Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2

We report single-molecule folding studies of a small, single-domain protein, chymotrypsin inhibitor 2 (CI2). CI2 is an excellent model system for protein folding studies and has been extensively studied, both experimentally (at the ensemble level) and theoretically. Conformationally assisted ligation methodology was used to synthesize the proteins and site-specifically label them with donor and acceptor dyes. Folded and denatured subpopulations were observed by fluorescence resonance energy transfer (FRET) measurements on freely diffusing single protein molecules. Properties of these subpopulations were directly monitored as a function of guanidinium chloride concentration. It is shown that new information about different aspects of the protein folding reaction can be extracted from such subpopulation properties. Shifts in the mean transfer efficiencies are discussed, FRET efficiency distributions are translated into potentials, and denaturation curves are directly plotted from the areas of the FRET peaks. Changes in stability caused by mutation also are measured by comparing pseudo wild-type CI2 with a destabilized mutant (K17G). Current limitations and future possibilities and prospects for single-pair FRET protein folding investigations are discussed.

Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy

We report single-molecule measurements on the folding and unfolding conformational equilibrium distributions and dynamics of a disulfide crosslinked version of the two-stranded coiled coil from GCN4. The peptide has a fluorescent donor and acceptor at the N termini of its two chains and a Cys disulfide near its C terminus. Thus, folding brings the two N termini of the two chains close together, resulting in an enhancement of fluorescent resonant energy transfer. End-to-end distance distributions have thus been characterized under conditions where the peptide is nearly fully folded (0 M urea), unfolded (7.4 M urea), and in dynamic exchange between folded and unfolded states (3.0 M urea). The distributions have been compared for the peptide freely diffusing in solution and deposited onto aminopropyl silanized glass. As the urea concentration is increased, the mean end-to-end distance shifts to longer distances both in free solution and on the modified surface. The widths of these distributions indicate that the molecules are undergoing millisecond conformational fluctuations. Under all three conditions, these fluctuations gave nonexponential correlations on 1- to 100-ms time scale. A component of the correlation decay that was sensitive to the concentration of urea corresponded to that measured by bulk relaxation kinetics. The trajectories provided effective intramolecular diffusion coefficients as a function of the end-to-end distances for the folded and unfolded states. Single-molecule folding studies provide information concerning the distributions of conformational states in the folded, unfolded, and dynamically interconverting states.

The effect of the geomagnetic field on cosmic ray energy estimates and large scale anisotropy searches on data from the Pierre Auger Observatory

We present a comprehensive study of the influence of the geomagnetic field on the energy estimation of extensive air showers with a zenith angle smaller than 60 degrees, detected at the Pierre Auger Observatory. the geomagnetic field induces an azimuthal modulation of the estimated energy of cosmic rays up to the similar to 2% level at large zenith angles. We present a method to account for this modulation of the reconstructed energy. We analyse the effect of the modulation on large scale anisotropy searches in the arrival direction distributions of cosmic rays. At a given energy, the geomagnetic effect is shown to induce a pseudo-dipolar pattern at the percent level in the declination distribution that needs to be accounted for.

NaOH and KOH for preparing activated carbons used in energy and environmental applications

Alkaline hydroxides, especially sodium and potassium hydroxides, are multi-million-ton per annum commodities and strong chemical bases that have large scale applications. Some of them are related with their consequent ability to degrade most materials, depending on the temperature used. As an example, these chemicals are involved in the manufacture of pulp and paper, textiles, biodiesels, soaps and detergents, acid gases removal (e.g., SO2) and others, as well as in many organic synthesis processes. Sodium and potassium hydroxides are strong and corrosive bases, but they are also very stable chemicals that can melt without decomposition, NaOH at 318ºC, and KOH at 360ºC. Hence, they can react with most materials, even with relatively inert ones such as carbon materials. Thus, at temperatures higher than 360ºC these melted hydroxides easily react with most types of carbon-containing raw materials (coals, lignocellulosic materials, pitches, etc.), as well as with most pure carbon materials (carbon fibers, carbon nanofibers and carbon nanotubes). This reaction occurs via a solid-liquid redox reaction in which both hydroxides (NaOH or KOH) are converted to the following main products: hydrogen, alkaline metals and alkaline carbonates, as a result of the carbon precursor oxidation. By controlling this reaction, and after a suitable washing process, good quality activated carbons (ACs), a classical type of porous materials, can be prepared. Such carbon activation by hydroxides, known since long time ago, continues to be under research due to the unique properties of the resulting activated carbons. They have promising high porosity developments and interesting pore size distributions. These two properties are important for new applications such as gas storage (e.g., natural gas or hydrogen), capture, storage and transport of carbon dioxide, electricity storage demands (EDLC-supercapacitors-) or pollution control. Because these applications require new and superior quality activated carbons, there is no doubt that among the different existing activating processes, the one based on the chemical reaction between the carbon precursor and the alkaline hydroxide (NaOH or KOH) gives the best activation results. The present article covers different aspects of the activation by hydroxides, including the characteristics of the resulting activated carbons and their performance in some environment-related applications. The following topics are discussed: i) variables of the preparation method, such as the nature of the hydroxide, the type of carbon precursor, the hydroxide/carbon precursor ratio, the mixing procedure of carbon precursor and hydroxide (impregnation of the precursor with a hydroxide solution or mixing both, hydroxide and carbon precursor, as solids), or the temperature and time of the reaction are discussed, analyzing their effect on the resulting porosity; ii) analysis of the main reactions occurring during the activation process, iii) comparative analysis of the porosity development obtained from different activation processes (e.g., CO2, steam, phosphoric acid and hydroxides activation); and iv) performance of the prepared activated carbon materials on a few applications, such as VOC removal, electricity and gas storages.

Neutron cross sections: angular distributions

"Expansion of the limited amount of angular

The development of uniform distributions of uranium in beryllium by means of powder metallurgy /

"Contract AT-30-1 GEN 366."

Determination of relative power distributions in CANEL critical assemblies using catcher foil techniques /

"Contract AT(30-1)-2789."

Interpretation of the relationship between benthic fauna, geologic distributions, and methane seeps at Southern Hydrate Ridge, Oregon continental margin

Senior thesis written for Oceanography 445

Analysis of stirred mill performance using DEM simulation: Part 1 - Media motion, energy consumption and collisional environment

Stirred mills are becoming increasingly used for fine and ultra-fine grinding. This technology is still poorly understood when used in the mineral processing context. This makes process optimisation of such devices problematic. 3D DEM simulations of the flow of grinding media in pilot scale tower mills and pin mills are carried out in order to investigate the relative performance of these stirred mills. Media flow patterns and energy absorption rates and distributions are analysed here. In the second part of this paper, coherent flow structures, equipment wear and mixing and transport efficiency are analysed. (C) 2006 Published by Elsevier Ltd.

Electronic energy-transfer rate constants for geometrical isomers of a bichromophoric macrocyclic complex

The rate of electronic energy transfer (EET) between a naphthalene donor and an anthracene acceptor in [ZnL3]-(ClO4)(2) and [ZnL4](ClO4)(2) was determined by time-resolved fluorescence measurements, where L 3 and L 4 are the geometrical isomers of 6-[(anthracen-9-ylmethyl)amino]-trans-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane-13-amine (L-2), substituted with either a naphthalen-1-ylmethyl or naphthalen-2-ylmethyl donor, respectively. The energy transfer rate constant, k(EET), was determined to be (0.92 +/- 0.02) x 10(9) s(-1) for the naphthalen-1-ylmethyl-substituted isomer, while that for the naphthalen-2-ylmethyl-substituted isomer is somewhat faster, with k(EET) = (1.31 +/- 0.01) x 10(9) s(-1). The solid-state structure of [(ZnLCl)-Cl-3]ClO4 has been determined, and using molecular modeling calculations, the likely distributions of solution conformations in CH3CN have been evaluated for both complexes. The calculated conformational distributions in the common trans-III N-based isomeric form gave Forster EET rate constants that account for the differences observed and are in excellent agreement with the experimental values. It is shown that the full range of conformers must be considered to accurately reproduce the observed EET kinetics.

Techniques to improve forecasting models: applications to energy demand and price

This thesis is a study of three techniques to improve performance of some standard fore-casting models, application to the energy demand and prices. We focus on forecasting demand and price one-day ahead. First, the wavelet transform was used as a pre-processing procedure with two approaches: multicomponent-forecasts and direct-forecasts. We have empirically compared these approaches and found that the former consistently outperformed the latter. Second, adaptive models were introduced to continuously update model parameters in the testing period by combining ?lters with standard forecasting methods. Among these adaptive models, the adaptive LR-GARCH model was proposed for the fi?rst time in the thesis. Third, with regard to noise distributions of the dependent variables in the forecasting models, we used either Gaussian or Student-t distributions. This thesis proposed a novel algorithm to infer parameters of Student-t noise models. The method is an extension of earlier work for models that are linear in parameters to the non-linear multilayer perceptron. Therefore, the proposed method broadens the range of models that can use a Student-t noise distribution. Because these techniques cannot stand alone, they must be combined with prediction models to improve their performance. We combined these techniques with some standard forecasting models: multilayer perceptron, radial basis functions, linear regression, and linear regression with GARCH. These techniques and forecasting models were applied to two datasets from the UK energy markets: daily electricity demand (which is stationary) and gas forward prices (non-stationary). The results showed that these techniques provided good improvement to prediction performance.

Experimental deuteron momentum distributions with reduced final state interactions

This dissertation presents a study of the D( e, e′p)n reaction carried out at the Thomas Jefferson National Accelerator Facility (Jefferson Lab) for a set of fixed values of four-momentum transfer Q 2 = 2.1 and 0.8 (GeV/c)2 and for missing momenta pm ranging from pm = 0.03 to pm = 0.65 GeV/c. The analysis resulted in the determination of absolute D(e,e′ p)n cross sections as a function of the recoiling neutron momentum and it's scattering angle with respect to the momentum transfer [vector] q. The angular distribution was compared to various modern theoretical predictions that also included final state interactions. The data confirmed the theoretical prediction of a strong anisotropy of final state interaction contributions at Q2 of 2.1 (GeV/c)2 while at the lower Q2 value, the anisotropy was much less pronounced. At Q2 of 0.8 (GeV/c)2, theories show a large disagreement with the experimental results. The experimental momentum distribution of the bound proton inside the deuteron has been determined for the first time at a set of fixed neutron recoil angles. The momentum distribution is directly related to the ground state wave function of the deuteron in momentum space. The high momentum part of this wave function plays a crucial role in understanding the short-range part of the nucleon-nucleon force. At Q2 = 2.1 (GeV/c)2, the momentum distribution determined at small neutron recoil angles is much less affected by FSI compared to a recoil angle of 75°. In contrast, at Q2 = 0.8 (GeV/c)2 there seems to be no region with reduced FSI for larger missing momenta. Besides the statistical errors, systematic errors of about 5–6 % were included in the final results in order to account for normalization uncertainties and uncertainties in the determi- nation of kinematic veriables. The measurements were carried out using an electron beam energy of 2.8 and 4.7 GeV with beam currents between 10 to 100 &mgr; A. The scattered electrons and the ejected protons originated from a 15cm long liquid deuterium target, and were detected in conicidence with the two high resolution spectrometers of Hall A at Jefferson Lab.^

Additional evidence for fisheries acoustics : small cameras and angling gear provide tilt angle distributions and other relevant data for mackerel surveys

Acknowledgements This work received funding from the Marine Alliance for Science and Technology for Scotland (MASTS) pooling initiative and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. We thank Joshua Lawrence and Niall Fallon for their assistance in collecting some of the video data.

An Empirically Based Stochastic Turbulence Simulator with Temporal Coherence for Wind Energy Applications

In this dissertation, we develop a novel methodology for characterizing and simulating nonstationary, full-field, stochastic turbulent wind fields.

In this new method, nonstationarity is characterized and modeled via temporal coherence, which is quantified in the discrete frequency domain by probability distributions of the differences in phase between adjacent Fourier components.

The empirical distributions of the phase differences can also be extracted from measured data, and the resulting temporal coherence parameters can quantify the occurrence of nonstationarity in empirical wind data.

This dissertation (1) implements temporal coherence in a desktop turbulence simulator, (2) calibrates empirical temporal coherence models for four wind datasets, and (3) quantifies the increase in lifetime wind turbine loads caused by temporal coherence.

The four wind datasets were intentionally chosen from locations around the world so that they had significantly different ambient atmospheric conditions.

The prevalence of temporal coherence and its relationship to other standard wind parameters was modeled through empirical joint distributions (EJDs), which involved fitting marginal distributions and calculating correlations.

EJDs have the added benefit of being able to generate samples of wind parameters that reflect the characteristics of a particular site.

Lastly, to characterize the effect of temporal coherence on design loads, we created four models in the open-source wind turbine simulator FAST based on the \windpact turbines, fit response surfaces to them, and used the response surfaces to calculate lifetime turbine responses to wind fields simulated with and without temporal coherence.

The training data for the response surfaces was generated from exhaustive FAST simulations that were run on the high-performance computing (HPC) facilities at the National Renewable Energy Laboratory.

This process was repeated for wind field parameters drawn from the empirical distributions and for wind samples drawn using the recommended procedure in the wind turbine design standard \iec.

The effect of temporal coherence was calculated as a percent increase in the lifetime load over the base value with no temporal coherence.

A Molecular-scale Programmable Stochastic Process Based On Resonance Energy Transfer Networks: Modeling And Applications

While molecular and cellular processes are often modeled as stochastic processes, such as Brownian motion, chemical reaction networks and gene regulatory networks, there are few attempts to program a molecular-scale process to physically implement stochastic processes. DNA has been used as a substrate for programming molecular interactions, but its applications are restricted to deterministic functions and unfavorable properties such as slow processing, thermal annealing, aqueous solvents and difficult readout limit them to proof-of-concept purposes. To date, whether there exists a molecular process that can be programmed to implement stochastic processes for practical applications remains unknown.

In this dissertation, a fully specified Resonance Energy Transfer (RET) network between chromophores is accurately fabricated via DNA self-assembly, and the exciton dynamics in the RET network physically implement a stochastic process, specifically a continuous-time Markov chain (CTMC), which has a direct mapping to the physical geometry of the chromophore network. Excited by a light source, a RET network generates random samples in the temporal domain in the form of fluorescence photons which can be detected by a photon detector. The intrinsic sampling distribution of a RET network is derived as a phase-type distribution configured by its CTMC model. The conclusion is that the exciton dynamics in a RET network implement a general and important class of stochastic processes that can be directly and accurately programmed and used for practical applications of photonics and optoelectronics. Different approaches to using RET networks exist with vast potential applications. As an entropy source that can directly generate samples from virtually arbitrary distributions, RET networks can benefit applications that rely on generating random samples such as 1) fluorescent taggants and 2) stochastic computing.

By using RET networks between chromophores to implement fluorescent taggants with temporally coded signatures, the taggant design is not constrained by resolvable dyes and has a significantly larger coding capacity than spectrally or lifetime coded fluorescent taggants. Meanwhile, the taggant detection process becomes highly efficient, and the Maximum Likelihood Estimation (MLE) based taggant identification guarantees high accuracy even with only a few hundred detected photons.

Meanwhile, RET-based sampling units (RSU) can be constructed to accelerate probabilistic algorithms for wide applications in machine learning and data analytics. Because probabilistic algorithms often rely on iteratively sampling from parameterized distributions, they can be inefficient in practice on the deterministic hardware traditional computers use, especially for high-dimensional and complex problems. As an efficient universal sampling unit, the proposed RSU can be integrated into a processor / GPU as specialized functional units or organized as a discrete accelerator to bring substantial speedups and power savings.