Jaehee Kim

Control of 1,3-cyclohexadiene photoisomerization using light-induced conical intersections.

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.

Ab initio multiple spawning on laser-dressed states: a study of 1,3-cyclohexadiene photoisomerization via light-induced conical intersections

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.

Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers

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.

Ultrafast ring opening in 1,3-cyclohexadiene investigated by simplex-based spectral unmixing.

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.

Enhancement of strong-field multiple ionization in the vicinity of the conical intersection in 1,3-cyclohexadiene ring opening

Nonradiative energy dissipation in electronically excited polyatomic molecules proceeds through conical intersections, loci of degeneracy between electronic states. We observe a marked enhancement of laser-induced double ionization in the vicinity of a conical intersection during a non-radiative transition. We measured double ionization by detecting the kinetic energy of ions released by laser-induced strong-field fragmentation during the ring-opening transition between 1,3-cyclohexadiene and 1,3,5-hexatriene. The enhancement of the double ionization correlates with the conical intersection between the HOMO and LUMO orbitals.

Linkage disequilibrium connects genetic records of relatives typed with disjoint genomic marker sets

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.

Mathematical and Simulation-Based Analysis of the Behavior of Admixed Taxa in the Neighbor-Joining Algorithm

The neighbor-joining algorithm for phylogenetic inference (NJ) has been seen to have three specific properties when applied to distance matrices that contain an admixed taxon: (1) antecedence of clustering, in which the admixed taxon agglomerates with one of its source taxa before the two source taxa agglomerate with each other; (2) intermediacy of distances, in which the distance on an inferred NJ tree between an admixed taxon and either of its source taxa is smaller than the distance between the two source taxa; and (3) intermediacy of path lengths, in which the number of edges separating the admixed taxon and either of its source taxa is less than or equal to the number of edges between the source taxa. We examine the behavior of neighbor-joining on distance matrices containing an admixed group, investigating the occurrence of antecedence of clustering, intermediacy of distances, and intermediacy of path lengths. We first mathematically predict the frequency with which the properties are satisfied for a labeled unrooted binary tree selected uniformly at random in the absence of admixture. We then introduce a taxon constructed by a linear admixture of distances from two source taxa, examining three admixture scenarios by simulation: a model in which distance matrices are chosen at random, a model in which an admixed taxon is added to a set of taxa that reflect treelike evolution, and a model that introduces a perturbation of the treelike scenario. In contrast to previous conjectures, we observe that the three properties are sometimes violated by distance matrices that include an admixed taxon. However, we also find that they are satisfied more often than is expected by chance when the distance matrix contains an admixed taxon, especially when evolution among the non-admixed taxa is treelike. The results contribute to a deeper understanding of the nature of evolutionary trees constructed from data that do not necessarily reflect a treelike evolutionary process.