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Medical imaging, a key component in clinical diagnosis of and research on numerous medical conditions, is very costly and can generate massive datasets. For instance, a single scanned subject produces hundreds of thousands of images and millions of key-value metadata pairs that must be verified to ensure instrument and research protocol compliance. Many projects lack funds to reacquire images if data quality issues are detected later. Data quality assurance (QA) requires continuous involvement by all stakeholders and use of specific quality control (QC) methods to identify data issues likely to require post-processing correction or real-time re-acquisition. While many useful QC methods exist, they are often designed for specific use-cases with limited scope and documentation, making integration with other setups difficult. We present the Scalable Quality Assurance for Neuroimaging (SQAN), an open-source software suite developed by Indiana University for protocol quality control and instrumental validation on medical imaging data. SQAN includes a comprehensive QC Engine that ensures adherence to a research study’s protocol. A modern, intuitive web portal serves a wide range of users including researchers, scanner technologists and data scientists, each of whom approach QC with unique priorities, expertise, insights and expectations. Since Fall 2017, a fully operational SQAN instance has supported 50+ research projects, and has QC’d ∼3.5 million images and over 700 million metadata tags. SQAN is designed to scale to any imaging center’s QC needs, and to extend beyond protocol QC toward image-level QC and integration with pipeline and non-imaging database systems.

Virtual delineation of white matter bundles in the human brain is of paramount importance for multiple applications, such as pre-surgical planning and connectomics. A substantial body of literature is related to methods that automatically segment bundles from diffusion Magnetic Resonance Imaging (dMRI) data indirectly, by exploiting either the idea of connectivity between regions or the geometry of fiber paths obtained with tractography techniques, or, directly, through the information in volumetric data. Despite the remarkable improvement in automatic segmentation methods over the years, their segmentation quality is not yet satisfactory, especially when dealing with datasets with very diverse characteristics, such as different tracking methods, bundle sizes or data quality. In this work, we propose a novel, supervised streamline-based segmentation method, called Classifyber, which combines information from atlases, connectivity patterns, and the geometry of fiber paths into a simple linear model. With a wide range of experiments on multiple datasets that span from research to clinical domains, we show that Classifyber substantially improves the quality of segmentation as compared to other state-of-the-art methods and, more importantly, that it is robust across very diverse settings. We provide an implementation of the proposed method as open source code, as well as web service.

We describe the Open Diffusion Data Derivatives (O3D) repository: an integrated collection of preserved brain data derivatives and processing pipelines, published together using a single digital-object-identifier. The data derivatives were generated using modern diffusion-weighted magnetic resonance imaging data (dMRI) with diverse properties of resolution and signal-to-noise ratio. In addition to the data, we publish all processing pipelines (also referred to as open cloud services). The pipelines utilize modern methods for neuroimaging data processing (diffusion-signal modelling, fiber tracking, tractography evaluation, white matter segmentation, and structural connectome construction). The O3D open services can allow cognitive and clinical neuroscientists to run the connectome mapping algorithms on new, user-uploaded, data. Open source code implementing all O3D services is also provided to allow computational and computer scientists to reuse and extend the processing methods. Publishing both data-derivatives and integrated processing pipeline promotes practices for scientific reproducibility and data upcycling by providing open access to the research assets for utilization by multiple scientific communities., Design Type(s)data integration objective • database creation objectiveMeasurement Type(s)brainTechnology Type(s)magnetic resonance imagingFactor Type(s)Voxel SizeSample Characteristic(s)Homo sapiens • brain Machine-accessible metadata file describing the reported data (ISA-Tab format)

Diffusion-weighted magnetic resonance imaging (dMRI) allows for non-invasive, detailed examination of the white matter structures of the brain. White matter tract specific measures based on either the diffusion tensor model (e.g. FA, ADC, and MD) or tractography (e.g. volume, streamline count or density) are often compared between groups of subjects to localize differences within the white matter. Less commonly examined is the shape of the individual white matter tracts. In this paper, we propose to use the Laplace-Beltrami (LB) spectrum as a descriptor of the shape of white matter tracts. We provide an open, automated pipeline for the computation of the LB spectrum on segmented white matter tracts and demonstrate its efficacy through machine learning classification experiments. We show that the LB spectrum allows for distinguishing subjects diagnosed with bipolar disorder from age and sex matched healthy controls, with classification accuracy reaching 95%. We further demonstrate that the results cannot be explained by traditional measures, such as tract volume, streamline count, or mean and total length. The results indicate that there is valuable information in the anatomical shape of the human white matter tracts.

We describe the SpArc science gateway for spectral data obtained during the period from 1975 through 1995 at the Kitt Peak National Observatory using the Fourier Transform Spectrometer (FTS) in operation at the Mayall 4-m telescope. SpArc is hosted by Indiana University Bloomington and is available for public access. The archive includes nearly 10,000 individual spectra of more than 800 different astronomical sources including stars, nebulae, galaxies, and Solar System objects. We briefly describe the FTS instrument itself, and summarize the conversion of the original interferograms into spectral data and the process for recovering the data into FITS files. The architecture of the archive is discussed, and the process for retrieving data from the archive is introduced. Sample use cases showing typical FTS spectra are presented., Accepted for publication in the PASP

The Astronomy scientific community has embraced Big Data processing challenges, e.g. associated with time-domain astronomy, and come up with a variety of novel and efficient data processing solutions. However, data processing is only a small part of the Big Data challenge. Efficient knowledge discovery and scientific advancement in the Big Data era requires new and equally efficient tools: modern user interfaces for searching, identifying and viewing data online without direct access to the data; tracking of data provenance; searching, plotting and analyzing metadata; interactive visual analysis, especially of (time-dependent) image data; and the ability to execute pipelines on supercomputing and cloud resources with minimal user overhead or expertise even to novice computing users. The Trident project at Indiana University offers a comprehensive web and cloud-based microservice software suite that enables the straight forward deployment of highly customized Scalable Compute Archive (SCA) systems; including extensive visualization and analysis capabilities, with minimal amount of additional coding. Trident seamlessly scales up or down in terms of data volumes and computational needs, and allows feature sets within a web user interface to be quickly adapted to meet individual project requirements. Domain experts only have to provide code or business logic about handling/visualizing their domain's data products and about executing their pipelines and application work flows. Trident's microservices architecture is made up of light-weight services connected by a REST API and/or a message bus; a web interface elements are built using NodeJS, AngularJS, and HighCharts JavaScript libraries among others while backend services are written in NodeJS, PHP/Zend, and Python. The software suite currently consists of (1) a simple work flow execution framework to integrate, deploy, and execute pipelines and applications (2) a progress service to monitor work flows and sub-work flows (3) ImageX, an interactive image visualization service (3) an authentication and authorization service (4) a data service that handles archival, staging and serving of data products, and (5) a notification service that serves statistical collation and reporting needs of various projects. Several other additional components are under development. Trident is an umbrella project, that evolved from the One Degree Imager, Portal, Pipeline, and Archive (ODI-PPA) project which we had initially refactored toward (1) a powerful analysis/visualization portal for Globular Cluster System (GCS) survey data collected by IU researchers, 2) a data search and download portal for the IU Electron Microscopy Center's data (EMC-SCA), 3) a prototype archive for the Ludwig Maximilian University's Wide Field Imager. The new Trident software has been used to deploy (1) a metadata quality control and analytics portal (RADY-SCA) for DICOM formatted medical imaging data produced by the IU Radiology Center, 2) Several prototype work flows for different domains, 3) a snapshot tool within IU's Karst Desktop environment, 4) a limited component-set to serve GIS data within the IU GIS web portal. Trident SCA systems leverage supercomputing and storage resources at Indiana University but can be configured to make use of any cloud/grid resource, from local workstations/servers to (inter)national supercomputing facilities such as XSEDE.

Processing astronomical data to science readiness was and remains a challenge, in particular in the case of multi detector instruments such as wide-field imagers. One such instrument, the WIYN One Degree Imager, is available to the astronomical community at large, and, in order to be scientifically useful to its varied user community on a short timescale, provides its users fully calibrated data in addition to the underlying raw data. However, time-efficient re-processing of the often large datasets with improved calibration data and/or software requires more than just a large number of CPU-cores and disk space. This is particularly relevant if all computing resources are general purpose and shared with a large number of users in a typical university setup. Our approach to address this challenge is a flexible framework, combining the best of both high performance (large number of nodes, internal communication) and high throughput (flexible/variable number of nodes, no dedicated hardware) computing. Based on the Advanced Message Queuing Protocol, we a developed a Server-Manager- Worker framework. In addition to the server directing the work flow and the worker executing the actual work, the manager maintains a list of available worker, adds and/or removes individual workers from the worker pool, and re-assigns worker to different tasks. This provides the flexibility of optimizing the worker pool to the current task and workload, improves load balancing, and makes the most efficient use of the available resources. We present performance benchmarks and scaling tests, showing that, today and using existing, commodity shared- use hardware we can process data with data throughputs (including data reduction and calibration) approaching that expected in the early 2020s for future observatories such as the Large Synoptic Survey Telescope.

The One Degree Imager - Portal, Pipeline, and Archive (ODI-PPA) has included the Image Explorer interactive image visualization tool since it went operational. Portal users were able to quickly open up several ODI images within any HTML5 capable web browser, adjust the scaling, apply color maps, and perform other basic image visualization steps typically done on a desktop client like DS9. However, the original design of the Image Explorer required lossless PNG tiles to be generated and stored for all raw and reduced ODI images thereby taking up tens of TB of spinning disk space even though a small fraction of those images were being accessed by portal users at any given time. It also caused significant overhead on the portal web application and the Apache webserver used by ODI-PPA. We found it hard to merge in improvements made to a similar deployment in another project's portal. To address these concerns, we re-architected Image Explorer from scratch and came up with ImageX, a set of microservices that are part of the IU Trident project software suite, with rapid interactive visualization capabilities useful for ODI data and beyond. We generate a full resolution JPEG image for each raw and reduced ODI FITS image before producing a JPG tileset, one that can be rendered using the ImageX frontend code at various locations as appropriate within a web portal (for example: on tabular image listings, views allowing quick perusal of a set of thumbnails or other image sifting activities). The new design has decreased spinning disk requirements, uses AngularJS for the client side Model/View code (instead of depending on backend PHP Model/View/Controller code previously used), OpenSeaDragon to render the tile images, and uses nginx and a lightweight NodeJS application to serve tile images thereby significantly decreasing the Time To First Byte latency by a few orders of magnitude. We plan to extend ImageX for non-FITS images including electron microscopy and radiology scan images, and its featureset to include basic functions like image overlay and colormaps. Users needing more advanced visualization and analysis capabilities could use a desktop tool like DS9+IRAF on another IU Trident project called StarDock, without having to download Gigabytes of FITS image data.

Surging data volumes make it increasingly unfeasible to transfer astronomical datasets to the local systems of individual scientists. Centralized pipelines offer some relief, but lack flexibility to fulfill the needs of all users. We have developed a system that leverages the Docker container application virtualization software. Along with a suite of commonly used astronomy applications, users can configure a container with their own custom software and analysis tools. Our StarDock system will move the users container to the data, and expose the requested dataset, allowing our users to safely and securely process their data without needlessly transferring hundreds of gigabytes.

Static and dynamic structures of water molecules have been inspected in aqueous solutions of di-and penta-α- and -β- d -glucopyranose (maltose, cellobiose, maltopentaose, and cellopentaose) outside the first hydration shell around the saccharides, using a molecular dynamics simulation which includes all degrees of freedom concerning atomic motion. The aim is to inspect the solute effect on water molecules in the aqueous solution systems corresponding to the length or the kind of the glycosidic linkage. We use the partial radial distribution function and two kinds of angular distribution functions for the static analysis, and find peculiarities in the solutions of both α-linked saccharides, maltose and maltopentaose. The broadness of the hydrogen bond network distribution in the maltose solution is particularly related to the translational motion of water molecules which is slowest in the maltose solution. The rotational motion of water molecules is significantly slow in the cellopentaose solution. The solute effect can be detected outside the first hydration shell around the solute, and is most noticeable in the translational motion.

A molecular dynamics simulation, which includes all degrees of freedom of atomic motion, has been carried out for aqueous maltose and cellobiose solutions in order to investigate whether the solvent as a background of solutes changes its dynamic characteristics or not. Mean square displacement, velocity autocorrelation function, rotational correlation function, and newly defined hydrogen bond correlation function have been calculated for the whole solvent from which the first hydration shell of the solute was omitted. The first three functions concern motions of each water molecule, and the last one reveals relative motions of water molecules. Translational and rotational motions of water molecules are restricted more in the solution than in the bulk water, because the network defects, which weaken the power of a water molecule to retain others, exist less in the solution than in the bulk water. Between two solution systems, this tendency is stronger in the maltose solution than in the cellobiose one. The difference between two solution systems is clearly demonstrated in the present study dealing with the dynamic structure, although it was not clear in the static structure revealed in our previous paper.

The Open Science Grid (OSG) relies upon the network as a critical part of the distributed infrastructures it enables. In 2012, OSG added a new focus area in networking with a goal of becoming the primary source of network information for its members and collaborators. This includes gathering, organizing, and providing network metrics to guarantee effective network usage and prompt detection and resolution of any network issues, including connection failures, congestion, and traffic routing. In September of 2015, this service was deployed into the OSG production environment. We will report on the creation, implementation, testing, and deployment of the OSG Networking Service. Starting from organizing the deployment of perfSONAR toolkits within OSG and its partners, to the challenges of orchestrating regular testing between sites, to reliably gathering the resulting network metrics and making them available for users, virtual organizations, and higher level services, all aspects of implementation will be reviewed. In particular, several higher-level services were developed to bring the OSG network service to its full potential. These include a web-based mesh configuration system, which allows central scheduling and management of all the network tests performed by the instances; a set of probes to continually gather metrics from the remote instances and publish it to different sources; a central network datastore (esmond), which provides interfaces to access the network monitoring information in close to real time and historically (up to a year) giving the state of the tests; and a perfSONAR infrastructure monitor system, ensuring the current perfSONAR instances are correctly configured and operating as intended. We will also describe the challenges we encountered in ongoing operations of the network service and how we have evolved our procedures to address those challenges. Finally we will describe our plans for future extensions and improvements to the service.

The One Degree Imager-Portal, Pipeline, and Archive (ODI-PPA) is a web science gateway that provides astronomers a modern web interface that acts as a single point of access to their data, and rich computational and visualization capabilities. Its goal is to support scientists in handling complex data sets, and to enhance WIYN Observatory's scientific productivity beyond data acquisition on its 3.5m telescope. ODI-PPA is designed, with periodic user feedback, to be a compute archive that has built-in frameworks including: (1) Collections that allow an astronomer to create logical collations of data products intended for publication, further research, instructional purposes, or to execute data processing tasks (2) Image Explorer and Source Explorer, which together enable real-time interactive visual analysis of massive astronomical data products within an HTML5 capable web browser, and overlaid standard catalog and Source Extractor-generated source markers (3) Workflow framework which enables rapid integration of data processing pipelines on an associated compute cluster and users to request such pipelines to be executed on their data via custom user interfaces. ODI-PPA is made up of several light-weight services connected by a message bus; the web portal built using Twitter/Bootstrap, AngularJS and jQuery JavaScript libraries, and backend services written in PHP (using the Zend framework) and Python; it leverages supercomputing and storage resources at Indiana University. ODI-PPA is designed to be reconfigurable for use in other science domains with large and complex datasets, including an ongoing offshoot project for electron microscopy data.

This paper, the first of a series of papers, examines equilibrium properties of N2O4⇌NO2 in liquid state by classical molecular dynamics simulations of liquid NO2. An ab initio MO calculation has been carried out to elucidate NO2–NO2 potential, and an orientation-sensitive pairwise potential (OSPP), which can reproduce highly anisotropic character of covalent bonding between N–N, has been formulated. The OSPP potential is parameterized by the well depth De and by two anisotropy factors: Aθ (0⩽Aθ⩽1) the anisotropy factor for the rocking angle between NN bond and ONO direction, and Aτ (0⩽Aτ⩽1) for torsional angle of the two NO2 about NN bond. The reactive liquid N2O4 is modeled as liquid NO2 which interacts with the OSPP potential between N–N atoms and Lennard-Jones potentials between N–O and O–O atoms. Equilibrium properties were found to be very sensitive to the well depth De and anisotropy factors of OSPP. The population of more than the NO2 dimer (3-mer, 4-mer,…) is considerable when anisotropy factors ...

Infrared (IR) spectra of the Langmuir monolayers of stearic acid were simulated by the molecular dynamics (MD) method, for the first time, where the translational, rotational, and vibrational degrees of freedom of all atoms in the monolayer were considered. The IR spectra simulated by this method completely reproduced surface area dependence of the monolayer structure and the chain axis orientation. The characteristics of the spectra were also consistent with the chain orientation evaluated by in situ experimental techniques. In addition, the simulated spectra gave evidence of no area dependence of the head group orientation in the monolayer.

A molecular dynamics (MD) simulation, which includes all degrees of freedom of atomic motion, has been carried out in order to investigate the temperature dependence of single particle dynamics such as translational and reorientational motions of liquid benzene (C 6 H 6 ). The translational diffusion coefficients D and first and second rank reorientational correlation times τ l R ( l =1, 2) of liquid C 6 H 6 are simulated at 366.12, 322.69, 295.00 and 198.54 K. Except for the simulation at 198.54 K, all three motions are characteristic of typical molecular liquids. Although these simulated D and τ l R values slightly deviate from experimental ones, both activation energies E a of simulated and experimental ones are in agreement with each other. The Stokes–Einstein–Debye (SED) equations, which are based on a hydrodynamics model, have also been checked for the D and τ l R values with changing temperature. It has been found that the SED equations hold for both values, and the hydrodynamical model is effective for the simulated liquid C 6 H 6 .

A molecular dynamics (MD) simulation, which includes all degrees of freedom of atomic motion, has been carried out in order to investigate the temperature dependence of single particle dynamics such as translational and reorientational motions of liquid carbon disulfide (CS 2 ). The translational diffusion coefficients D and first and second rank reorientational correlation times τ lr ( l = 1, 2) of liquid CS 2 are simulated at three temperatures. Both motions are characteristics of the typical molecular liquids, and these simulated D and τ lR values and the activation energies of them are close to the experimental ones. The Stokes-Einstein-Debye (SED) equations, which are based on a hydrodynamics model, have also been checked for the D and τ lR values with changing the temperature. It has been found that the SED equations hold for both values, and the hydrodynamical model is effective for the simulated liquid CS 2 .

We have applied our theory of the division of the viscosity B coefficient to the n-hexane-n-heptane, -n-octane, -n-decane, -n-undecane, and -n-dodecane systems at 25°C, and to the n-hexane-n-hexadecane system at 25, 45, 65, and 85 °C. Similar to the investigation of benzene regular solutions, a linear relation holds between the Bn term and the equimolar excess enthalpy HxaE = 0.5, and it has been clarified that the Bn term and the temperature coefficient of Bn for these systems are controlled by solute-solvent interaction.

A molecular dynamics (MD) simulation, which includes all degrees of freedom of atomic motion, has been carried out in order to investigate the temperature dependence of single particle dynamics such as translational and reorientational motions of liquid tetrachloromethane (CCl 4 ). The translational diffusion coefficients D and first and second rank reorientational correlation times τ lR ( l = 1, 2) of liquid CCl 4 are simulated at three temperatures. Both motions are characteristics of the typical molecular liquids, and these simulated D and τ lR values and their activation energies are close to the experimental ones. The Stokes-Einstein-Debye (SED) equations, which are based on a hydrodynamics model, have also been checked for the D and τ lR values with changing the temperatures. It has been found that the SED equations hold for both values, and the hydrodynamical model is effective for the simulated liquid CCl 4 .

Vibrational effects on structural parameters obtained by solid-state NMR are studied by theoretical calculations and molecular-dynamics simulations. The structural parameters treated contain internuclear distances between directly bonded or remote nuclei including nonproton pairs in a molecule and bond and dihedral angles. In addition to the intramolecular normal mode vibrations, the libration of the whole molecule is considered in the theory. It is shown that the molecular libration as well as the intramolecular vibrations reduce dipolar interactions, and consequently lengthen the internuclear distances obtained from the dipolar interactions (RNMR). In contrast, the internuclear distances obtained by single crystal x-ray or neutron diffraction (Rcor) are proved to be shortened by the molecular libration. Molecular-dynamics simulations for glycine molecules in the crystal at room temperature reveal that RNMR are 1%–4% longer than Rcor, confirming the theoretical results. It is also demonstrated that the e...

The polarized infrared spectra of water in the middle phase of Triton X100 aqueous solution were compared with those of poly(ethylene oxide) in the crystalline state. The oxyethylene chain of TX100 orients approximately perpendicular to the direction of the stream (parallel to the direction of growth of the liquid crystal), while that of poly(ethylene oxide) orients parallel to the stretching direction. However, in both cases the water molecule prefers the perpendicular orientation of its bisector to the oxyethylene chain. The OH stretching frequency of water in Triton X100 sharply increases with increasing water content up to about 10 wt% and decreases suddenly up to about 40 wt%, after which it stays constant. The initial increment in the OH stretching frequency is due to the progression of the hydrogen bonding between water and the ether oxygen in the oxyethylene groups of Triton X100 and the subsequent reduction is the result of the linkage between the waters. On the other hand, the increase in intensity and the decrease in band-width of the 949 cm−1band up to a constant value at about 40 wt% H2O suggest the progression of the ordered GTTG helical conformation in the oxyethylene group of Triton X100. The appearance of the middle phase of Triton X100 results in the formation of the hydrogen-bonding network of the (2:1) complex at about 40 wt% H2O. In the middle phase of 40–60 wt% H2O, water added in excess gradually dissolves the linkage among the adjacent oxyethylene chains, but the system partially remains in the liquid crystal phase. Above 60 wt% H2O (water:oxyethylene = 5:1), the water added in excess interrupts the hydrogen-bond linkage of the 2:1 complex and destroys the middle phase. However, the helical conformation resides in this aqueous solution, because the oxyethylene group prefers the helical conformation in the aqueous solution rather than in the neat or molten state. The13C chemical shifts ensured the concurrence of hydration to the various oxygen atoms in the oxyethylene chain and the existence of the helical conformation. In the middle phase, the weak orientation of water and TX100 is due to the directional distributions of the helical axis in the quasi-spherical micelle.

Molecular dynamics simulations were performed for the dissociation and association (D/A) reactions N 2 O 4 2NO 2 in the gas and liquid phases. The transition state of the D/A reactions was identified as the phase space surface E T =0, where E T is the sum of the potential and kinetic energies of the interfragment motion. The dissociation reaction in liquid N 2 O 4 is found to occur by two steps: first, a reactant is activated by intermolecular energy transfer from solvent to reactant, and second, the dissociation occurs by energy transfer from intrafragment vibrational and rotational modes to interfragment translational mode. The association reaction proceeds by two steps: interfragment translational energy of an encounter NO 2 pair is transferred to intrafragment modes and then the associated N 2 O 4 is deactivated by intermolecular energy transfer from product to solvent.

The journey of a monitoring probe from its development phase to the moment its execution result is presented in an availability report is a complex process. It goes through multiple phases such as development, testing, integration, release, deployment, execution, data aggregation, computation, and reporting. Further, it involves people with different roles (developers, site managers, VO[1] managers, service managers, management), from different middleware providers (ARC[2], dCache[3], gLite[4], UNICORE[5] and VDT[6]), consortiums (WLCG[7], EMI[11], EGI[15], OSG[13]), and operational teams (GOC[16], OMB[8], OTAG[9], CSIRT[10]). The seamless harmonization of these distributed actors is in daily use for monitoring of the WLCG infrastructure. In this paper we describe the monitoring of the WLCG infrastructure from the operational perspective. We explain the complexity of the journey of a monitoring probe from its execution on a grid node to the visualization on the MyWLCG[27] portal where it is exposed to other clients. This monitoring workflow profits from the interoperability established between the SAM[19] and RSV[20] frameworks. We show how these two distributed structures are capable of uniting technologies and hiding the complexity around them, making them easy to be used by the community. Finally, the different supported deployment strategies, tailored not only for monitoring the entire infrastructure but also for monitoring sites and virtual organizations, are presented and the associated operational benefits highlighted.

In order to explain the large permittivity of liquid cyanogen consisting of centrosymmetric molecules, a molecular dynamics simulation which includes all degrees of freedom of vibration, rotation, and translation has been performed. The intramolecular potential energy is expressed in terms of the internal coordinates with quadratic, cubic, and quartic force constants. The intermolecular potential consists of an atom–atom pair potential with Coulombic and Buckingham terms. The simulation has given an adequate value of self‐diffusion coefficient and a typical form of radial distribution function for the liquid state. The simulation has reproduced well the large value of the permittivity observed in experiments, suggesting that the value results from the extraordinarily large atomic polarization brought by the intramolecular bending motion in an antisymmetric mode. The simulation has also suggested that the nitrogen atoms collide with each other more frequently than with carbon atoms and the collision shifts the normal frequencies related to the N≡C bond to higher frequency. The infrared and Raman spectra together with the real and imaginary parts of the refractive index have also been calculated.

Vibrational spectra of benzene and benzene-d6 in the gas and liquid phase have been simulated by a molecular mechanics method including the calculation of equilibrium structures, thermodynamic quantities, normal frequencies and vibrational transition probabilities. The potential parameters have been estimated by referring to the observed frequencies of benzene, benzene-d6 and 1,3,5-benzene-d3 and also to results of ab initio calculations. Four and ten independent parameters are required, respectively, for elucidating the infrared absorption and Raman intensities of these compounds in the gas and liquid phase. The infrared absorption spectrum of benzene-d1 is reproduced well by using the potential and the intensity parameters estimated for benzene and benzene-d6. The change of relative band intensities on the phase change has been elucidated in terms of the change of various intensity parameters.

Polarized infrared spectra of well-oriented crystalline thin films of dodecylbutyldimethylammonum bromide monohydrate (DBDM·H 2 O) were recorded in the region 5400-250 cm −1 . From the results of the polychroism measurements and the X-ray analysis, water bands were divided into three symmetry species ( A 1 , B 1 , and B 2 ). With the aid of frequencies and isotopic frequency ratios, the water bands were assigned to the three fundamental vibrations, two librations, and their overtones and combinations. In the crystalline environment, we have observed the doublets for each of the vibrationally isolated OH and OD stretching bands of HOD in isotopically diluted monohydrates DBDM·HOD. This spectral feature suggests the presence of two distinct configurations of the water molecule, one forming a strong and linear O 1 H ⋯ Br 1 hydrogen bond and the other forming a weak and slightly bent O 1 H ⋯ Br 2 hydrogen bond. The results in this work are discussed in connection with previous work. The OH stretcing bands in DBDM·H 2 O appear at higher frequency than in dodecylpropyldimethylammonium bromide (DPDM)·H 2 O or in DPDM· 1 2 H 2 O, while the HOH scissoring, rocking, and wagging modes occur at lower frequency. These are consistent with the weaker hydrogen bond of the water molecule and the longer O ⋯ Br hydrogen bond distance in DBDM·H 2 O than in the DPDM hydrates. Correlation between ν(OD) and the O ⋯ Br distance is also argued.

Molecular dynamics simulations were performed for the dissociation and association (D/A) reactions N2O4■2 NO2 in the gas phase and in liquid N2O4. The trajectory was initialized from an equilibrium distribution of all variables in liquid N2O4, except the reactive mode, the NN distance of a reactant NO2 pair, was excited above the dissociation limit of the Morse‐like potential between NO2 fragments, and the dynamics were calculated for 500 fs both forward and backward in time. Characteristics of the translational and vibrational energy relaxations of the reactant were studied in detail. Energy ERT, which is defined to be the sum of the potential and kinetic energies of interfragment motion, is found to play a key role in the D/A dynamics; a reactant pair is associated when ERT

In order to study the cation dependence of the ionic dynamics in molten nitrates, molecular dynamics simulations including vibrational degrees of freedom were carried out for molten LiNO3, NaNO3, and RbNO3. Coulomb pair potential with Born‐type repulsion was adopted for the interionic interaction. The simulated diffusion coefficient was smaller for a larger cation, and that of nitrate ions did not change with changing cation species. The mean squared charge displacements showed that the static conductivity decreased considerably as the cation size increased from Li+ to Rb+. The simulated orientational correlation function of nitrate ions decayed more quickly as the cation size increased. Far infrared absorption spectrum simulated from the time evolution of the dipole moment (or the current) of the system showed that the peak shifted to the low energy side and the intensity decreased as the cation size increased. Results of the simulation were compared with the experimental diffusion constants, static and ...

An extended molecular mechanics calculation of thermodynamic quantities, structure parameters, infrared absorption spectra, and Raman spectra of normal fatty acids was carried out on the basis of t...

To study the microdynamics of translational, orientational and vibrational motions in liquid N2O4, molecular dynamics simulations, including all degrees of freedom of vibrating N2O4 molecules, were carried out. Atom-atom Lennard-Jones potentials with and without Coulomb potentials (LJ + C and LJ, respectively), were adopted in the simulation. When Coulomb interaction between atoms was included, mean-squared force and torque increased, the velocity and angular momentum correlation functions decayed faster to more evident negative parts, and both the translational and orientational diffusion slowed down. Simulated rotational correlation functions for LJ + C agreed reasonably with those derived from Raman spectroscopy, while those for LJ were found to decay too fast. Vibrational correlation functions for the NN stretching v 3 mode were calculated and the vibrational spectra were obtained from their Fourier transforms. Two simulations for the harmonic and the anharmonic intramolecular potentials, where anharm...

The Open Science Grid (OSG) is made up of researchers from several scientific domains that contribute hardware and software resources through Virtual Organizations (VOs). These VOs have developed a plethora of tools that have been found useful to members of the OSG. Unfortunately it is hard for everyone in the OSG community to keep up with all the tools, and their accessibility; Similarly OSG support staff and resource administrators have been known to have a hard time debugging an issue related to a reported issue because of the distributed nature of various tools; Additionally, new collaborators have repeatedly complained that most of the tools on the OSG are hard to discover; and even after they discover a tool, the interface is not uniform, and requires them to learn a new interface and its data format. MyOSG addresses these concerns: The primary idea is to use an authoritative source of information about OSG entities as a backbone, and organize data from different tools around this backbone to create a web portal. Further, MyOSG provides the ability for users to export / subscribe to a variety of information in formats such as XML, UWA -- an industry standard widget format, iCal -- for calendar type information, and others. This enables a user to construct Individual Information Centers (IIC) on tools such as iGoogle, Netvibes, Opera Widgets, and on mobile devices such as iPhone, etc. In summary, MyOSG is a highly customizable web portal that allows vastly different categories of users to access information they find important to their role in a format that is convenient to them.

Molecular dynamics simulation has been used to investigate the infrared spectra of ordered and disordered benzoic acid crystals consisting of various proportions of the A and B configurations, whose C–O and C=O bonds are approximately parallel to the a axis, respectively. The simulation reproduced well the splitting and the temperature dependence in intensity for the C=O stretching bands observed. The absorption coefficient of the lower frequency band was simulated as several times larger than that of the higher frequency band in accord with the observed. To interpret this peculiar result of the molecular dynamics simulation, a simple calculation of the band splitting has been made in terms of the transition dipole–transition dipole interaction. It has been shown that the interaction is an essential factor to produce the large difference in intensity and the splitting for the C=O stretching bands. The higher and lower bands are interpreted as due to the A configuration reduced in intensity by the B form, and due to the B form enhanced in intensity by the A form, respectively. Compression effect in the O⋅⋅⋅O distance of the hydrogen bond is also studied in comparison with the observed value.

In order to study the effect of the potential well on the single ion dynamics and the charge transport in molten LiNO3, a molecular dynamics simulation, which included all degrees of freedom of vibrating nitrate ions, was carried out. Simple Coulomb pair potential with Born‐type repulsion was adopted as a standard, and a potential well of varying depth between Li+ and O of NO−3 was added to the standard potential. As the well depth increased, both the translational and orientational diffusion were found to slow down, leading to solid like dynamics. The potential dependence of the ionic dynamics was studied from the translational, orientational, and current correlation functions. Results of the simulation were compared with the experimental diffusion constants, static conductivity, and rotational behavior revealed by Raman spectroscopy. Using the relation between the infrared absorption spectrum and the autocorrelation function of the dipole moment (or the current) of the system, we carried out the first s...

Gas gangrene, which is a severe and life-threatening disease, has been very rare in the head and neck region. A case of gas gangrene spreading within the bilateral cheek, oral floor, neck and upper mediastinum is reported. A 51-year-old man having a history of liver cirrhosis was admitted to Nagoya City University Hospital, due to persistent swelling and pain in his neck following gingibitis of his lower jaw, in spite of medical treatments involving antibiotics. He had high fever and jaundice. Severe swelling and redness were observed in his face, neck and upper chest wall. Macroscopic hematuria, leukocytosis, thrombocytopenia were also observed. He was recovered after transient shock with three times complementary surgical drainages and debridements under general anesthesia, supported by effective antibiotics. The foci of abscess were successfully oriented by computed tomography at every operation. Thus the computed tomography was very useful to determine the indication and suitable method of drainage and debridement of gas gangrene.