Non-Empirically Tuned Range-Separated DFT Accurately Predicts Both Fundamental and Excitation Gaps in DNA and RNA Nucleobases

Using a non-empirically tuned range-separated DFT approach, we study both the quasiparticle properties (HOMO-LUMO fundamental gaps) and excitation energies of DNA and RNA nucleobases (adenine, thymine, cytosine, guanine, and uracil). Our calculations demonstrate that a physically-motivated, first-principles tuned DFT approach accurately reproduces results from both experimental benchmarks and more computationally intensive techniques such as many-body GW theory. Furthermore, in the same set of nucleobases, we show that the non-empirical range-separated procedure also leads to significantly improved results for excitation energies compared to conventional DFT methods. The present results emphasize the importance of a non-empirically tuned range-separation approach for accurately predicting both fundamental and excitation gaps in DNA and RNA nucleobases.Comment: Accepted by the Journal of Chemical Theory and Computatio

PAMELA: An Open-Source Software Package for Calculating Nonlocal Exact Exchange Effects on Electron Gases in Core-Shell Nanowires

We present a new pseudospectral approach for incorporating many-body, nonlocal exact exchange interactions to understand the formation of electron gases in core-shell nanowires. Our approach is efficiently implemented in the open-source software package PAMELA (Pseudospectral Analysis Method with Exchange & Local Approximations) that can calculate electronic energies, densities, wavefunctions, and band-bending diagrams within a self-consistent Schrodinger-Poisson formalism. The implementation of both local and nonlocal electronic effects using pseudospectral methods is key to PAMELA's efficiency, resulting in significantly reduced computational effort compared to finite-element methods. In contrast to the new nonlocal exchange formalism implemented in this work, we find that the simple, conventional Schrodinger-Poisson approaches commonly used in the literature (1) considerably overestimate the number of occupied electron levels, (2) overdelocalize electrons in nanowires, and (3) significantly underestimate the relative energy separation between electronic subbands. In addition, we perform several calculations in the high-doping regime that show a critical tunneling depth exists in these nanosystems where tunneling from the core-shell interface to the nanowire edge becomes the dominant mechanism of electron gas formation. Finally, in order to present a general-purpose set of tools that both experimentalists and theorists can easily use to predict electron gas formation in core-shell nanowires, we document and provide our efficient and user-friendly PAMELA source code that is freely available at http://alum.mit.edu/www/usagiComment: Accepted by AIP Advance

Development of a computer model to predict platform station keeping requirements in the Gulf of Mexico using remote sensing data

Offshore operations such as oil drilling and radar monitoring require semisubmersible platforms to remain stationary at specific locations in the Gulf of Mexico. Ocean currents, wind, and waves in the Gulf of Mexico tend to move platforms away from their desired locations. A computer model was created to predict the station keeping requirements of a platform. The computer simulation uses remote sensing data from satellites and buoys as input. A background of the project, alternate approaches to the project, and the details of the simulation are presented

Using access information in the dynamic visualisation of web sites

Includes bibliographical references.Log file analysis provides a cost-effective means to detennine web site usage. However, current methods of displaying log analysis results tend to be limited in that they either contain no reference to a web site's structure, or else they portray this structure as a standard graph or tree. This dissertation presents a visual representation of web server log information, which addresses these limitations by incorporating log file data into a visualisation of a web site's layout. The devised visualisation utilizes properties unique to web sites in order to create a compromise between the clutter-prone network graph and the infonnation incomplete tree representations that have traditionally been used to depict web sites. As such, the visualisation emphasises typical web site features such as the home page, sub-sites and navigation bars. This approach pennitted the introduction of the concept of implying the presence of links without explicitly rendering them. This notion has many implications, not least of which is the reduction of cluttering. The visualisation combined several other techniques to address the issues of structure and data representation, data exploration, scalability and context maintenance. Assessment of the visualisation consisted of a heuristic evaluation by an expert from the web site usage industry, a test to detelmine the intuitiveness of the representation, and a series of user experiments. Results of the assessment were generally promising although a few areas of concern, such as the difficulty experienced by users in navigating the visualisation with a trackball, were identified. These issues should not prove to be too difficult to overcome however. The visualisation could thus be said to have successfully met the aim of developing a representation of web site usage infonnation that incorporates site structure and treats web sites as unique entities, thereby taking advantage of their particular characteristics. It is hoped such a visualisation will be of benefit to web site designers and administrators in analysing and ultimately improving their web sites

The Diamine Cation Is Not a Chemical Example Where Density Functional Theory Fails

In a recent communication, Weber and co-workers presented a surprising study on charge-localization effects in the N,N'-dimethylpiperazine (DMP+) diamine cation to provide a stringent test of density functional theory (DFT) methods. Within their study, the authors examined various DFT methods and concluded that "all DFT functionals commonly used today, including hybrid functionals with exact exchange, fail to predict a stable charge-localized state." This surprising conclusion is based on the authors' use of a self-interaction correction (namely, complex-valued Perdew-Zunger Self-Interaction Correction (PZ-SIC)) to DFT, which appears to give excellent agreement with experiment and other wavefunction-based benchmarks. Since the publication of this recent communication, the same DMP+ molecule has been cited in numerous subsequent studies as a prototypical example of the importance of self-interaction corrections for accurately calculating other chemical systems. In this correspondence, we have carried out new high-level CCSD(T) analyses on the DMP+ cation to show that DFT actually performs quite well for this system (in contrast to their conclusion that all DFT functionals fail), whereas the PZ-SIC approach used by Weber et al. is the outlier that is inconsistent with the high-level CCSD(T) (coupled-cluster with single and double excitations and perturbative triples) calculations. Our new findings and analysis for this system are briefly discussed in this correspondence.Comment: Accepted by Nature Communication