Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate ...

Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation ...

Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly ...

We describe a new, computationally effcient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed ...

BackgroundSequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the ...

... This system is designed to provide a faster and more accurate optical alignment of the pinhole and the device under test. ...

We use extreme-ultraviolet interferometry to measure the phase of high-order harmonic generation from transiently aligned CO(2) molecules. We unambiguously observe a reversal in phase of the high-order harmonic emission for higher harmonic orders with a sufficient degree of alignment. This results from molecular-scale quantum ...

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of ...

Alignment of macromolecules in nearly neutral aqueous lyotropic liquid-crystalline media such as bicelles, commonly used in macromolecular NMR studies, can be predicted accurately by a steric obstruction model (Zweckstetter and Bax, 2000). A simple extension of this model is described that results in improved predictions for both the ...

Page 1. Guidance Methods for Accurate In�Flight Alignment of Navy Theatre Wide Missiles 15 May 2001 ... Page 9. In-Flight Alignment Metric � ADOP � ...

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently ...

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently ...

Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

Efficient and safe operation of a laser requires precise alignment of the resonator. This paper describes a method for aligning an unstable resonator very accurately with off-axis injection of the alignment beam ultilizing multiple reflections of the Gaussian beam inside the resonator.

Comparing and classifying the three-dimensional (3D) structures of proteins is of crucial importance to molecular biology, from helping to determine the function of a protein to determining its evolutionary relationships. Traditionally, 3D structures are classified into groups of families that closely resemble the grouping according to their primary sequence. However, ...

For a laser driven molecule, we show that the ionization and the dissociation channels can be separated by preparing the molecule in a specific vibrational state. Specifically, we investigate the dynamics of the hydrogen molecular ion under a femtosecond infrared laser field aligned with the molecular axis. We find dissociation ...

... Title : Flat, Straight, Square, Parallel: Laser Alignment Tools Provide a Fast, Accurate Way to Keep Machine Tools in Line for Precision Cutting. ...

We report a magnetic determination of H_c2 for accurate alignment along the in-plane, inter-chain b-direction for the molecular organic superconductor (TMTSF)_2ClO_4. A number of recent studies, including resistively-determined H_c2 for this special direction, have indicated spin triplet superconductivity in this system. From ...

A measuring system is described for surveying and very accurately positioning objects with respect to a reference line. A principle use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a part...

The effects of electric fields on the molecular alignment in the liquid crystal p-(anisalamino)-phenyl acetate are discussed. The behavior of this material is similar to that of p-azoxyanisole in that the ordering which is normally observed shows an align...

. Adamantane Fragments This is a synthetic case created to test the molecular alignment functionality, where the pharmacophore points chosen have no chemical or therapeutic significance. The adamantane molecule, which has and the branching point of the chain, as shown in Figure 1. However, when they are aligned with adamantane

This report documents the design and operation of the particle beam alignment system developed for single event upset - Van de Graaff experiments. This system is designed to provide a faster and more accurate optical alignment of the pinhole and the devic...

This work provides a method of mechanical alignment of an array of single mode fibers to an array of optical devices. The technique uses a micromachined metal spring, which captures a vertical, pre- positioned fiber, moves it into accurate alignment, and ...

Understanding interface properties of nano- and hybrid- materials at molecular level is of critical importance for fostering technological advancements. While the density functional theory (DFT) continues to be an important method for investigating opto-electronic and excitation properties of materials, the DFT calculations in some cases fail to provide an ...

... Schmoker et al. for the stabilization of bone grafts following partial resection of tumors of the mandible. The technique of ...

and accurately aligned laser assembly that is capable of fast data Processing. producing ultra short pulses at a high repetition rate. It ...

SPAC (sequence protein alignment with composition) is a software that retrieve from protein or nucleic acid databases, the sequences corresponding to a protein or peptide whose only amino acid composition and molecular weight are known. By accurately matching a DNA or a protein sequence to candidate protein or peptide fragment, this ...

When aligning RNAs, it is important to consider both the secondary structure similarity and primary sequence similarity to find an accurate alignment. However, algorithms that can handle RNA secondary structures typically have high computational complexity that limits their utility. For this reason, there have been a number of attempts ...

The main peak in the autocorrelation function of bar codes is here utilized as the signal of accurate alignment. Attention is therefore directed to the problem of how to increase the contrast of the main autocorrelation peak above the remaining part of the correlation signal and to the problem concerned with the upper limit that the contrast may attain. To ...

We perform an accurate polarimetry measurement of high-order harmonic emission from aligned molecules. We find that harmonic emission from N2 can be strongly elliptically polarized even when driven by linearly polarized laser fields. These data have broad implications for understanding molecules in strong fields because they cannot be explained by simple ...

Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pairwise alignments are global ...

We directly measure the field-free molecular alignment of various room-temperature molecular gases based on alignment-induced spatial focusing and defocusing effects. By imaging the spatial profile of a time-delayed probe pulse with increased and decreased local intensity at the beam center, the parallel and ...

Comparing and classifying the three-dimensional (3D) structures of proteins is of crucial importance to molecular biology, from helping to determine the function of a protein to determining its evolutionary relationships. Traditionally, 3D structures are classified into groups of families that closely resemble the grouping according to their primary sequence. However, ...

The study purposed to determine if a navigation in total knee arthroplasty (TKA) leads to accurate limb alignment and component position than the conventional technique as measured by full length standing radiographs and to evaluate the correlation between navigation and radiographic measurements. A total of 160 knees underwent navigation (n = 80) or ...

1 Introduction In comparative structural biology studies, analyzing or predicting protein three-dimensional structure often begins with identifying patterns of amino acid substitution via protein sequence alignment. While the evolutionary informationobtained from alignments can provide insights into protein structure, constructing ...

We present a computational study of the rotational molecular dynamics of bromotrifluoromethane (CF{sub 3}Br) molecules in gas phase. The rotation is manipulated with an off-resonant 800 nm laser. The molecules are treated as rigid rotors. Frequently, we use a computationally efficient linear rotor model for CF{sub 3}Br, which we compare with selected results for full ...

We present a computational study of the rotational molecular dynamics of bromotrifluoromethane (CF3Br) molecules in gas phase. The rotation is manipulated with an offresonant, 800nm laser. The molecules are treated as rigid rotors. Frequently, we use a computationally efficient linear rotor model for CF3Br which we compare with selected results for full symmetric-rotor ...

We study molecular alignment by trains of strong, ultrashort laser pulses. Single-pulse alignment is analyzed both in classical and quantum-mechanical regimes. Moreover, we suggest multipulse excitation schemes leading to dramatically enhanced molecular alignment, and define conditions for ...

and inappropriate ordering of the molecular drug-resistance tests. The molecular drug-resistance testing services should be aligned or coordinated with the services of the TB...

Laser-optic alignment systems are fast becoming cost-effective devices that improve the accuracy and speed of machinery shaft alignment. Because of the difficulty, if not impossibility, of aligning operating machinery, cold alignment specifications must be determined to compensate for thermal growth so that the ...

This paper discusses how laser-optic alignment systems can be employed effectively to detect and accurately measure rotary machinery shaft alignment while the machinery is running. These measurements can be used to maintain proper alignment at operating conditions. One of the many significant factors influencing ...

The quantitative rescattering theory (QRS) for high-order harmonic generation (HHG) by intense laser pulses is presented. According to the QRS, HHG spectra can be expressed as a product of a returning electron wave packet and the photorecombination differential cross section of the laser-free continuum electron back to the initial bound state. We show that the shape of the returning electron wave ...

We propose a novel method for detecting sites of molecular recombination in multiple alignments. Our approach is a compromise between previous extremes of computationally prohibitive but mathematically rigorous methods and imprecise heuristic methods. Using a combined algorithm for estimating tree structure and hidden Markov model parameters, our program ...

We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDC) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein ...

We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While ...

The chemical shifts of nuclei that have chemical shielding anisotropy, such as the 15N amide in a protein, show significant changes in their chemical shifts when the sample is altered from an isotropic state to an aligned state. Such orientation-dependent chemical shift changes provide information on the magnitudes and orientation of the chemical shielding tensors relative to ...

BackgroundAccurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resulting in alignments that are not always correct. Refinement of existing ...

To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions ...

We report an experimental study of the control of molecular alignment of N{sub 2} by use of spectrally modulated pulses at an intensity regime below the intrinsic saturation of the alignment. By manipulating the relative timing of the alignment revival pattern arising from the even subset of the thermal ensemble as ...

... Title : Microsatellite Alterations as Molecular Markers in Breast ... lack of early and accurate markers of disease. ... utility of a novel marker, the enzyme ...

... Title : Microsatellite Alterations as Molecular Markers in Breast ... lack of early and accurate markers of disease. ... utility of a novel marker, the enzyme ...

Multiple sequence alignment as a means of comparing DNA, RNA, or amino acid sequences is an essential precondition for various analyses, including structure prediction, modeling binding sites, phylogeny, or function prediction. This range of applications implies a demand for versatile, flexible, and specialized methods to compute accurate ...

The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider. For the reconstruction of charged particles, and their production and their decay vertices, ATLAS is equipped with a sophisticated tracking system, unprecedented in size and complexity. Full exploitation of both the Inner Detector and the muon ...

Interferometrically measured system wavefronts combined with a differential ray-traced lens model are used to determine alignment adjustments to a lens system. This is achieved by minimizing the difference between measured and ray-traced wavefronts by means of a damped least-squares method, without information regarding individual surface shapes or misalignment sources in the ...

Effects of high pressure or radiation-induced cross-linking of synthetic rubbers and polymerization of methacrylates and acrylonitrile (AN) have been studied paying attention to molecular motion and alignment. The following were revealed from radiation-in...

Steric effect for the XeBr* (B, C) formation in the oriented Xe*(3P2, MJ=2)+oriented CF3Br reaction has been observed as a function of the mutual configuration between the molecular orientation and the atomic orientation in the collision frame. Molecular steric opacity function has been determined as a function of the atomic orbital ...

A simple and accurate stowage drum and capstan alignment system and method for the Deployable Array Work Group (DAWG) is provided. The system includes a drum reference point fixture for obtaining the drum centerline, a drum sighting assembly and a capstan...

A structural alignment sensor (SAS) was developed for use with large deployable antenna systems for contour measurement and/or active control. The SAS is a laser ranging system using frequency modulation and accurate phase measurement to determine distanc...

Accurate alignment and focus of mirror facets are critical for the integration of concentrators and receivers in many of the low-cost stretched-membrane concentrators currently under development. In this report, the theoretical development of computer sof...

Distributed point-focusing solar concentrators are being developed for dish-Stirling systems and other applications. Many of these concentrators make use of faceted mirrors that have to be accurately aligned. Some of the solar concentrator designs use str...

There are two major goals driving the requirements for alignment and measurement of the detector being designed by the Solenoidal Detector Collaboration (SDC). First is each subsystem's goal of measuring its particular physics data as accurately as possib...

2D measurement of human joint motion involves analysis of 3D displacements in an observer selected measurement plane. Accurate marker placement and alignment of joint motion plane with the observer plane are difficult. Alignment of the two planes is essen...

Accurate alignment of pencil beam eye shields to protect the lens of the eye may be made easier by means of a simple modification of existing apparatus. This involves drilling a small hole through the center of the shield to isolate the rayline directed to the lens and fabricating a suitable plug for this hole.

We apply density functional theory with empirical Hubbard U parameter (DFT+U) to study Mn-based molecular magnets. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the spin density onto acetate ligands due to pi-back bonding, inverting spin ...

We apply density functional theory with empirical Hubbard U parameter (DFT+U) to study Mn-based molecular magnets. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the spin density onto acetate ligands due to ?-back bonding, inverting spin ...

... the application. Acknowledgements This work is supported in part by US AOARD-05-4057 and Samsung Electronics. SH ...

The creation of materials with sub-100 nm functional architectures is a challenge in nanotechnology. Two ways to create nanostructures are: (i) self-assembly of small molecules into supramolecular structures; and (ii) design of shape-persistent macromolecules. Molecular brushes are ideal candidates as one can control size, shape, interior structure, and surface composition ...

In this article, we introduce PicXAA-Web, a web-based platform for accurate probabilistic alignment of multiple biological sequences. The core of PicXAA-Web consists of PicXAA, a multiple protein/DNA sequence alignment algorithm, and PicXAA-R, an extension of PicXAA for structural alignment of RNA sequences. Both ...

Two approaches for directly computing a molecular heat of formation based on sophisticated ab initio

... Descriptors : *ENERGETIC PROPERTIES, QUANTUM ... MOLECULAR DYNAMICS, CHEMICAL REACTIONS ... THRUST, QUANTUM CHEMISTRY ...

Accurate placement of hundreds of focused laser beams on target is necessary to achieve success in the National Ignition Facility (NIF). The current system requirement is {le}7 {mu}rad error in output pointing and {le}1 mm error in focusing. To accommodate several system shots per day, a target alignment system must be able to align ...

MOTIVATION: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new ...

The spindle assemble checkpoint (SAC) is critical for accurate chromosome segregation. Hec1 contributes to chromosome segregation in part by mediating SAC signaling and chromosome alignment. However, the molecular mechanism for Hec1 to modulate checkpoint signaling and alignment remains poorly understood. We found ...

To achieve accurate registration, the transformations which locate the tracking system components with respect to the environment must be known. These transformations relate the base of the tracking system to the virtual world and the tracking system's se...

Image 1: I managed to accurately polar align my mount such that the comet spent an additional ten minutes placed behind the neighbor's air conditioner after ...

7.2.2 GPS Analysis, IVP Determination, Alignment and SINEX. ... accurate connections and their associated variance covariance matrix, and provided an un- ...

Meadowlark Optics, A liquid beam steerer to align accurately laser beams for precise distant measurement (metrology). Pixel Vision, A 20000-frame-per-second ...

Parallax of a thin rotatable glass plate gives accurate compensation of the position of a laser beam used in the outside illumination of a sample in a vacuum system. (Author)

This study aimed to determine limb and component alignment after computer-assisted total knee arthroplasty in 30 patients (32 limbs) with an altered hip center due to a prior hip implant or deformed femoral head. There were no outliers greater than �3� in the postoperative coronal alignment of the limb and the femoral component in relation to the ...

A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the �structural alignment� space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a ...

It is attempted to show that the Stieltjes-moment-theory provides a practical and a reasonably accurate method for calculating the widths of molecular resonances. The method seems to possess a number of advantages for molecular applications, since it avoi...

The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which ...

We report theoretical calculations of high-order harmonic generation (HHG) by intense infrared lasers in atomic and molecular targets taking into account the macroscopic propagation of both fundamental and harmonic fields. On the examples of Ar and N2, we demonstrate that these ab initio calculations are capable of accurately reproducing available ...

Polarimetry in the far-infrared and submillimeter has been valuable in tracing magnetic fields in bright Galactic Clouds. We discuss the techniques we have developed and trends we have found in polarization vs column density, and vs wavelength. The polarization spectrum has proven to be more interesting than had been anticipated. It is potentially valuable in explaining grain ...

Many future mission models require large space (LSS) which have accurate surfaces and/or the capability of being accurately aligned. If ground test approaches which will provide adequate confidence of the structrual performance to the program managers are...

A three-dimensional registration and alignment algorithm was developed to align single photon emission computed tomography examinations and magnetic resonance images. Operators manipulated images interactively with real-time visual feedback, with use of both internal and surface features to achieve accurate ...

Accurate alignment of the electron and ion beams in the RHIC electron cooling solenoids is crucial for well-optimized cooling. Because of the greatly differing rigidities of the electron and ion beams, to achieve the specified alignment accuracy it is required that transverse magnetic fields resulting from imperfections in solenoid ...

Three exciting new methods that address the accurate prediction of processes and properties of large molecular systems are discussed. The systematic fragmentation method (SFM) and the fragment molecular orbital (FMO) method both decompose a large molecula...

The CORBA-based Simulator was a Laboratory Directed Research and Development (LDRD) project that applied simulation techniques to explore critical questions about distributed control systems. The simulator project used a three-prong approach that studied object-oriented distribution tools, computer network modeling, and simulation of key control system scenarios. The National Ignition ...

We propose a scheme to enhance the field-free molecular alignment by shaping the femtosecond laser pulse with cubic phase modulation. We show that the molecular alignment can be obtained adiabatically during the shaped pulse and can be revived at the full rotational periods with the same degree as that at the peak ...

BackgroundAccurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence ...

The surface molecular alignment in a sandwich cell showing V-shaped switching has been investigated using a photocontrolling method. The results indicate that the molecules on the rubbed surface are aligned parallel to the rubbing direction as in an open cell with an air--liquid crystal boundary. This alignment is ...

As the global market for fisheries and aquaculture products expands, mislabeling of these products has become a growing concern in the food safety arena. Molecular species identification techniques hold the potential for rapid, accurate assessment of proper labeling. Here we developed and evaluated DNA barcodes for use in differentiating United States ...

A local text alignment algorithm is introduced in this work for synchronizing transcripts. The proposed algorithm can be used for any transcript alignment process where high computational complexity is a concern. Dynamic programming is typically used to align a set of transcripts: however, the computational complexity of dynamic ...

Errors in the inferred multiple sequence alignment may lead to false prediction of positive selection. Recently, methods for detecting unreliable alignment regions were developed and were shown to accurately identify incorrectly aligned regions. While removing unreliable alignment regions is ...

We present two heuristics for speeding up a time series alignment algorithm that is related to dynamic time warping (DTW). In previous work, we developed our multisegment alignment algorithm to answer similarity queries for toxicogenomic time-series data. Our multisegment algorithm returns more accurate alignments ...

This work provides a method of mechanical alignment of an array of single mode fibers to an array of optical devices. The technique uses a micromachined metal spring, which captures a vertical, pre-positioned fiber, moves it into accurate alignment, and holds it for attachment. The spring is fabricated from electroplated nickel, using ...

In this paper, we propose a square laser pulse to realize the field-free alignment in linear molecules. We show that the molecular alignment after the laser pulse can be obtained in both non-adiabatic and adiabatic regimes. Comparing with the conventional Gaussian laser pulse, the maximum degree of the molecular ...

The design concept and operation performance of a novel alignment system for accurate electron density profile measurement is presented, which has been developed on the basis of the original method for adjusting quantitatively and actively an object field of collection fiber optics to a laser-beam axis. The quantitative expression needed for an appropriate ...

the molecule to align. In the case of a linearly polarized laser field, the most polarizable axis is aligned polarizations.12�15 In the case of polar molecules, confinement of the molecular axes is not sufficient polarized beam, the largest polarizability axis of the molecule is expected to be aligned along the ...

This paper shows that transient alignment of linear molecules in a dense collisional environment can result from the formation of trapped aligned �dark� states in a laser field constituting either a comb of resonant short pulses or a sinusoidally frequency-modulated wave with a continuous flux. Simulation of the laser-induced dynamics of CO molecules ...

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue ...

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue ...

through MBBA in its nematic state. Thus an or- dered bulk fluid does not necessarily lead to an orientedControlling molecular alignment in an organic monolayer with a sacrificial liquid crystal template molecular adsorption and molecular ordering and disordering at surfaces. Films of the liquid crystal 40

BackgroundProtein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant pairs, structure ...

rr : contribution due to molecular (Rayleigh) scattering, which can be accurately modeled. MODIS requires accurate measurement of change in its mirror ...

of linear molecules, at least approximately. Accurate a priori calculation of relaxation times requires an accurate knowledge of the molecular phrenology, ...

Orientational restraints such as residual dipolar couplings promise to overcome many of the problems that traditionally limited liquid-state nuclear magnetic resonance spectroscopy. Recently, we developed methods to predict a molecular alignment tensor and thus residual dipolar couplings for a given molecular structure. This provides ...

.e. misalignment of the word CAT. T- Coffee is a progressive alignment with an ability to consider information fromBase categories (CE in Cat1 and 2, CL for Cat3, T-Coffee: a Method for Sequence Alignment 211 #12;Table 1. The effect considering the unweighted average accuracy over the �ve cat- egories (Table 2, Total2) T-Coffee is 9.7 % more

Accurate alignment and focus of mirror facets are critical for the integration of concentrators and receivers in many of the low-cost stretched-membrane concentrators currently under development. In this report, the theoretical development of computer software that traces light rays from a source to a facet of a point-focusing solar concentrator and then ...

A system for welding fiber optic waveguides is disclosed. The ends of the two fibers to be joined are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45/sup 0/ angle to the optical axis of a stereomicroscope mounted for ...

A system for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45.degree. angle to the optical axis of a stereomicroscope mounted ...

A technique is described for maintaining the highly precise alignment needed for accurate density profile measurements with the TFTR Thomson scattering system. The method uses the transverse coherence of the fiber bundles in the collection optics to encode the alignment information in the spatial distribution of the scattered light ...

The purpose of the present study is to establish a rapid and effective PCR method for the identification of B. multicinctus. Based on sequence alignment of B. multicinctus and its adulterants, we found that Cyt b gene is a good molecular genetic marker for the authentication of B. multicinctus. On the basis of the sequence data, a pair of highly ...

Biology is encoded in molecular sequences: deciphering this encoding remains a grand scientific challenge. Functional regions of DNA, RNA, and protein sequences often exhibit characteristic but subtle motifs; thus, computational discovery of motifs in sequences is a fundamental and much-studied problem. However, most current algorithms do not allow for insertions or deletions ...

Microsatellite length mutations are often modeled using the generalized stepwise mutation process, which is a type of random walk. If this model is sufficiently accurate, one can estimate the coalescence time between alleles of a locus after a mathematical transformation of the allele lengths. When large-scale microsatellite genotyping first became possible, there was ...

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75?bp) and ...

BackgroundLong term survivorship in total knee arthroplasty is significantly dependant on prosthesis alignment. Our aim was determine which alignment guide was more accurate in positioning of the tibial component in total knee arthroplasty. We also aimed to assess whether there was any difference in short term patient outcome.MethodA ...

It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a ...

BackgroundWhen accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental ...

The dynamics of gas-surface interactions are explored through the rotational analysis of nitric oxide molecules scattered from a Pt(111) surface. For the temperature range of 350-550 K, this system demonstrates two distinct dynamical regimes: trapping/desorption and direct inelastic scattering. The rotational dynamics of these processes are investigated through the measurement of both the ...

Research by other investigators has established that insulin-like growth factor?1 receptor (IGF-1R) is a key oncological target, and that derivatives of 1, 3-disubstituted-imidazo[1,5-?] pyrazine are potent IGF-1R inhibitors. In this paper, we report on our three-dimensional quantitative structure activity relationship (3D-QSAR) studies for this series of compounds. We validated the 3D-QSAR ...

BackgroundGenomic sequence alignment is a powerful method for genome analysis and annotation, as alignments are routinely used to identify functional sites such as genes or regulatory elements. With a growing number of partially or completely sequenced genomes, multiple alignment is playing an increasingly important role in these ...

BackgroundAccurate and efficient structural alignment of non-coding RNAs (ncRNAs) has grasped more and more attentions as recent studies unveiled the significance of ncRNAs in living organisms. While the Sankoff style structural alignment algorithms cannot efficiently serve for multiple sequences, mostly progressive schemes are used to ...

Methods for significantly increasing the molecular weight of polyaniline are described. The conductivity of doped polyaniline is shown to be more directly dependent on its degree of alignment/crystallinity than on its molecular weight. The tensile strengt...

The enhancement of the x-ray scattering signal from partially aligned molecular samples is investigated. The alignment properties of the studied molecular system are modeled based on the method of laser alignment. With the advances in the area of laser alignment of ...

The enhancement of the x-ray scattering signal from partially aligned molecular samples is investigated. The alignment properties of the studied molecular system are modeled based on the method of laser alignment. With the advances in the area of laser alignment of ...

An electro-optically active polymer gel material comprising a high molecular weight alignment polymer adapted to be homogeneously dispersed throughout a liquid crystal to control the alignment of the liquid crystal molecules and/or confer mechanical stabi...

Substitutional OH(-) ions in alkali halides have become, by recent extended work, a prototype for a molecular electric dipole center which exhibits paraelectric alignment behavior to very low temperatures due to orientational tunneling. The understanding ...

Precise pre- and postoperative anatomic measurements are necessary to plan, perform, and evaluate total knee arthroplasty (TKA). We evaluated the relationship between radiographic and navigation alignment measurements, identified sources of error in radiographic and navigated alignment assessment, and determined the differences between desired and ...

Abstract. We have developed a multiple genome alignment algorithm by using a sequence clustering algorithm to combine local pairwise genome sequence matches produced by pairwise genome alignments, e.g, BLASTZ. Sequence clustering algorithms often generate clusters of sequences such that there exists a common shared region among all sequences in each ...

A procedure is described for preparing relief alignment marks with precisely degraded quality that are then used to calibrate alignment performance. Alignment degrades with mark quality, eventually failing when the marks are no longer found. Using conventional processes it is difficult to accurately find this ...

We define a �threaded blockset,� which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for �threaded blockset aligner�) builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are ...

National Ignition Facility (NIF) is a high-energy laser facility comprised of 192 laser beams focused with enough power and precision on a hydrogen-filled spherical, cryogenic target to initiate a fusion reaction. The target container, or hohlraum, must be accurately aligned to an x-ray imaging system to allow careful monitoring of the frozen fuel layer in ...

National Ignition Facility (NIF) is a high-energy laser facility comprised of 192 laser beams focused with enough power and precision on a hydrogen-filled spherical, cryogenic target to initiate a fusion reaction. The target container, or hohlraum, must be accurately aligned to an x-ray imaging system to allow careful monitoring of the frozen fuel layer in ...

The existence of states for which molecular alignment can be maintained for long periods of time is shown. These states, consisting of coherent superpositions of rotational states, are found among cyclic states of the generalized Floquet operator corresponding to a molecule in a short nonresonant laser pulse. For a single pulse ...

The difficulty of aligning bent-core liquid crystals at a surface is addressed from three directions: We form Langmuir monolayers of bent core molecules at the air-water interface, and explore their orientation and packing. We transfer these films by Langmuir-Schaefer techniques to a solid surface, and test them for the alignment of bulk liquid crystal. We ...

We demonstrate control on nonadiabatic molecular alignment by using a spectrally phase-shaped laser pulse. An evolutionary algorithm in a closed feedback loop has been used in order to find pulse shapes that maximize a given effect. In particular, this scheme has been applied to the optimization of total alignment, and to the control ...

This study presents a two-laser alignment approach for facilitating the precise alignment of various imaging and measuring components with respect to the x-ray beam. The first laser constantly pointed to the output window of the source, in a direction parallel to the path along which the components are placed. The second laser beam, originating from the ...

Quantitative analyses of low molecular weight (100-200) polar compounds [1-methyl-4-phenylpyridine (MPP+), 2-amino-3-(methylamino)propanoic acid (synonyms, beta-(methyl-amino)-L-alanine or BMAA), and tryptophan] were conducted on a triple-stage quadrupole mass spectrometer configured for continuous flow liquid secondary ion mass spectrometry ionization (CF L-SIMS). It is shown ...

Molecular ADK model (MO-ADK) [1] has been successfully used to study the ionization of molecules in recent years. However, there is indication that the model does not predict the correct alignment dependence of the ionization rates for CO2 molecules [2]. In the MO-ADK model, the wavefunction of the highest-occupied orbital at large distance is needed in ...

Equation of state and structure of hard-sphere fluids confined in a cylindrical hard pore were investigated at the vicinity of fluid-solid transition via molecular dynamics simulation. By constructing artificial closed-packed structures in a cylindrical pore, we explicitly capture the fluid-solid phase transition and coexistence for the pore diameters from 2.17sigma to ...

Purpose: To evaluate the impact of the number and location of intraprostatic fiducial markers on the accuracy and reproducibility of daily prostate target alignment and to evaluate the migration of such markers. Methods and Materials: Three gold fiducial markers were implanted transrectally under ultrasound guidance near the apex, middle, and base of the prostate in 10 ...

Protein sequence alignment has become an essential task in modern molecular biology research. A number of alignment techniques have been documented in literature and their corresponding tools are made available as freeware and commercial software. The choice and use of these tools for sequence alignment ...

Polypeptide based molecular diode with high rectification ratio (~122 at +/-0.422 V) is formed by controlling molecular order and orientation. A film of tethered poly(?-benzyl-L-glutamate) (PBLG) with high degree of molecular orientation was formed by solvent pair (good/bad) treatment. I-V characterization of the well ...

The underlying objective of this work is to develop molecular models that accurately describe the polymer-carbon black composite films used in the ENose ...

BackgroundIn this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead, it defines a set of optimal and suboptimal alignments at each step during ...

As the IC product scribe line of logic 90nm (L90) technology shrinks from 80�m to 62?m, the wafer quality (W.Q.), will become weak and less distinguishable during the subsequent ASML scanner stepper's photo mask aligning. Many wafers having photo mask aligning errors will eventually lead to wafer scrapping. In order to improve the photo ...

Biological control requires specific tools for the accurate detection and identification of natural enemies, and to detect unusual variations in their density, which may follow changes in agricultural practices. Here we have developed specific molecular markers to detect Lydella thompsoni (Herting) and Pseudoperichaeta nigrolineata (Walker) (Diptera: ...

A comprehensive literature search was conducted to obtain the most accurate values for the molecular and the spectral parameters, including Franck-Cordon ...

... outcome. Proper interpretation of genetic testing results requires correlation with accurate clinical information. Inappropriate interpretation can result ...

A comprehensive literature search was conducted to obtain the most accurate values for the molecular and the spectral parameters, including Franck-Cordon ...

... relaxation times in molecular crystals. ... are certainly the most accurate crystal absorption spectra ... of the electronic structure of very large molecules.

... systems of three and four ion pairs, to illustrate the effectiveness of the FMO method in accurately describing complex molecular clusters, with the ...

... along with systems of three ion pairs, to illustrate the effectiveness of the FMO method in accurately describing complex molecular clusters, with the ...

The method is based upon molecular line parameters and makes use of a far wing scaling approximation

Hybrid (quantum mechanics/molecular mechanics) theoretical techniques will be discussed that may allow to obtain accurate vibrational spectra of ...

times requires an accurate knowledge of the molecular phrenology, characterized by Pd; such information is not generally available. ...

We experimentally demonstrate field-free, spin-selective alignment of ortho- and para molecular spin isomers at room temperature. By means of two nonresonant, strong, properly delayed femtosecond pulses within a four wave mixing arrangement, we observed selective alignment for homonuclear diatomics composed of spin 1/2 (15N) or spin 1 ...

We experimentally demonstrate field-free, spin-selective alignment of ortho- and para molecular spin isomers at room temperature. By means of two nonresonant, strong, properly delayed femtosecond pulses within a four wave mixing arrangement, we observed selective alignment for homonuclear diatomics composed of spin 1/2 ({sup 15}N) or ...

We study the effect of molecular alignment on the performance of organic photovoltaic devices (OPV) by using two porphyrin molecules of etioporphyrin-I (HOX) and octaethylporphyrin (HOEP) with similar chemical structures. Due to the minor differences in their peripheral substituents, the two porphyrin molecules form crystalline films of different ...

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple ...

We describe a new global multiple-alignment program capable of aligning a large number of genomic regions. Our progressive-alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein-based anchoring of ab-initio gene predictions, and constraints ...

This paper proposes a novel mechanism for the initial alignment of low-cost INS aided by GPS. For low-cost INS, the initial alignment is still a challenging issue because of the high noises from low-cost inertial sensors. In this paper, a two-stage Kalman Filtering mechanism is proposed for the initial alignment of low-cost INS. The ...

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential ...

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential ...

A technique is presented with which the alignment of molecular angular momenta in molecular beam scattering can be measured. In principle the method can be applied to any molecule as long as the polarization of an absorbed or emitted photon is related directly to the orientation of the molecular angular momentum ...

self-aligned electroless metallization by molecular self-assembly. Langmuir 18, no. 25:9625-9628. 19

Molecular biologists have recently developed the technology required to determine the genetic information of complete organisms. They are now faced with a number of interesting computational problems as they attempt to process data. We are interested in d...

For use in low-voltage, high frequency electro-optic modulators, such materials require the internal nanoscale alignment of molecular dipoles. ...