Angstrom Unit Research Articles

Python-based Program for Analysing Lattice Parameter of Cubic and Tetragonal Crystal Structure

A program for analysing lattice parameter of a crystal structure has been successfully created based on Python programming language using the Google Collaboratory service, so it can be accessed through a PC or smartphone as long as internet access is available. This program can be used to calculate lattice parameter of a crystal structure with x-ray diffraction data as the input. Crystal structures that can be calculated for its lattice parameter are cubic and tetragonal. The program will ask for the type of crystal structure of the data, along with diffraction angles and miller indices. The input will be processed using the Cramer-Cohen method according to the previously entered crystal structure. By also entering the wavelength used, the output of this program is the lattice parameter in the angstrom unit. The percentage of error of this program’s output is extremely low.

Estabilidad estructural y electrónica para la adsorción de Nb sobre la superficie polar del AlN


 
 
 
 Se reportan cálculos de primeros principios con el fin de analizar la adsorción y la difusión de un átomo de Nb en la superficie AlN (0001) con una geometría 2 × 2, la cual se construye con el modelo de supercelda. En los cálculos se resuelven las ecuaciones de Konh-Sham con una base de ondas planas y pseudopontenciales atómicos, para lo cual se utiliza la aproximación del gradiente generalizado (GGA) para describir la interacción electrón-electrón, dentro del marco de la teoría del funcional de la densidad (DFT). Con el propósito de estudiar el modelo de adsorción más favorable, se consideran los sitios de alta simetría T1, T4 y H3. Se encuentra que las estructuras energéticamente más favorables corresponden a la de un átomo de Nb localizado en los sitos H3 y T4, mientras que la adsorción del Nb sobre un átomo de aluminio (sitio T1) es desfavorable. La difusión del Nb sobre la superficie muestra una energía de activación de 0.453 eV de T4 hacia H3. Los resultados de las reconstrucciones adsorbato-superficie en los diferentes puntos de alta simetría presentan una relajación lateral de unas centésimas de angstrom con relación a su configuración más estable. Finalmente, se comparan la densidad de estados de la superficie limpia AlN(0001) y las reconstrucciones que presentan mayor favorabilidad energética.
 
 
 

Functional Nanomaterials: From Basic Science to Emerging Applications

Moores law predicts the reduction of the device elements size and the advancement of physics with time for the next generation microelectronic industries. Materials and devices sizes and enriched physics are strongly correlated phenomena. Everyday physics moves a step forward from microscale classical physics toward nanoscale quantum phenomenon. Similarly, the vast micro/nanoelectronics needs advancement in growth and characterization techniques and unexplored physics to cope with the 21stcentury market demands. The continuous size reduction of devices stimulates the researchers and technocrats to work on nanomaterials and devices for the next generation technology. The semiconductor industry is also facing the problem of size limitation and has followed Moores law which predicts 16 nm nodes for next generation microelectronic industries. Nanometer is known as the 10 times of an Angstrom unit, where it is common consensus among the scientists that any materials and devices having physical dimensions less than 1000 times of an Angstrom will come under the umbrella of Nanotechnology. This review article focuses on the fundamental aspects of nanoscale materials and devices: (i) definitions and different categories of nanomaterials, (ii) quantum scale physics and technology, (iii) self-assembed nanostructures, (iv) growth conditions and techniques of 0D, 1D, 2D, and 3D dimensional materials, (v) understanding of the multifunctionalities of the nanomaterials, (vi) nanoscale devices for low energy consumption and fast response, (vii) integration of nanoscale materials with Si-based systems, and (viii) major technical challenges.

In Silico Docking of HNF-1a Receptor Ligands.

Background. HNF-1a is a transcription factor that regulates glucose metabolism by expression in various tissues. Aim. To dock potential ligands of HNF-1a using docking software in silico. Methods. We performed in silico studies using HNF-1a protein 2GYP·pdb and the following softwares: ISIS/Draw 2.5SP4, ARGUSLAB 4.0.1, and HEX5.1. Observations. The docking distances (in angstrom units: 1 angstrom unit (Å) = 0.1 nanometer or 1 × 10−10 metres) with ligands in decreasing order are as follows: resveratrol (3.8 Å), aspirin (4.5 Å), stearic acid (4.9 Å), retinol (6.0 Å), nitrazepam (6.8 Å), ibuprofen (7.9 Å), azulfidine (9.0 Å), simvastatin (9.0 Å), elaidic acid (10.1 Å), and oleic acid (11.6 Å). Conclusion. HNF-1a domain interacted most closely with resveratrol and aspirin

Semiempirical evaluation of the global hardness of the atoms of 103 elements of the periodic table using the most probable radii as their size descriptors

AbstractRelying upon the fact that the density functional computation of the global hardness of the atoms of the elements are still at large and there is some mathematical in congruency between the theory and operational formula of finite difference approximation, we have suggested a radial‐dependent ansatz for evaluating global hardness of atoms as: η=a(7.2/r)+b (in eV), where, “a” and “b” are the constants and r is the absolute radius of atoms in angstrom unit. The ansatz is invoked to evaluate the global hardness of atoms of 103 element of the periodic table. The evaluated new set of global hardness is found to satisfy the sine qua non of a reasonable scale of hardness by exhibiting perfect periodicity of periods and groups and correlating the gross physicochemical properties of elements. The inertness of Hg and extreme reactivity Cs atoms are nicely correlated. The chemical reactivity and its variation in small steps in the series of lanthanide elements are also nicely reproduced. The results of the present semiempirical calculation also have strong correlation with the result of some sophisticated DFT calculation for a set of atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Adaptive Brownian Dynamics for Shape Estimation of Sodium Ion Channels

Ion channels are protein macromolecules that form biological nanotubes across the membranes of living cells. Given many possible geometrical shapes of an ion channel, we propose a computational scheme of selecting the model that best replicates experimental observations, using adaptive Brownian dynamics simulations together with discrete optimization algorithms. Brownian dynamics simulations emulate the propagation of individual ions through the sodium channel nanotube at a femto time second time scale and Angstrom unit (10(-10) meter) spatial scale.

Adaptive Brownian Dynamics Simulation for Estimating Potential Mean Force in Ion Channel Permeation

Ion channels are biological nanotubes formed by large protein molecules in the cell membrane. This paper presents a novel multiparticle simulation methodology, which we call adaptive controlled Brownian dynamics, for estimating the force experienced by a permeating ion at each discrete position along the ion-conducting pathway. The profile of this force, commonly known as the potential of mean force, results from the electrostatic interactions between the ions in the conduit and all the charges carried by atoms forming the channel the protein, as well as the induced charges on the protein wall. The current across the channel is solely determined by the potential of mean force encountered by the permeant ions. The simulation algorithm yields consistent estimates of this profile. The algorithm operates on an angstrom unit spatial scale and femtosecond time scale. Numerical simulations on the gramicidin ion channel show that the algorithm yields the potential of mean force profile that accurately reproduces experimental observations.

SHAPE ESTIMATION OF BIOLOGICAL NANOTUBES USING CONTROLLED BROWNIAN DYNAMICS SIMULATION ALGORITHM

Ion channels are protein macromolecules that form biological nanotubes in the cell membrane of living cells. In this paper we use a parameterized molecular structure to formulate the ion channel shape estimation as a discrete stochastic optimization problem. We use Brownian dynamics simulations controlled with discrete stochastic optimization algorithms to estimate the shape of Sodium ion channels. The Brownian dynamics simulation emulates the propagation of individual ions through the Sodium ion channel nanotube at a femto time second time scale and Angstrom unit (10–10 meter) spatial scale. The algorithms presented in this paper are provably convergent. In numerical studies that use experimental measurements of an actual Sodium ion channel, we show that the proposed algorithms efficiently learn the shape of Sodium ion channels.

Research in Medical Sciences

THE experiments of Faraday on electricity and of Helmholtz on heat and on light were incorporated during the latter half of the nineteenth century into a comprehensive electromagnetic theory inter relating light and electric and magnetic fields. Clerk Maxwell (1831-79) proposed the theory that light waves consist of oscillating electric fields at right angles to which are magnetic fields. The velocity of light, three hundred million meters (or 186,000 miles) per second, is the same for impulses of short and long wave-lengths and is one of the most impor tant of physical constants, comparable in its universality to the force of gravity. Indeed Einstein, in 1905, deduced, in terms of the velocity of light, the relation between mass and energy which made possible the prediction of atomic fission. Since the velocity is the same for all electromagnetic waves, includ ing light, differences in property are associated with the length of the wave or with its frequency. The propagation of electromagnetic waves, first studied by Hertz (1857-94), led to wireless telegraphy. Improve ments in technique have made it possible to transmit both very long and very short wave-lengths, ranging from centimeters to thousands of meters. The bands of the modern radio generally extend from 150 to 600 meters. Waves of these lengths may be absorbed by biological sys tems and give rise to considerable heating effects. Radio waves are very long in comparison with those of visible light, which range from about 0.0000007 meters, characteristic of red light, to about 0.0000004 meters for violet light. For convenience, different units are generally used in describing waves of short length, namely Angstrom units, one Angstrom unit being equal to one billionth of a meter. In these terms, red light has a wave length of 7,000 and violet light of 4,000 Angstrom units. The visibility of cells through the microscope depends upon the fact that their diameters are of the same order as the wave-length of light. Objects smaller than cells cannot be observed with ordinary light even through the most powerful microscope. In 1895, Wilhelm R?ntgen (1845-1923), studying the discharge of electricity through gases, noted that photographic plates, placed near the tubes, fogged when the gas in the tubes was largely exhausted. The action was not due to light, but to very short electromagnetic waves which passed through the tubes. The chance nature of the observation of this previously unknown type of radiation, X ray, is reminiscent of Galvani's earlier observation of the nature of electricity and of Bec querel^ later observation of radioactivity. In each instance, discoveries in new fields of the greatest importance were made because, to quote the

Mercury intrusion porosimetry, nitrogen adsorption, and scanning electron microscopy analysis of pores in skin.

Stability of collagenous matrixes such as skin and leather with respect to changes in their dimensions on heating has long been correlated with degree and type of cross links formed and short-range ordering in angstrom unit scales. Macroscopic dimensional changes may be expected to involve alterations in the long-range order as well as supramolecular assemblies in skin and leather. This study relates thermal shrinkage of skin matrixes with alterations observed in micro-, meso-, and macroporic structures. Changes in the pore structure of skin associated with thermal shrinkage have been studied using nitrogen adsorption and mercury intrusion porosimetry measurements. A comparison of results obtained using both techniques has been made. These results indicate that although the percentage porosity of the matrix decreases, the BET specific surface area increases on shrinkage. An insight into the changes in the pore systems of skin induced by thermal shrinkage has been gained.

Is the reduction of mental phenomena an attainable goal?

In science, whenever a lower level explanation is sufficient, it becomes paramount. This paper addresses the proposition that the same will happen for human behaviour. The author considers differen...

X-ray standing waves—a new method of studying the structure of crystals

The physical nature, potentialities, and prospects of application of a new method of studying the structure of crystals and thin surface layers is discussed. It is based on recording secondary radiations such as external and internal photoelectron emission, as well as x-ray fluorescence, under conditions of dynamic x-ray diffraction in single crystals, in which the intensity of the radiation field in the crystal reproduces the periodicity of the crystal lattice in the form of a standing wave along the diffraction vector. The method allows one to measure the absolute displacements of atomic planes in the crystal in fractions of an Angstrom unit, and also to determine the degree of order in the arrangement of atoms in the surface layer. In addition to presenting the history of the problem and reviewing the most important studies published in this field in the past twenty years, the problems of the theory and the experimental technique of the method of standing x-ray waves are presented in considerable detail.

Prospects for a gamma-ray laser

Lasers generating wavelengths shorter than one angstrom unit would have many important applications. Ever since the discovery of the Mössbauer effect it has been realized that we would be able to stimulate nuclear transitions suitable for lasers in this range if we could prepare the population inversion on which lasers depend, and it has also long been known that some nuclear isomers are producible in a state of population inversion. Why then do we not yet have any operating gamma-ray lasers?

A proton magnetic relaxation study of ferrimyoglobin in aqueous ionic solutions

Proton magnetic longitudinal T 1 relaxation times have been measured for acid (horse) ferrimyoglobin solutions [0.1 M NaCl and KH 2PO 4, 2 M NaCl and 1 M MgCl 2] from 5°C to 35°C in dependence on myoglobin concentration up to 6 mM. The enhancement of the relaxation rate due to the paramagnetic haem iron. which is observed in this temperature range is compared with analogous data for the ferrihaemoglobin solution. The conclusion is that the protons exchanging from the haem pocket with bulk solvent are not those from the water molecule at the sixth ligand site of haem iron. The exchanging protons are more than 4 Å away from the haem iron being closer to it in ferrimyoglobin than in ferrihaemogiobin. This distance becomes larger in solutions with higher salt concentration, the largest difference between 0.1 M NaCl and 1 M MgCl 2 being over one Angstrom unit. This indicates a conformational change of the haem pocket, possibly its tightening.

Liquid Surface Tension near the Triple Point

It is shown that the product of the isothermal compressibility ξ and surface tension Σ of a liquid near its triple point may be expected to be a fundamental length characteristic of the liquid. From experimental data on 30 liquids (including liquid metals) it is observed that while ξ and Σ separately vary by a factor of 150, the product ξΣ varies by a factor of less than 3 and is equal always to a few tenths of an angstrom unit.

Nuclear magnetic resonance determination of ligand-induced conformational changes in myoglobin

We report the results of a high-resolution proton nuclear magnetic resonance at 220 MHz of deoxymyoglobin and three diamagnetic complexes of myoglobin with oxygen, carbon monoxide and ethylisocyanide. We emphasize the resonances which are shifted from their normal positions by ring currents from aromatic rings, particularly the porphyrin ring, because these ring current shifts are very sensitive to changes of the relative co-ordinates of the observed protons and the ring. A specific resonance at −6.1 p.p.m., with intensity of about three protons, has been attributed to the protons of an aromatic residue, shifted upfield by the ring currents of the heme group. A possible origin of this resonance is Phe CD1. The observed change of this resonance of 0.2 p.p.m. upon oxygenation corresponds to a movement of a few tenths of an angstrom unit. Slightly larger shifts upon oxygenation of resonances attributed to methyl groups of aliphatic residues are interpreted in terms of movements of about 0.5 Å. A comparison of the complete spectra of Mb ‡ and MbO 2 shows that there are many small differences of 0.1 to 0.2 p.p.m. which indicate widespread small structural changes upon oxygenation. Differences in the ring-current-shifted resonances amongst various ligated forms including cyanoferrimyoglobin, indicate the existence of structural differences in the protein when the ligand is changed.

X-ray Moiré Topography of Lattice Defects in Quartz

The X-ray moire topograph displays a map of mismatch between the lattices of two crystals. From moire fringe patterns the lattice displacements due to dislocations and other crystal defects can be measured to a fraction of an Angstrom unit.

EFFECT OF ACCESSORY ELEMENTS ON THE UNIT CELL EDGE OF β ZnS MINERALS

Sixty sphalerite samples were collected from various mines in Japan. Ore deposits of Oe (Hokkaido), Toyoha (Hokkaido), Namariyama (Akita Prefecture), Nikkatsu (Akita Pref.) and Kuroiwa mines (Fukushima Pref.) are vein type deposits, those of Hanawa (Akita Pref.), Yoshino (Yamagata Pref) Yonaihata (Fukushima Pref.) and Kidogasawa (Tochigi Pref.) mines are so-called Kuroko type deposits, while Hitachi mine is a Kieslager type deposit. From the results of chemical analyses and X-ray measurements on sixty sphalerite samples, it has been recognized that natural β ZnS minerals consist of the β1 sphalerite and β2 sphalerite. The unit cell edges in β1 sphalerites are determined by Fe, Mn and Cd content dissolved in this minerals, and the equations of relation between unit cell edges and FeS content in this minerals are shown a0=5.4103+0.000717 X and a0=5.4124+0.000349X. a0 is in Angstrom unit and X is mole % FeS, and both these equations are continuous. The solubility of Mn in β1 sphalerite increase with an increasing FeS content, so that it is a function of the temperature and pressure as well as the variation of FeS content. The correlation between Fe and Cd is random, but the variation of Cd solubility is constant. From the variations of Fe, Mn and Cd content, β1 ZnS system is divided into β1 (Zn, Fe, Cd)S and β1 (Sn, Fe, Mn)S system. Also the equation of β2 sphalerite is shown by a0=5.4093+0.000290X.

A NEW METHOD OF POLARIZATION MICROSCOPIC ANALYSIS. I. SCANNING WITH A BIREFRINGENCE DETECTION SYSTEM.

A new method of polarized light analysis is described in which a highly sensitive electronic detector specific for birefringence is used to identify the crystalline axes of an object and then measure its phase retardation due to birefringence. The microscopic system employed in the method consists of an electronic birefringence detection system (BDS), a microscope with strain-free lenses, and a driven stage for passing the specimen at appropriate velocities across the image of an aperture placed at the field stop and imaged in the specimen plane by the condenser. The detector registers retardations directly as voltage at a constant deflection sensitivity of ca. 1.1 v per angstrom unit over a range of 120 angstrom units. The basal rms noise level is 0.002 A for a spot 36 micro in diameter formed by a 95 x, N. A. 1.25 objective pair, and increases in proportion to the reciprocal of the diameter of the scanning spot. The increase in noise with high resolution scanning can be offset by increasing the instrumental time constant, which is adjustable in decades between 0.004 and 0.4 seconds. A number of difficult problems in high extinction polarization microscopy are avoided by the use of modulated light and a rapid electronic detector. For example: (a) The measured distribution of birefringence is unaffected by the usual diffraction anomaly; therefore polarization rectifiers are not required. (b) The detector is selective for birefringence, so that there is no problem in separating contrast due to different optical properties (e.g. dichroism, light scattering). (c) The speed and sensitivity are both increased by between one and two orders of magnitude over that attainable by visual or photographic methods, thereby rendering a vast number of weakly birefringent, light-scattering, and motile objects readily analyzable for the first time with polarized light.

Effect of Specimen Delocalization in Electron Diffraction Studies of Gas Molecules

The effect upon a normal electron diffraction pattern of an extraneous uniform distribution of the gaseous specimen is considered quantitatively. It is shown that the delocalization of gas may lead to errors in internuclear distances of several thousandths of an Angstrom unit or more in conventional experiments. Equations are presented for the correction of experimental data.