Gary E. Gorbet

Characterization of size, anisotropy, and density heterogeneity of nanoparticles by sedimentation velocity.

A critical problem in materials science is the accurate characterization of the size dependent properties of colloidal inorganic nanocrystals. Due to the intrinsic polydispersity present during synthesis, dispersions of such materials exhibit simultaneous heterogeneity in density ρ, molar mass M, and particle diameter d. The density increments ∂ρ/∂d and ∂ρ/∂M of these nanoparticles, if known, can then provide important information about crystal growth and particle size distributions. For most classes of nanocrystals, a mixture of surfactants is added during synthesis to control their shape, size, and optical properties. However, it remains a challenge to accurately determine the amount of passivating ligand bound to the particle surface post synthesis. The presence of the ligand shell hampers an accurate determination of the nanocrystal diameter. Using CdSe and PbS semiconductor nanocrystals, and the ultrastable silver nanoparticle (M4Ag44(p-MBA)30), as model systems, we describe a Custom Grid method implemented in UltraScan-III for the characterization of nanoparticles and macromolecules using sedimentation velocity analytical ultracentrifugation. We show that multiple parametrizations are possible, and that the Custom Grid method can be generalized to provide high resolution composition information for mixtures of solutes that are heterogeneous in two out of three parameters. For such cases, our method can simultaneously resolve arbitrary two-dimensional distributions of hydrodynamic parameters when a third property can be held constant. For example, this method extracts partial specific volume and molar mass from sedimentation velocity data for cases where the anisotropy can be held constant, or provides anisotropy and partial specific volume if the molar mass is known.

A parametrically constrained optimization method for fitting sedimentation velocity experiments.

A method for fitting sedimentation velocity experiments using whole boundary Lamm equation solutions is presented. The method, termed parametrically constrained spectrum analysis (PCSA), provides an optimized approach for simultaneously modeling heterogeneity in size and anisotropy of macromolecular mixtures. The solutions produced by PCSA are particularly useful for modeling polymerizing systems, where a single-valued relationship exists between the molar mass of the growing polymer chain and its corresponding anisotropy. The PCSA uses functional constraints to identify this relationship, and unlike other multidimensional grid methods, assures that only a single molar mass can be associated with a given anisotropy measurement. A description of the PCSA algorithm is presented, as well as several experimental and simulated examples that illustrate its utility and capabilities. The performance advantages of the PCSA method in comparison to other methods are documented. The method has been added to the UltraScan-III software suite, which is available for free download from http://www.ultrascan.uthscsa.edu.

The apache airavata application programming interface: overview and evaluation with the UltraScan science gateway

We present an overview of the Apache Airavata Application Programming Interface (API), describe the design choices and implementation details, and describe how API methods map to the UltraScan Science Gateway use case. The Airavata API is designed to standardize access to Airavata services that provide gateways with scientific application metadata and execution management. The API also represents an important milestone in the development of Science Gateway Platform as a Service (SciGaP), a hosted, multi-tenanted gateway service based on open source Airavata software. The UltraScan gateway is a production XSEDE gateway that has been using Airavata services for over three years through customized interfaces and represents a stringent test of the API design and implementation.

Analytical Ultracentrifugation Data Analysis with UltraScan-III

The current status of the UltraScan-III (US3) data analysis software suite is described. An overview of the US3 concepts, software layout, the data workflows and US3 components is presented, followed by a discussion of the analysis methods and their applications. Also described are visualization modules for analysis results, US3’s utilities and simulation tools, as well as the collaboration environments for online data and result exchange.

Next-Generation AUC : Analysis of Multiwavelength Analytical Ultracentrifugation Data

We describe important advances in methodologies for the analysis of multiwavelength data. In contrast to the Beckman-Coulter XL-A/I ultraviolet-visible light detector, multiwavelength detection is able to simultaneously collect sedimentation data for a large wavelength range in a single experiment. The additional dimension increases the data density by orders of magnitude, posing new challenges for data analysis and management. The additional data not only improve the statistics of the measurement but also provide new information for spectral characterization, which complements the hydrodynamic information. New data analysis and management approaches were integrated into the UltraScan software to address these challenges. In this chapter, we describe the enhancements and benefits realized by multiwavelength analysis and compare the results to those obtained from the traditional single-wavelength detector. We illustrate the advances offered by the new instruments by comparing results from mixtures that contain different ratios of protein and DNA samples, representing analytes with distinct spectral and hydrodynamic properties. For the first time, we demonstrate that the spectral dimension not only adds valuable detail, but when spectral properties are known, individual components with distinct spectral properties measured in a mixture by the multiwavelength system can be clearly separated and decomposed into traditional datasets for each of the spectrally distinct components, even when their sedimentation coefficients are virtually identical.

Next-Generation AUC

We describe important advances in methodologies for the analysis of multiwavelength data. In contrast to the Beckman-Coulter XL-A/I ultraviolet-visible light detector, multiwavelength detection is able to simultaneously collect sedimentation data for a large wavelength range in a single experiment. The additional dimension increases the data density by orders of magnitude, posing new challenges for data analysis and management. The additional data not only improve the statistics of the measurement but also provide new information for spectral characterization, which complements the hydrodynamic information. New data analysis and management approaches were integrated into the UltraScan software to address these challenges. In this chapter, we describe the enhancements and benefits realized by multiwavelength analysis and compare the results to those obtained from the traditional single-wavelength detector. We illustrate the advances offered by the new instruments by comparing results from mixtures that contain different ratios of protein and DNA samples, representing analytes with distinct spectral and hydrodynamic properties. For the first time, we demonstrate that the spectral dimension not only adds valuable detail, but when spectral properties are known, individual components with distinct spectral properties measured in a mixture by the multiwavelength system can be clearly separated and decomposed into traditional datasets for each of the spectrally distinct components, even when their sedimentation coefficients are virtually identical.

Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures

The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation experiments. Since 2006, the UltraScan scientific gateway has been used with Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. UltraScan supports its users with a scientific gateway in order to leverage the power of supercomputing. In this contribution, we will focus on several advancements of the UltraScan scientific gateway architecture with a standardized job management while retaining its lightweight design and end user interaction experience. This paper also presents insights into a production deployment of UltraScan in Europe. The approach is based on open standards with respect to job management and submissions to the Extreme Science and Engineering Discovery Environment in the USA and to similar infrastructures in Europe such as the European Grid Infrastructure or the Partnership for Advanced Computing in Europe (PRACE). Our implementation takes advantage of the Apache Airavata framework for scientific gateways that lays the foundation for easy integration into several other scientific gateways. Copyright

Improvements of the UltraScan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures

The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation (AUC) experiments. Since 2006, the UltraScan scientific gateway has been used with ordinary Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. Unlike other applications, UltraScan is implemented on a gateway architecture and leverages the power of supercomputing to extract very high resolution information from the experimental data. In this contribution, we will focus on several improvements of the UltraScan scientific gateway that enable a standardized job submission and management to computational resources while retaining its lightweight design in order to not disturb the established workflows of its end-users. This paper further presents a walkthrough of the architectural design including one real installation deployment of UltraScan in Europe. The aim is to provide evidence for the added value of open standards and resulting interoperability enabling not only UltraScan application submissions to resources offered in the US cyber infrastructure Extreme Science and Engineering Discovery Environment (XSEDE), but also submissions to similar infrastructures in Europe and around the world. The use of the Apache Airavata framework for scientific gateways within our approach bears the potential to have an impact on several other scientific gateways too.

Multi-speed sedimentation velocity implementation in UltraScan-III

A framework for the global analysis of multi-speed analytical ultracentrifugation sedimentation velocity experiments is presented. We discuss extensions to the adaptive space–time finite element fitting methods implemented in UltraScan-III to model sedimentation velocity experiments where a single run is performed at multiple rotor speeds, and describe extensions in the optimization routines used for fitting experimental data collected at arbitrary multi-speed profiles. Our implementation considers factors such as speed dependent rotor stretching, the resulting radial shifting of the finite element solution’s boundary conditions, and changes in the associated time-invariant noise. We also address the calculation of acceleration rates and acceleration zones from existing radial acceleration and time records, as well as utilization of the time state object available at high temporal resolution from the new Beckman Optima AUC instrument. Analysis methods in UltraScan-III support unconstrained models that extract reliable information for both the sedimentation and the diffusion coefficients. These methods do not rely on any assumptions and allow for arbitrary variations in both sedimentation and diffusion transport. We have adapted these routines for the multi-speed case, and developed optimized and general grid based fitting methods to handle changes in the information content of the simulation matrix for different speed steps. New graphical simulation tools are presented that assist the investigator to estimate suitable grid metrics and evaluate information content based on edit profiles for individual experiments.

Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge

Interactions between nucleic acids and proteins are critical for many cellular processes, and their study is of utmost importance to many areas of biochemistry, cellular biology, and virology. Here, we introduce a new analytical method based on sedimentation velocity (SV) analytical ultracentrifugation, in combination with a novel multiwavelength detector to characterize such interactions. We identified the stoichiometry and molar mass of a complex formed during the interaction of a West Nile virus RNA stem loop structure with the human T cell-restricted intracellular antigen-1 related protein. SV has long been proven as a powerful technique for studying dynamic assembly processes under physiological conditions in solution. Here, we demonstrate, for the first time, how the new multiwavelength technology can be exploited to study protein-RNA interactions, and show how the spectral information derived from the new detector complements the traditional hydrodynamic information from analytical ultracentrifugation. Our method allows the protein and nucleic acid signals to be separated by spectral decomposition such that sedimentation information from each individual species, including any complexes, can be clearly identified based on their spectral signatures. The method presented here extends to any interacting system where the interaction partners are spectrally separable.