubes to introduce different impurity atoms into these structures, in order to gain control on their electronic character. Ion irradiation is shown to be a very efficient method to replace carbon atoms with boron or nitrogen impurities in single-walled nanotubes. Furthermore, potassium irradiation of multi-walled and fullerene-filled nanotubes is demonstrated to result in small potassium clusters in the hollow parts of these structures. Molecular dynamic simulations are further used to give an example on using irradiation to improve contacts between a nanotube and a silicon substrate. Methods based on the density-functional theory are used to gain insight on the defect structures inevitably created during the irradiation. Finally, a new simulation code utilizing the kinetic Monte Carlo method is introduced to follow the time evolution of irradiation-induced defects on carbon nanotubes on macroscopic time scales. Overall, the molecular dynamic simulations presented in this thesis show that ion irradiation is a promisingmethod for tailoring the nanotube properties in a controlled manner. The calculations made with density-functional-theory based methods indicate that it is energetically favorable for even relatively large defects to transform to keep the atomic configuration as close to the pristine nanotube as possible. The kinetic Monte Carlo studies reveal that elevated temperatures during the processing enhance the self-healing of nanotubes significantly, ensuring low defect concentrations after the treatment with energetic ions. Thereby, nanotubes can retain their desired properties also after the irradiation. Throughout the thesis, atomistic simulations combining different levels of theory are demonstrated to be an important tool for determining the optimal conditions for irradiation experiments, because the atomic-scale processes at short time scales are extremely difficult to study by any other means.

Applications of Gauge/Gravity Duality to QCD and Heavy Ion Collisions

The description of quarks and gluons, using the theory of quantum chromodynamics (QCD), has been known for a long time. Nevertheless, many fundamental questions in QCD remain unanswered. This is mainly due to problems in solving the theory at low energies, where the theory is strongly interacting. AdS/CFT is a duality between a specific string theory and a conformal field theory. Duality provides new tools to solve the conformal field theory in the strong coupling regime. There is also some evidence that using the duality, one can get at least qualitative understanding of how QCD behaves at strong coupling. In this thesis, we try to address some issues related to QCD and heavy ion collisions, applying the duality in various ways.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa

Purpose: Mutations in IDH3B, an enzyme participating in the Krebs cycle, have recently been found to cause autosomal recessive retinitis pigmentosa (arRP). The MDH1 gene maps within the RP28 arRP linkage interval and encodes cytoplasmic malate dehydrogenase, an enzyme functionally related to IDH3B. As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28. Methods: With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). PCR products were then sequenced by short-read UHTs with no further processing. Computer-based mapping of the reads and mutation detection were performed by three independent software packages. Results: Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. The two patients were homozygous for all DNA variants identified in the region, which confirms previous linkage and homozygosity mapping results, but had different haplotypes, indicating genetic or allelic heterogeneity. None of the DNA changes detected could be associated with the disease. Conclusions: The MDH1 gene is not the cause of RP28-linked arRP. Our experimental strategy shows that long-range genomic PCR followed by UHTs provides an excellent system to perform a thorough screening of candidate genes for hereditary retinal degeneration.