Ab initio electronic structure theory as an aid to understanding excited state hydrogen transfer in moderate to large systems

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Best practices for the maintenance and distribution of GAMESS are also discussed.

The somatic autosomal mutation matrix in cancer genomes

DNA damage in somatic cells originates from both environmental and endogenous sources, giving rise to mutations through multiple mechanisms. When these mutations affect the function of critical genes, cancer may ensue. Although identifying genomic subsets of mutated genes may inform therapeutic options, a systematic survey of tumor mutational spectra is required to improve our understanding of the underlying mechanisms of mutagenesis involved in cancer etiology. Recent studies have presented genome-wide sets of somatic mutations as a 96-element vector, a procedure that only captures the immediate neighbors of the mutated nucleotide. Herein, we present a 32 × 12 mutation matrix that captures the nucleotide pattern two nucleotides upstream and downstream of the mutation. A somatic autosomal mutation matrix (SAMM) was constructed from tumor-specific mutations derived from each of 909 individual cancer genomes harboring a total of 10,681,843 single-base substitutions. In addition, mechanistic template mutation matrices (MTMMs) representing oxidative DNA damage, ultraviolet-induced DNA damage, (5m)CpG deamination, and APOBEC-mediated cytosine mutation, are presented. MTMMs were mapped to the individual tumor SAMMs to determine the maximum contribution of each mutational mechanism to the overall mutation pattern. A Manhattan distance across all SAMM elements between any two tumor genomes was used to determine their relative distance. Employing this metric, 89.5% of all tumor genomes were found to have a nearest neighbor from the same tissue of origin. When a distance-dependent 6-nearest neighbor classifier was used, 10.4% of the SAMMs had an Undetermined tissue of origin, and 92.2% of the remaining SAMMs were assigned to the correct tissue of origin. [corrected]. Thus, although tumors from different tissues may have similar mutation patterns, their SAMMs often display signatures that are characteristic of specific tissues.

Optical operation by chromophores featuring 4,5-dicyanoimidazole embedded within poly(methyl methacrylate) matrices

We have studied photoinduced absorption, birefringence, and optical second-harmonic generation in poly(methyl methacrylate) (PMMA) films doped by organic chromophores featuring 4,5-dicyanoimidazole in the weight content equal to 5%. The chromophores indicated as IM1-IM6 were synthesized from 2-bromo-1-methylimidazole-4,5-dicarbonitrile by either nucleophilic substitution or Suzuki-Miyaura cross-coupling reaction. The samples were obtained as films of several micrometers thickness by the spin-coating method on a quartz substrate. Measurements of the optically induced birefringence were done by the Senarmont method at wavelength 1150 nm, and photoinduced absorption was studied in the spectral range 250-700 nm under optical treatment by 300 mW cw 532 nm laser. Photoinduced optical effects were studied by bicolor 1064 and 532 nm coherent laser pulses. The maximal changes were observed for the ratio between fundamental and writing beam intensities equal to about 7:1. To interpret the observed experimental measurements, theoretical simulations of photoinduced optical properties were performed by quantum chemical computational methods.