We have studied the photoinduced isomerization from 1,3-cyclohexadiene to 1,3,5-hexatriene in the presence of an intense ultrafast laser pulse. We find that the laser field maximally suppresses isomerization if it is both polarized parallel to the excitation dipole and present 50 fs after the initial photoabsorption, at the time when the system is expected to be in the vicinity of a conical intersection that mediates this structural transition. A modified ab initio multiple spawning (AIMS) method shows that the laser induces a resonant coupling between the excited state and the ground state, i.e., a light-induced conical intersection. The theory accounts for the timing and direction of the effect.

Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

We extend the ab initio multiple spawning method to include both field-free and field-induced nonadiabatic transitions. We apply this method to describe ultrafast pump-probe experiments of the photoinduced ring-opening of gas phase 1,3-cyclohexadiene. In the absence of a control field, nonadiabatic transitions mediated by a conical intersection (CoIn) lead to rapid ground state recovery with both 1,3-cyclohexadiene and ring-opened hexatriene products. However, application of a control field within the first 200 fs after photoexcitation results in suppression of the hexatriene product. We demonstrate that this is a consequence of population dumping prior to reaching the CoIn and further interpret this in terms of light-induced CoIns created by the control field.

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SUMMARY In familial searching in forensic genetics, a query DNA profile is tested against a database to determine whether it represents a relative of a database entrant. We examine the potential for using linkage disequilibrium to identify pairs of profiles as belonging to relatives when the query and database rely on nonoverlapping genetic markers. Considering data on individuals genotyped with both microsatellites used in forensic applications and genome-wide SNPs, we find that ~30-32% of parent–offspring pairs and ~35-36% of sib pairs can be identified from the SNPs of one member of the pair and the microsatellites of the other. The method suggests the possibility of performing familial searches of microsatellite databases using query SNP profiles, or vice versa. It also reveals that privacy concerns arising from computations across multiple databases that share no genetic markers in common entail risks not only for database entrants, but for their close relatives as well.

The prospect of utilizing CRISPR-based gene-drive technology for controlling populations has generated much excitement. However, the potential for spillovers of gene-drive alleles from the target population to non-target populations has raised concerns. Here, using mathematical models, we investigate the possibility of limiting spillovers to non-target populations by designing differential-targeting gene drives, in which the expected equilibrium gene-drive allele frequencies are high in the target population but low in the non-target population. We find that achieving differential targeting is possible with certain configurations of gene drive parameters, but, in most cases, only under relatively low migration rates between populations. Under high migration, differential targeting is possible only in a narrow region of the parameter space. Because fixation of the gene drive in the non-target population could severely disrupt ecosystems, we outline possible ways to avoid this outcome. We apply our model to two potential applications of gene drives—field trials for malaria-vector gene drives and control of invasive species on islands. We discuss theoretical predictions of key requirements for differential targeting and their practical implications.

Genealogical tree modeling is essential for estimating evolutionary parameters in population genetics and phylogenetics. Recent mathematical results concerning ranked genealogies without leaf labels unlock opportunities in the analysis of evolutionary trees. In particular, comparisons between ranked genealogies facilitate the study of evolutionary processes of different organisms sampled at multiple time periods. We propose metrics on ranked tree shapes and ranked genealogies for lineages isochronously and heterochronously sampled. Our proposed tree metrics make it possible to conduct statistical analyses of ranked tree shapes and timed ranked tree shapes or ranked genealogies. Such analyses allow us to assess differences in tree distributions, quantify estimation uncertainty, and summarize tree distributions. We show the utility of our metrics via simulations and an application in infectious diseases.

We use spectral unmixing to determine the number of transient photoproducts and to track their evolution following the photo-excitation of 1,3-cyclohexadiene (CHD) to form 1,3,5-hexatriene (HT) in the gas phase. The ring opening is initiated with a 266 nm ultraviolet laser pulse and probed via fragmentation with a delayed intense infrared 800 nm laser pulse. The ion time-of-flight (TOF) spectra are analyzed with a simplex-based spectral unmixing technique. We find that at least three independent spectra are needed to model the transient TOF spectra. Guided by mathematical and physical constraints, we decompose the transient TOF spectra into three spectra associated with the presence of CHD, CHD(+), and HT, and show how these three species appear at different times during the ring opening.