Modeling of Magic Water Clusters(H20)2 and (H20)21H+ with the PM3 Quantum-Mechanical Method

The PM3 quantum-mechanical method is able to model the magic water clusters (H20),, and (H20)&+. Results indicate that the H30+ ion is tightly bound within the (H20),, cluster by multiple hydrogen bonds, causing deformation to the symmetric (HzO),, pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H20)21H+ clusters are presented.

Semiempirical Study of the Bergman Reaction: Towards a Computationally Efficient and Accurate Method for Modeling Enediyne Anticancer Antibiotics

Over the past 7 years, the enediyne anticancer antibiotics have been widely studied due to their DNA cleaving ability. The focus of these antibiotics, represented by kedarcidin chromophore, neocarzinostatin chromophore, calicheamicin, esperamicin A, and dynemicin A, is on the enediyne moiety contained within each of these antibiotics. In its inactive form, the moiety is benign to its environment. Upon suitable activation, the system undergoes a Bergman cycloaromatization proceeding through a 1,4-dehydrobenzene diradical intermediate. It is this diradical intermediate that is thought to cleave double-stranded dna through hydrogen atom abstraction. Semiempirical, semiempiricalci, Hartree–Fock ab initio, and mp2 electron correlation methods have been used to investigate the inactive hex-3-ene-1,5-diyne reactant, the 1,4-dehydrobenzene diradical, and a transition state structure of the Bergman reaction. Geometries calculated with different basis sets and by semiempirical methods have been used for single-point calculations using electron correlation methods. These results are compared with the best experimental and theoretical results reported in the literature. Implications of these results for computational studies of the enediyne anticancer antibiotics are discussed.

Structure and function of the glucose PTS transporter from Escherichia coli

The glucose transporter IICB of the Escherichia coli phosphotransferase system (PTS) consists of a polytopic membrane domain (IIC) responsible for substrate transport and a hydrophilic C-terminal domain (IIB) responsible for substrate phosphorylation. We have overexpressed and purified a triple mutant of IIC (mut-IIC), which had recently been shown to be suitable for crystallization purposes. Mut-IIC was homodimeric as determined by blue native-PAGE and gel-filtration, and had an eyeglasses-like structure as shown by negative-stain transmission electron microscopy (TEM) and single particle analysis. Glucose binding and transport by mut-IIC, mut-IICB and wildtype-IICB were compared with scintillation proximity and in vivo transport assays. Binding was reduced and transport was impaired by the triple mutation. The scintillation proximity assay allowed determination of substrate binding, affinity and specificity of wildtype-IICB by a direct method. 2D crystallization of mut-IIC yielded highly-ordered tubular crystals and made possible the calculation of a projection structure at 12Å resolution by negative-stain TEM. Immunogold labeling TEM revealed the sidedness of the tubular crystals, and high-resolution atomic force microscopy the surface structure of mut-IIC. This work presents the structure of a glucose PTS transporter at the highest resolution achieved so far and sets the basis for future structural studies.

Frog oocytes to unveil the structure and supramolecular organization of human transport proteins

Structural analyses of heterologously expressed mammalian membrane proteins remain a great challenge given that microgram to milligram amounts of correctly folded and highly purified proteins are required. Here, we present a novel method for the expression and affinity purification of recombinant mammalian and in particular human transport proteins in Xenopus laevis frog oocytes. The method was validated for four human and one murine transporter. Negative stain transmission electron microscopy (TEM) and single particle analysis (SPA) of two of these transporters, i.e., the potassium-chloride cotransporter 4 (KCC4) and the aquaporin-1 (AQP1) water channel, revealed the expected quaternary structures within homogeneous preparations, and thus correct protein folding and assembly. This is the first time a cation-chloride cotransporter (SLC12) family member is isolated, and its shape, dimensions, low-resolution structure and oligomeric state determined by TEM, i.e., by a direct method. Finally, we were able to grow 2D crystals of human AQP1. The ability of AQP1 to crystallize was a strong indicator for the structural integrity of the purified recombinant protein. This approach will open the way for the structure determination of many human membrane transporters taking full advantage of the Xenopus laevis oocyte expression system that generally yields robust functional expression.

German Validation of the Conners Adult ADHD Rating Scale-Self-Report: Confirmation of Factor Structure in a Large Sample of Participants With ADHD

Objective: The Conners Adult ADHD Rating Scales (CAARS) assess symptoms specific to adults that are frequently used and have been translated into German. The current study tests the factor structure of the CAARS in a large sample of German adults with ADHD and compares the means of the CAARS subscales with those of healthy German controls. Method: CAARS were completed by 466 participants with ADHD and 851 healthy control participants. Confirmatory factor analysis was used to establish model fit with the American original. Comparisons between participants with ADHD and healthy controls and influences of gender, age, and degree of education were analyzed. Results: Confirmatory factor analysis showed a very good fit with the model for the American original. Differences between ADHD participants and healthy controls on all Conners Adult ADHD Rating Scales-Self-Report (CAARS-S) subscales were substantial and significant. Conclusion: The factor structure of the original American model was successfully replicated in this sample of adult German ADHD participants. (J. of Att. Dis. 2012; XX(X) 1-XX).

Assessment Of Dynamic Properties Of A Crowd Model For Human-Structure Interaction Modeling

As lightweight and slender structural elements are more frequently used in the design, large scale structures become more flexible and susceptible to excessive vibrations. To ensure the functionality of the structure, dynamic properties of the occupied structure need to be estimated during the design phase. Traditional analysis method models occupants simply as an additional mass; however, research has shown that human occupants could be better modeled as an additional degree-of- freedom. In the United Kingdom, active and passive crowd models are proposed by the Joint Working Group as a result of a series of analytical and experimental research. It is expected that the crowd models would yield a more accurate estimation to the dynamic response of the occupied structure. However, experimental testing recently conducted through a graduate student project at Bucknell University indicated that the proposed passive crowd model might be inaccurate in representing the impact on the structure from the occupants. The objective of this study is to provide an assessment of the validity of the crowd models proposed by JWG through comparing the dynamic properties obtained from experimental testing data and analytical modeling results. The experimental data used in this study was collected by Firman in 2010. The analytical results were obtained by performing a time-history analysis on a finite element model of the occupied structure. The crowd models were created based on the recommendations from the JWG combined with the physical properties of the occupants during the experimental study. During this study, SAP2000 was used to create the finite element models and to implement the analysis; Matlab and ME¿scope were used to obtain the dynamic properties of the structure through processing the time-history analysis results from SAP2000. The result of this study indicates that the active crowd model could quite accurately represent the impact on the structure from occupants standing with bent knees while the passive crowd model could not properly simulate the dynamic response of the structure when occupants were standing straight or sitting on the structure. Future work related to this study involves improving the passive crowd model and evaluating the crowd models with full-scale structure models and operating data.

A MICROFLUIDIC METHOD TO MEASURE DIFFUSION IN HYDROGELS

A novel microfluidic method is proposed for studying diffusion of small molecules in a hydrogel. Microfluidic devices were prepared with semi-permeable microchannels defined by crosslinked poly(ethylene glycol) (PEG). Uptake of dye molecules from aqueous solutions flowing through the microchannels was observedoptically and diffusion of the dye into the hydrogel was quantified. To complement the diffusion measurements from the microfluidic studies, nuclear magnetic resonance(NMR) characterization of the diffusion of dye in the PEG hydrogels was performed. The diffusion of small molecules in a hydrogel is relevant to applications such asdrug delivery and modeling transport for tissue-engineering applications. The diffusion of small molecules in a hydrogel is dependent on the extent of crosslinking within the gel, gel structure, and interactions between the diffusive species and the hydrogel network. These effects were studied in a model environment (semi-infinite slab) at the hydrogelfluid boundary in a microfluidic device. The microfluidic devices containing PEG microchannels were fabricated using photolithography. The unsteady diffusion of small molecules (dyes) within the microfluidic device was monitored and recorded using a digital microscope. The information was analyzed with techniques drawn from digital microscopy and image analysis to obtain concentration profiles with time. Using a diffusion model to fit this concentration vs. position data, a diffusion coefficient was obtained. This diffusion coefficient was compared to those from complementary NMR analysis. A pulsed field gradient (PFG) method was used to investigate and quantify small molecule diffusion in gradient (PFG) method was used to investigate and quantify small molecule diffusion in hydrogels. There is good agreement between the diffusion coefficients obtained from the microfluidic methods and those found from the NMR studies. The microfluidic approachused in this research enables the study of diffusion at length scales that approach those of vasculature, facilitating models for studying drug elution from hydrogels in blood-contacting applications.

Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared to its bound form

The first step of coagulation factor XIII (FXIII) activation involves cleavage of the FXIII activation peptide (FXIII-AP) by thrombin. However, it is not known whether the FXIII-AP is released into plasma upon cleavage or remains attached to activated FXIII. The aim of the present work was to study the structure of free FXIII-AP, develop an assay for FXIII-AP determination in human plasma, and to answer the question whether FXIII-AP is released into plasma. We used ab-initio modeling and molecular dynamics simulations to study the structure of free FXIII-AP. We raised monoclonal and polyclonal antibodies against FXIII-AP and developed a highly sensitive and specific ELISA method for direct detection of FXIII-AP in human plasma. Structural analysis showed a putative different conformation of the free FXIII-AP compared to FXIII-AP bound to the FXIII protein. We concluded that it might be feasible to develop specific antibodies against the free FXIII-AP. Using our new FXIII-AP ELISA, we found high levels of FXIII-AP in in-vitro activated plasma samples and serum. We showed for the first time that FXIIIAP is detached from activated FXIII and is released into plasma, where it can be directly measured. Our findings may be of major clinical interest in regard to a possible new marker in thrombotic disease.

Vibro-acoustical analysis and design of a multiple-layer constrained viscoelastic damping structure

The goal of this research is to provide a framework for vibro-acoustical analysis and design of a multiple-layer constrained damping structure. The existing research on damping and viscoelastic damping mechanism is limited to the following four mainstream approaches: modeling techniques of damping treatments/materials; control through the electrical-mechanical effect using the piezoelectric layer; optimization by adjusting the parameters of the structure to meet the design requirements; and identification of the damping material’s properties through the response of the structure. This research proposes a systematic design methodology for the multiple-layer constrained damping beam giving consideration to vibro-acoustics. A modeling technique to study the vibro-acoustics of multiple-layered viscoelastic laminated beams using the Biot damping model is presented using a hybrid numerical model. The boundary element method (BEM) is used to model the acoustical cavity whereas the Finite Element Method (FEM) is the basis for vibration analysis of the multiple-layered beam structure. Through the proposed procedure, the analysis can easily be extended to other complex geometry with arbitrary boundary conditions. The nonlinear behavior of viscoelastic damping materials is represented by the Biot damping model taking into account the effects of frequency, temperature and different damping materials for individual layers. A curve-fitting procedure used to obtain the Biot constants for different damping materials for each temperature is explained. The results from structural vibration analysis for selected beams agree with published closed-form results and results for the radiated noise for a sample beam structure obtained using a commercial BEM software is compared with the acoustical results of the same beam with using the Biot damping model. The extension of the Biot damping model is demonstrated to study MDOF (Multiple Degrees of Freedom) dynamics equations of a discrete system in order to introduce different types of viscoelastic damping materials. The mechanical properties of viscoelastic damping materials such as shear modulus and loss factor change with respect to different ambient temperatures and frequencies. The application of multiple-layer treatment increases the damping characteristic of the structure significantly and thus helps to attenuate the vibration and noise for a broad range of frequency and temperature. The main contributions of this dissertation include the following three major tasks: 1) Study of the viscoelastic damping mechanism and the dynamics equation of a multilayer damped system incorporating the Biot damping model. 2) Building the Finite Element Method (FEM) model of the multiple-layer constrained viscoelastic damping beam and conducting the vibration analysis. 3) Extending the vibration problem to the Boundary Element Method (BEM) based acoustical problem and comparing the results with commercial simulation software.

Analytical investigation of squeeze film dampers

Squeeze film damping effects naturally occur if structures are subjected to loading situations such that a very thin film of fluid is trapped within structural joints, interfaces, etc. An accurate estimate of squeeze film effects is important to predict the performance of dynamic structures. Starting from linear Reynolds equation which governs the fluid behavior coupled with structure domain which is modeled by Kirchhoff plate equation, the effects of nondimensional parameters on the damped natural frequencies are presented using boundary characteristic orthogonal functions. For this purpose, the nondimensional coupled partial differential equations are obtained using Rayleigh-Ritz method and the weak formulation, are solved using polynomial and sinusoidal boundary characteristic orthogonal functions for structure and fluid domain respectively. In order to implement present approach to the complex geometries, a two dimensional isoparametric coupled finite element is developed based on Reissner-Mindlin plate theory and linearized Reynolds equation. The coupling between fluid and structure is handled by considering the pressure forces and structural surface velocities on the boundaries. The effects of the driving parameters on the frequency response functions are investigated. As the next logical step, an analytical method for solution of squeeze film damping based upon Green’s function to the nonlinear Reynolds equation considering elastic plate is studied. This allows calculating modal damping and stiffness force rapidly for various boundary conditions. The nonlinear Reynolds equation is divided into multiple linear non-homogeneous Helmholtz equations, which then can be solvable using the presented approach. Approximate mode shapes of a rectangular elastic plate are used, enabling calculation of damping ratio and frequency shift as well as complex resistant pressure. Moreover, the theoretical results are correlated and compared with experimental results both in the literature and in-house experimental procedures including comparison against viscoelastic dampers.

Reconstruction of the palatal aponeurosis with autogenous fascia lata in secondary radical intravelar veloplasty: a new method

Velopharyngeal insufficiency in cleft patients with muscular insufficiency detected by nasendoscopy is commonly treated by secondary radical intravelar veloplasty, in which the palatal muscles are reoriented and positioned backwards. The dead space between the retro-displaced musculature and the posterior borders of the palatal bone remains problematic. Postoperatively, the surgically achieved lengthening of the soft palate often diminishes due to scar tissue formation in the dead space, leading to reattachment of the reoriented muscles to the palatal bone and to decreased mobility of the soft palate. To avoid this, the dead space should be restored by a structure imitating the function of the missing palatal aponeurosis. The entire dead space was covered using a double layer of autogenous fascia lata harvested from the lateral thigh, which should allow sufficient and permanent sliding of the retro-positioned musculature. A clinical case of a 9-year-old boy who underwent the operation is reported. Postoperatively, marked functional improvements were observable in speech assessment, nasendoscopy and nasometry. The case reported here suggests that the restoration of the dead space may be beneficial for effective secondary palatal repair. Fascia lata seems to be a suitable graft for this purpose.

Two dimensional Lattice Boltzmann simulation of fluid flow through an idealized micro-structure of disordered media

This technical report discusses the application of Lattice Boltzmann Method (LBM) in the fluid flow simulation through porous filter-wall of disordered media. The diesel particulate filter (DPF) is an example of disordered media. DPF is developed as a cutting edge technology to reduce harmful particulate matter in the engine exhaust. Porous filter-wall of DPF traps these soot particles in the after-treatment of the exhaust gas. To examine the phenomena inside the DPF, researchers are looking forward to use the Lattice Boltzmann Method as a promising alternative simulation tool. The lattice Boltzmann method is comparatively a newer numerical scheme and can be used to simulate fluid flow for single-component single-phase, single-component multi-phase. It is also an excellent method for modelling flow through disordered media. The current work focuses on a single-phase fluid flow simulation inside the porous micro-structure using LBM. Firstly, the theory concerning the development of LBM is discussed. LBM evolution is always related to Lattice gas Cellular Automata (LGCA), but it is also shown that this method is a special discretized form of the continuous Boltzmann equation. Since all the simulations are conducted in two-dimensions, the equations developed are in reference with D2Q9 (two-dimensional 9-velocity) model. The artificially created porous micro-structure is used in this study. The flow simulations are conducted by considering air and CO2 gas as fluids. The numerical model used in this study is explained with a flowchart and the coding steps. The numerical code is constructed in MATLAB. Different types of boundary conditions and their importance is discussed separately. Also the equations specific to boundary conditions are derived. The pressure and velocity contours over the porous domain are studied and recorded. The results are compared with the published work. The permeability values obtained in this study can be fitted to the relation proposed by Nabovati [8], and the results are in excellent agreement within porosity range of 0.4 to 0.8.

A new method to monitor visual field defects caused by photoreceptor degeneration by quantitative optical coherence tomography

PURPOSE: To correlate the dimension of the visual field (VF) tested by Goldman kinetic perimetry with the extent of visibility of the highly reflective layer between inner and outer segments of photoreceptors (IOS) seen in optical coherence tomography (OCT) images in patients with retinitis pigmentosa (RP). METHODS: In a retrospectively designed cross-sectional study, 18 eyes of 18 patients with RP were examined with OCT and Goldmann perimetry using test target I4e and compared with 18 eyes of 18 control subjects. A-scans of raw scan data of Stratus OCT images (Carl Zeiss Meditec, AG, Oberkochen, Germany) were quantitatively analyzed for the presence of the signal generated by the highly reflective layer between the IOS in OCT images. Starting in the fovea, the distance to which this signal was detectable was measured. Visual fields were analyzed by measuring the distance from the center point to isopter I4e. OCT and visual field data were analyzed in a clockwise fashion every 30 degrees , and corresponding measures were correlated. RESULTS: In corresponding alignments, the distance from the center point to isopter I4e and the distance to which the highly reflective signal from the IOS can be detected correlate significantly (r = 0.75, P < 0.0001). The greater the distance in VF, the greater the distance measured in OCT. CONCLUSIONS: The authors hypothesize that the retinal structure from which the highly reflective layer between the IOS emanates is of critical importance for visual and photoreceptor function. Further research is warranted to determine whether this may be useful as an objective marker of progression of retinal degeneration in patients with RP.

Unresolved Problems with the "I", the "A" and the "T": Logical and Psychometric Critique of the Implicit Association Test (IAT)

The Implicit Association Test (IAT) had already gained the status of a prominent assessment procedure before its psychometric properties and underlying task structure were understood. The present critique addresses five major problems that arise when the IAT is used for diagnostic inferences: (1) the asymmetry of causal and diagnostic inferences; (2) the viability of the underlying association model; (3) the lack of a testable model underlying IAT-based inferences; (4) the difficulties of interpreting difference scores; and (5) the susceptibility of the IAT to deliberate faking and strategic processing. Based on a theoretical reflection of these issues, and a comprehensive survey of published IAT studies, it is concluded that a number of uncontrolled factors can produce (or reduce) significant IAT scores independently of the personality attribute that is supposed to be captured by the IAT procedure.

Multi-scale micro-structure generation strategy for up-scaling transport in clays

Clays and claystones are used as backfill and barrier materials in the design of waste repositories, because they act as hydraulic barriers and retain contaminants. Transport through such barriers occurs mainly by molecular diffusion. There is thus an interest to relate the diffusion properties of clays to their structural properties. In previous work, we have developed a concept for up-scaling pore-scale molecular diffusion coefficients using a grid-based model for the sample pore structure. Here we present an operational algorithm which can generate such model pore structures of polymineral materials. The obtained pore maps match the rock’s mineralogical components and its macroscopic properties such as porosity, grain and pore size distributions. Representative ensembles of grains in 2D or 3D are created by a lattice Monte Carlo (MC) method, which minimizes the interfacial energy of grains starting from an initial grain distribution. Pores are generated at grain boundaries and/or within grains. The method is general and allows to generate anisotropic structures with grains of approximately predetermined shapes, or with mixtures of different grain types. A specific focus of this study was on the simulation of clay-like materials. The generated clay pore maps were then used to derive upscaled effective diffusion coefficients for non-sorbing tracers using a homogenization technique. The large number of generated maps allowed to check the relations between micro-structural features of clays and their effective transport parameters, as is required to explain and extrapolate experimental diffusion results. As examples, we present a set of 2D and 3D simulations and investigated the effects of nanopores within particles (interlayer pores) and micropores between particles. Archie’s simple power law is followed in systems with only micropores. When nanopores are present, additional parameters are required; the data reveal that effective diffusion coefficients could be described by a sum of two power functions, related to the micro- and nanoporosity. We further used the model to investigate the relationships between particle orientation and effective transport properties of the sample.