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Show moreComputing ab initio molecular linear response properties, e.g., electronic excitation energies and transition moments, requires the solution of large eigenvalue problems or large systems of equations. These large eigenvalue problems or large systems of equations are commonly solved iteratively using Krylov space algorithms, such as the Davidson algorithm for eigenvalue problems. A critical ingredient in Krylov space algorithms is the preconditioner which is used to generate optimal update vectors in each iteration. We propose to use semiempirical approximations as preconditioners to accelerate the calculation of ab initio properties. The crucial advantage to improving the preconditioner is that the converged result is unchanged, so there is no tradeoff between accuracy and speedup. Furthermore, the structure of the algorithm is retained so existing implementations of Krylov space algorithms require only minimal modifications to incorporate the proposed semiempirical preconditioner. We demonstrate our approach by accelerating the calculation of electronic excitation energies and electric polarizabilities from linear response time-dependent density functional theory using the simplified time-dependent density functional theory semiempirical model. For excitation energies, the semiempirical preconditioner reduces the number of iterations on average by 37% and up to 70%. The semiempirical preconditioner reduces the number of iterations for computing the polarizability by 15% on average and up to 33%. We show that the preconditioner can be further improved by tuning the empirical parameters defining the semiempirical model, leading to an additional reduction in the number of iterations by about 20%. Our approach bridges the gap between semiempirical models and ab initio methods and charts a path towards combining the speed of semiempirical models with the accuracy of ab initio methods.
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Show moreIntramolecular BO-chelated azadipyrromethenes are promising organic semiconductors. Here, we evaluated the electron and hole mobility of a series of BO-chelated azadipyrromethenes using the Space Charge Limited Current(SCLC) method. In order to determine the mobility of the material, Mott Gurney’s law was applied using the film thickness and slope of the J1/2 versus voltage plot in the SCLC graph. The best electron mobility observed for BO-chelated materials is 4.64×10-6 cm2V-1s-1 and the best hole mobility is 7.38×10-4 cm2V-1s-1. These results suggest that BO-chelated materials are promising p-type semiconductors for electronic applications.
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Show moreTitanium dioxide nanoparticles (TiO2 NPs) are non-toxic and biocompatible materials that are used for a wide range of applications such as pigments, sunscreens, cosmetics, and food colorings. TiO2 possesses a large band gap (3.2 eV) which, by heteroatom doping or by molten salt/hydrogen assisted reduction, can be narrowed to allow for activity within the visible light spectrum making them optimal candidates for use in bacterial biofilm eradication. Nitrogen-doped and reduced TiO2 NPs have been explored in this study due to their narrowed band gap. The narrowed band gap allows for the formation of excitons upon the absorption of light within the visible range. The excited charge carriers are transported to the NP surface where they react to form reactive oxygen species (ROS). These ROS interact with microbial membranes and cause cell wall damage, resulting in cell death. A study by the Samia Lab exploited and improved existing synthetic approaches and post-synthetic processing techniques to produce TiO2 NPs with enhanced visible light photoactivity for anti-biofilm applications using the mode of action described above. The most effective disruption of S. aureus biofilm was observed with the use of treated Nitrogen-doped TiO2 (N-TiO2), which included Magnesium-reduced (Mg-N-TiO2) and Hydrogen annealed Mg-N-TiO2 NPs (H-Mg-N-TiO2 NPs), under visible irradiation over 30 minutes. Future studies hope to expand upon these results with the optimization of reduced N-TiO2 concentration, light excitation intensity, and duration of treatment for a variety of bacterial biofilms.
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Show moreThis project aims to understand how surface polishing affects different materials in the context of art conservation. These materials include both those used in the creation and preservation of art objects, and those used to house and display them in a museum. Conservators at SBE Conservation and Cooper Hewitt have been working on two series of art objects, Still Life #46 and Still Life #54 by Tom Wesselman, for the past 6 years. The two sculptures are identical with the difference being that those from the Still Life #46 series were backlit while the others were not. Working with conservators from the Cleveland Museum of Art and Cooper Hewitt Smithsonian Design Museum, we are investigating characterization methods to rapidly and quantitatively evaluate polishing protocols to preserve these art objects. These sculptures are made out of plastic, specifically cellulose acetate butyrate (CAB), which is commercially known as UVEX. These sculptures, made in the mid 1960s, have scratches and abrasions from time and wear that need to be polished and conserved. There are three polishing materials (Novus 1, Novus 2, and Novus 3) used in three different combinations that have been tested in this study.
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Show moreRNA viruses are major threats to global society and mass outbreaks can cause long-lasting damage to international economies. RNA and related retro viruses represent a large and diverse family that contribute to the onset of human diseases such as AIDS; certain cancers like T cell lymphoma; severe acute respiratory illnesses as seen with COVID-19; and others. The hallmark of this viral family is the storage of genetic material in the form of RNA, and upon infecting host cells, their RNA genomes reprogram the cellular environment to favor productive viral replication. RNA is a multifunctional biomolecule that not only stores and transmits heritable information, but it also has the capacity to catalyze complex biochemical reactions. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. Efforts to subvert RNA viruses therefore requires a deep understanding of the mechanisms by which these pathogens usurp cellular machinery. Here, we briefly summarize several experimental techniques that individually inform on key physicochemical features of viral RNA genomes and their interactions with proteins. Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. These vivid descriptions should expedite the identification of novel therapeutic targets.
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Show moreThe photophysical properties of the canonical DNA/RNA nucleobases can be modified by selective functionalization. The carbonyl functional group at the C6 position of guanine or 2-amino-6-oxopurine, for example, can be removed to form 2-aminopurine, thus replacing the ultrafast internal conversion pathway to the ground state observed in guanine with slow internal conversion and intersystem crossing pathways in 2-aminopurine.1–3 Similarly, substitution of the carbonyl oxygen in guanine with a heavier atom results in a redshift of the absorption spectrum and a remarkable modulation of the electronic relaxation pathways of the DNA nucleobase. More specifically, sulfur substitution redshifts the absorption spectrum of guanine and allows for efficient population of the reactive triplet state upon ultraviolet excitation.4 This reactive triplet state makes 6-thioguanine useful in photodynamic therapy applications, as it can participate in reactive oxygen species generation. Substitution of the carbonyl oxygen with an even heavier selenium atom further redshifts the absorption spectrum of guanine, while also increasing the molar absorptivity coefficients in the near visible wavelengths (350-400 nm).5 If the excited state properties of 6-selenoguanine are also conducive to reactive oxygen species generation then this DNA derivative could be used as a potentially superior topical photodynamic therapy agent. The rationale for this hypothesis is that a redshift in the absorption spectrum allows for deeper penetration of light into tissue during a photodynamic treatment.
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