Exact quantum quasiclassical, and semiclassical reaction probabilities for the collinear F+D_2 → FD+D reaction

Exact quantum, quasiclassical, and semiclassical reaction probabilities and rate constants for the collinear reaction F+D_2 → FD+D are presented. In all calculations, a high degree of population inversion is predicted with P^R_(03) and P^R(04) being the dominant reaction probabilities. In analogy with the F+H_2 reaction (preceding paper), the exact quantum 0→3 and 0→4 probabilities show markedly different energy dependence with PR03 having a much smaller effective threshold energy (E_T=0.014 eV) than P^R_(04) (0.055 eV). The corresponding quasiclassical forward probabilities P^R_(03) and P^R_(04) are in poor agreement with the exact quantum ones, while their quasiclassical reverse and semiclassical counterparts provide much better approximations to the exact results. Similar comparisons are also made in the analysis of the corresponding EQ, QCF, QCR, and USC rate constants. An information theoretic analysis of the EQ and QCF reaction probabilities indicates nonlinear surprisal behavior as well as a significant isotope dependence. Additional quantum results at higher energies are presented and discussed in terms of threshold behavior and resonances. Exact quantum reaction probabilities for the related F+HD → FH+D and F+DH → FD+H reactions are given and an attempt to explain the observed isotope effects is made

Large quantum effects in the collinear F+H2-->FH+H reaction

We have performed accurate quantum mechanical calculations of reaction probabilities for the collinear F+H2-->FH+H reaction as well as corresponding quasiclassical trajectory calculations. A comparison of these results shows that very significant quantum mechanical effects are present in this reaction

Computational thinking in the era of big data biology

It is fall again, and another class of students has arrived in the Watson School of Biological Sciences at Cold Spring Harbor Laboratory (CSHL). Building on the lab's 100-year history as a leading center for research and education, the Watson School was established in 1998 as a graduate program in biology with a focus on molecular, cellular and structural biology, and neuroscience, cancer, plant biology and genetics. All students in the program complete the same courses, centered around these research topics, with an emphasis on the principles of scientific reasoning and logic, as well as the importance of ethics and effective communication. Three years ago the curriculum was expanded to include a new course on quantitative biology (QB) and I, along with my co-instructor Mickey Atwal and other members of the QB program, have been teaching it ever since

Biological data sciences in genome research

The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score

Motivation: Genome resequencing and short read mapping are two of the primary tools of genomics and are used for many important applications. The current state-of-the-art in mapping uses the quality values and mapping quality scores to evaluate the reliability of the mapping. These attributes, however, are assigned to individual reads and do not directly measure the problematic repeats across the genome. Here, we present the Genome Mappability Score (GMS) as a novel measure of the complexity of resequencing a genome. The GMS is a weighted probability that any read could be unambiguously mapped to a given position and thus measures the overall composition of the genome itself. Results: We have developed the Genome Mappability Analyzer to compute the GMS of every position in a genome. It leverages the parallelism of cloud computing to analyze large genomes, and enabled us to identify the 5-14% of the human, mouse, fly and yeast genomes that are difficult to analyze with short reads. We examined the accuracy of the widely used BWA/SAMtools polymorphism discovery pipeline in the context of the GMS, and found discovery errors are dominated by false negatives, especially in regions with poor GMS. These errors are fundamental to the mapping process and cannot be overcome by increasing coverage. As such, the GMS should be considered in every resequencing project to pinpoint the 'dark matter' of the genome, including of known clinically relevant variations in these regions

Metassembler: merging and optimizing de novo genome assemblies

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for meta-assembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source at http://metassembler.sourceforge.net

Quantum mechanical reactive scattering for planar atom plus diatom systems. I. Theory

A method is presented for accurately solving the Schrödinger equation for the reactive collision of an atom with a diatomic molecule on a space-fixed plane. The procedure consists primarily of two steps. First, the Schrödinger equation in each of the three arrangement channel regions is transformed into a set of coupled differential equations and numerically integrated in each of these regions to generate primitive solutions. The rotational part of the vibration–rotation basis functions involved is not changed from its asymptotic form during this propagation, but the vibrational eigenfunctions as well as the integration variable are changed periodically so as to follow the vibrational motions in a nearly adiabatic manner. In the second step, the primitive solutions generated in each of the three arrangement channels are smoothly matched to each other on a set of appropriately chosen matching surfaces. The resulting solutions are then linearly combined to satisfy the proper asymptotic boundary conditions, and the scattering matrix, scattering amplitudes, and cross sections are determined. Application of this procedure to the special case of the H+H2 reaction is discussed in detail including simplifications arising from the additional symmetries involved, and the inclusion of effects resulting from indistinguishability of identical particles

The advantages of SMRT sequencing

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes

The DNA60IFX contest

We present the full story of Genome Biology's recent DNA60IFX contest, as told by the curators and winner of what turned out to be a memorable and hotly contested bioinformatics challenge. Full solutions, including scripts, are available at http://genomebiology.com/about/update/DNA60_ANSWER