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Monthly Archives: March 2012

The interactions of zinc thiolate complexes and exogenous metal species: Investigations of thiolate bridging and metal exchange

Small molecule ZnII) complexes containing N- and S-donor environments may serve as appropriate models for mimicking Zn protein sites, and thus, their reactions with heavy metal ions such as PtII) and W0) may provide insight into possible adduct formation and zinc displacement. To study such possible interactions between zinc finger proteins and platinum-bound DNA, the ZnN2S2 dimeric complex, N,N-bis2-mercaptoethyl)-1,4-diazacycloheptane zinc II), [Zn-1]2, has been examined for Zn-bound thiolate reactivity in the presence of PtII) nitrogen-rich compounds. The reactions yielded Zn/Pt di- and tri-nuclear thiolate-bridged adducts and metal-exchanged products, which were initially observed via ESI-mass spectrometry ESI-MS) analysis of reaction solutions, and ultimately verified by comparison to the ESI-MS analysis, 195Pt NMR spectroscopy, and X-ray crystallography of directly synthesized complexes. The isolation of Zn-micro-SR)-Pt-bridged [Znbme-dach)Cl)Ptdien))]Cl adduct from these studies is, to our knowledge, the first Zn-Pt bimetallic thiolate-bridged model demonstrating the interaction between Zn-bound thiolates and PtII). Additional derivatives involving PdII) and AuIII) have been explored to parallel the experiments executed with PtII). The [Zn-1]2 was then modified by cleavage with Na ＋[ICH2CO2]- to produce N-3-Thiabutyl)-N-3-thiapentaneoate)-1,4-diazacycloheptane) zincII), Zn-1-Ac or ZnN2SSO, and 1,4-diazacycloheptane-1,4-diylbis3-thiapentanoato) zincII), Zn-1-Ac2 or ZnN2S2O 2, monomeric complexes where S ＝ thiolate, S ＝ thioether). The [Zn-1]2 di- and Zn-1-Ac mono-thiolato complexes demonstrated reactivity towards labile-ligand tungsten carbonyl species, THF)WCO) 5 and pip)2WCO)4, to yield, respectively, the [Zn-1-Cl)WCO)4]- complex and the [Zn-1-Ac)WCO)5]x coordination polymer. With the aid of CO ligands for IR spectral monitoring, the products were isolated and characterized spectroscopically, as well as by X-ray diffraction and elemental analysis. To examine the potential for zinc complexes or zinc-templated ligands) to possibly serve as a toxic metal remediation agents, Zn-1-Ac and Zn-1-Ac2 were reacted with NiBF4)2. The formation of Zn/Ni exchanged products confirmed the capability of “free” NiII) to displace ZnII) within the N-, S-, and O-chelate environment. The Zn/Ni exchanged complexes were analyzed by ESI-MS, UV-visible spectroscopy, IR spectroscopy of the acetate regions, and X-ray crystallography. They serve as foundation molecules for more noxious metal exchange/zinc displacement products.

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Higher-level canonical subgroups for P-divisible groups

Let R be a complete rank-1 valuation ring of mixed characteristic (0,p), and let K be its field of fractions. A g-dimensional truncated Barsotti-Tate group G of level n over R is said to have a level-n canonical subgroup if there is a K-subgroup of G &otimes；R K with geometric structure ( Z/pnZ)g consisting of points “closest to zero”. We give a nontrivial condition on the Hasse invariant of G that guarantees the existence of the canonical subgroup, which is analogous to a result of Katz and Lubin for elliptic curves.

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Space-time forecasting and evaluation of wind speed with statistical tests for comparing accuracy of spatial predictions

High-quality short-term forecasts of wind speed are vital to making wind power a more reliable energy source. Gneiting et al. 2006) have introduced a model for the average wind speed two hours ahead based on both spatial and temporal information. The forecasts produced by this model are accurate, and subject to accuracy, the predictive distribution is sharp, i.e., highly concentrated around its center. However, this model is split into nonunique regimes based on the wind direction at an off-site location. This work both generalizes and improves upon this model by treating wind direction as a circular variable and including it in the model. It is robust in many experiments, such as predicting at new locations. This is compared with the more common approach of modeling wind speeds and directions in the Cartesian space and use a skew-t distribution for the errors. The quality of the predictions from all of these models can be more realistically assessed with a loss measure that depends upon the power curve relating wind speed to power output. This proposed loss measure yields more insight into the true value of each models predictions. One method of evaluating time series forecasts, such as wind speed forecasts, is to test the null hypothesis of no difference in the accuracy of two competing sets of forecasts. Diebold and Mariano 1995) proposed a test in this setting that has been extended and widely applied. It allows the researcher to specify a wide variety of loss functions, and the forecast errors can be non-Gaussian, nonzero mean, serially correlated, and contemporaneously correlated. In this work, a similar unconditional test of forecast accuracy for spatial data is proposed. The forecast errors are no longer potentially serially correlated but spatially correlated. Simulations will illustrate the properties of this test, and an example with daily average wind speeds measured at over 100 locations in Oklahoma will demonstrate its use. This test is compared with a wavelet-based method introduced by Shen et al. 2002) in which the presence of a spatial signal at each location in the dataset is tested.

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Parking functions and generalized Catalan numbers

Since their introduction by Konheim and Weiss, parking functions have evolved into objects of surprising combinatorial complexity for their simple definitions. First, we introduce these structures, give a brief history of their development and give a few basic theorems about their structure. Then we examine the internal structures of parking functions, focusing on the distribution of descents and inversions in parking functions. We develop a generalization to the Catalan numbers in order to count subsets of the parking functions. Later, we introduce a generalization to parking functions in the form of k-blocked parking functions, and examine their internal structure. Finally, we expand on the extension to the Catalan numbers, exhibiting examples to explore its internal structure. These results continue the exploration of the deep structures of parking functions and their relationship to other combinatorial objects.

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Binary drop coalescence in liquids

Experiments on binary drop collisions within an index-matched liquid were conducted for Weber numbers We) of 1-50 and collision angles of 15-80&deg； below the horizontal. Drop pairs of water/glycerin mixture were injected into silicone oil and, due to gravitational effects, traveled on downward trajectories before colliding. A dual-field high-speed PIV measurement system was employed to quantify drop trajectories and overall collision conditions while simultaneously examining detailed velocity fields near the collision interface. In the We range examined, for equal size drops, both rebounding and coalescing behavior occurred. The drops coalesced for We ＞ 10 and rebounded for We &lt； 10, and this boundary was found to be insensitive to collision angle. Coalescence was found to result from a combination of vortical flow within drops and strong drop deformation characteristic of higher We. Flow through the centers of opposing ring vortices, strengthened by drop deformation, enhanced drainage of the thin film in the impact region, leading to film rupture and coalescence. The collision angle affected the eventual location of film rupture, with the rupture location moving higher in the thin film region as the collision angle increased. The film rupture location correlated closely with the location of maximum downward velocity in the thin film. The time between collision and rupture increases with We until We ＝ 30. For We ＞ 30, the time decreases as We increases. Unequal size drop collisions with drop size ratios Ds/D L) of 0.7 and 0.5 were also examined. Coalescence occurs above We* ＝ 11 similar to equal size drops. As drop size ratio decreases, the intervening film deforms more. If the velocity ratio uL/u s &lt； 1, the deformed interface becomes flat before coalescence. The rupture location varies due to the asymmetry of the drops. As collision offset increases B ＞ 0), the film rupture time is shortened and mixing of the fluid from both drops is enhanced after coalescence. The presence of tracer particles in the intervening film does not affect the minimum Weber number for coalescence, but the film ruptures earlier compared with cases lacking tracer particles.

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Data fusion in scientific data mining

Data fusion involves multi-sources or multi-presentations of a single source to perform inferences which are more comprehensive and accurate than those of any single method. Thus, data fusion makes it possible to create a synergistic process in which the consolidation of individual data creates a combined resource with a productive value greater than the sum of its parts. While considerable research has been done on data fusion in the past, most of them performed in the field of multi-sensor fusion. There has been relatively less work conducted in a data mining context. The goal of this dissertation is to develop a data fusion framework for predictive modeling, especially to the Quantitative Structure-Activity Relationship QSAR) problems, which includes a function-oriented model, general architecture paradigms and corresponding learning algorithms. Furthermore, kernel methods, e.g. kernel partial least squares K-PLS) ensemble with bagging and boosting is introduced as one of important decision level fusion methods. This approach can be applied to applications with multiple data sources available to obtain information of greater quality. In addition to the predefined three fusion levels, the kernel fusion method is further developed based on the properties of kernel in the feature space to take advantages of multiple physically different feature sets in order to build more accurate and robust predictive models. With Hessian-free and self-correction properties, the BFGS quasi-Newton method is employed for parameter tuning of kernel fusion. In addition to the regression algorithm applied in data fusion scheme introduced above, we also are trying to extend K-PLS to the classification, especially when the class distribution is highly skewed or changes dramatically over time. In this case, a probabilistic classifier with the capability to deal with high dimensional discrimination is desirable. To achieve this goal, a new kernel orthonormalized PLS logistic regression KOPLS-LR) and the corresponding ROC based adaptive threshold ROC-BAT) approach are proposed. KOPLS-LR inherits the advantages of K-PLS and logistic regression, while ROC-BAT provides an effective solution to predict observations in which the distribution dramatically changes over time. During the research process, a web-based modeling system has been designed and realized which integrates various learning methods, e.g. PLS, K-PLS and support vector machines SVM). Model selection parameter tuning) and performance estimation functionalities are also integrated in this online predictive modeling system. This predictive tool is open to the public and can be accessed at: http://reccr.chem.rpi.edu/Software/modeling/index.html

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Nuclear resonant scattering on nitrogenase, hydrogenase and model systems

Nitrogenase and hydrogenase are two critical iron-containing enzymes found in nature. Nitrogenase catalyzes the reduction of dinitrogen N 2) to ammonia, and hydrogenase catalyzes the evolution or consumption) of dihydrogen H2). A better understanding of these enzymes may have an impact on our ability to transition to more sustainable energy economy. Although X-ray crystallography has provided baseline structures of nitrogenase and hydrognease, and numerous spectroscopic studies and theoretical calculations have outlined catalytic mechanisms of these enzymes, the detailed mechanisms remain elusive. New spectroscopic techniques are needed. In this dissertation, three novel synchrotron radiation based nuclear resonant scattering techniques have been used to probe the metal sites of nitrogenase and hydrogenase. They are nuclear resonance vibrational spectroscopy NRVS), synchrotron radiation based perturbed angular correlations SRPAC), and nuclear forward scattering NFS, or synchrotron Mossbauer). Because of its unique selection rule, NRVS provides more detailed vibrational information about the Fe sites in metalloproteins than infrared and Raman spectroscopy. FeCO vibrations revealed by NRVS on a series of iron carbonyl complexes have been used to confirm a cis-FeCO)2 geometry in the iron center of Hmd hydrogenase. A possible water ligand has also been identified for the first time. In CO inhibited nitrogenase, NRVS revealed the relationship between the intensity of the strongest spectral feature at 188 cm-1 and the structural distortion of FeMo-co introduced by CO binding. NRVS also revealed a possible 7 iron structure for the VK cluster — a key FeMo-co precursor in the nitrogenase biosynthetic pathway. Selectively probing iron site vibrations in metalloproteins has been achieved for the first time by applying NRVS onto protein crystals from rubredoxin and MoFe protein of nitrogenase. SRPAC and NFS have been used for the first time to reveal nuclear hyperfine interactions on the metal sites of iron-sulfur proteins and related model complexes. These synchrotron radiation spectroscopic techniques demonstrate a great promise to obtain more detailed structural and electronic properties of the metal centers iron and nickel) in nitrogenase and hydrogenase than the conventional Mossbauer spectroscopy.

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Surface and bulk modification of poly(lactic acid)

The major drawbacks of PLA are its poor toughness and lack of readily reactable groups. Unfortunately, typical methods of PLA toughening are associated with significant modulus and/or ultimate tensile strength UTS) loss. The main objective of this research was to toughen PLA, with minimal modulus and/or UTS loss, and introduce reactive groups into the PLA matrix in one step. Initially, this objective was divided into two separate parts: PLA surface modification followed by toughening. PLA film was solvent cast from chloroform solution and was surface modified using a sequential two-step photografting approach. Benzophenone was photografted onto the film surface in Step 1 followed by photopolymerization of hydrophilic monomers, acrylic acid and acrylamide, from the film surface. The resultant films were characterized using ATR-FTIR spectroscopy, water contact angle goniometry, transmission FTIR microspectroscopy, and tensile testing. The effect of the reaction solvent ethanol and water) in Step 2 on PLA film surface and bulk properties was also studied. There was significant penetration of monomers into the films when ethanol was used as the reaction solvent, resulting in significant toughness loss. This monomer penetration into the films was successfully reduced by using water instead of ethanol as the reaction solvent in Step 2 and resultant films showed higher toughness than films surface-modified using ethanol as the reaction solvent in Step 2. It was also observed that solvent cast PLA film retained approximately 13 wt% chloroform, as characterized using thermogravimetric analyses TGA). The presence of residual chloroform in the film specimens is undesirable from a biocompatibility standpoint. Therefore, further work was conducted on melt-processed films where residual solvent from the film-formation method would not be an issue. Addition of a small amount of poly[3-hydroxybutyrate)-co-3-hydroxyhexanoate)] PHBHHx) to PLA improved the toughness of the resultant melt-processed blend from 4 ＋/- 2 MPa for neat PLA to 175 ＋/- 35 MPa for PLA-PHBHHx blend 90 wt% PLA). PLA-PHBHHx blend films were melt-processed using a single screw extruder. These polyblend films appeared to be non-compatible as characterized using dynamic mechanical analyses DMA). PLA-PHBHHx blend films underwent rapid physical aging losing their toughness from 175 ＋/- 35 MPa right after extrusion) to 68 ＋/- 34 MPa day 3). The blend films were surface modified using the sequential two-step photografting protocol using water as the reaction solvent in Step 2. PLA-PHBHHx blend films lost approximately 95% of their toughness on surface modification due to UV-assisted solvent induced crystallization as characterized using wide angle X-ray diffraction WAXD) analyses. A novel reactive blending approach was developed to toughen PLA with minimal modulus and UTS loss and introduce reactive groups into the PLA matrix. PLA was reactive blended with a stiffening polymer, polyacrylic acid) PAA), followed by physical blending with a toughening polymer, polyethylene glycol) PEG), in solution. The modified PLA was extruded into films using a co-rotating twin-screw extruder and characterized using tensile testing, differential scanning calorimetry DSC), DMA, and toluidine-blue-surface-staining. This material exhibited, for the first time, approximately 10 fold increase in PLAs toughness without significant modulus and/or UTS loss and also introduced a controlled concentration of surface modifiable reactive acid groups into the PLA matrix in one step.

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New directions in multivariate public key cryptography

Most public key cryptosystems used in practice are based on integer factorization or discrete logarithms in finite fields or elliptic curves). However, these systems suffer from two potential drawbacks. First, they must use large keys to maintain security, resulting in decreased efficiency. Second, if large enough quantum computers can be built, Shors algorithm will render them completely insecure. Multivariate public key cryptosystems MPKC) are one possible alternative. MPKC makes use of the fact that solving multivariate polynomial systems over a finite field is an NP-complete problem, for which it is not known whether there is a polynomial algorithm on quantum computers. The main goal of this work is to show how to use new mathematical structures, specifically polynomial identities from algebraic geometry, to construct new multivariate public key cryptosystems. We begin with a basic overview of MPKC and present several significant cryptosystems that have been proposed. We also examine in detail some of the most powerful attacks against MPKCs. We propose a new framework for constructing multivariate public key cryptosystems and consider several strategies for constructing polynomial identities that can be utilized by the framework. In particular, we have discovered several new families of polynomial identities. Finally, we propose our new cryptosystem and give parameters for which it is secure against known attacks on MPKCs.

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Falling through spacetime: Four studies in neutrino astrophysics

For a significant fraction of the history of the universe, neutrinos freely fall through spacetime. While they only weakly interact with matter, neutrinos have a significant impact in astrophysics. Experimental neutrino physics and observational cosmology are amidst an interesting era, where precision measurements in both fields have significantly improved scientific understanding of the standard model of particle physics and of the universe. Experiments in neutrino physics have not only discerned that neutrinos are massive particles, but have also measured their relative masses but not their absolute masses) and the quantum mechanical mixing matrix that is a consequence of these differing mass scales. Meanwhile, precision cosmological observations have determined the energy content of the universe, which in turn has presented a self-consistent story of the history and evolution of the universe and its contents. The topics discussed in this dissertation are based upon an interplay between these two fields, at times pushing the envelope, but always focused upon the basic physical processes that affect massive neutrinos in an expanding universe. A hearty, pedagogical introduction is presented to highlight the relevant neutrino physics described in this work and an overview of cosmology, strongly biased toward the early universe, the paradigm in which much of the work in this dissertation is based. Sterile neutrinos in different regimes of mass and mixing with active neutrinos are proposed as well as asymmetries between the number density of active neutrinos and antineutrinos in the early universe. The consequences of these two propositions are discussed in terms of observables such as primordial light element abundances and the observables related to a sterile neutrino dark matter candidate. Neutrino emission from high-entropy electron-positron plasmas are introduced, and the effects of this large flux of neutrinos and antineutrinos on hot hydrogen burning are explored. Finally, the nature of the cosmic neutrino background, a relic of the hot Big Bang, is discussed as they freely fall through spacetime from weak decoupling to the present epoch.

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