Observations of Coherence in Bacterial Reaction Centers Using Two-Dimensional Electronic Spectroscopy

Photosynthesis is the process by which plants and photosynthetic bacteria convert absorbed sunlight into usable chemical energy. In the first steps of photosynthesis, light energy absorbed by molecules embedded in photosynthetic proteins is rapidly transferred to a low-energy state in a type of protein called the reaction center. In the reaction center, this energy then converted into a charge separation which is followed by rapid and efficient movement of an electron out of the protein. Recent observations of coherent oscillatory signals (coherences) in photosynthetic proteins have been suggested to be responsible for the rapidity and efficiency of the energy and charge transfer processes in these systems. The reaction center of photosynthetic purple bacteria, the Bacterial Reaction Center (BRC), has long served as a model protein for understanding charge transfer processes due in part to the relatively well separated electronic peaks in its absorption spectrum and the availability of many mutants. Coherent oscillations previously observed in the BRC have been attributed to multiple conflicting origins. In this work we characterize the coherences present in the BRC using broadband Two-Dimensional Electronic Spectroscopy (2DES) with a nonlinear light source capable of generating pulses spanning the visible-NIR portion of the BRC spectrum. These 2DES experiments are some of the first to be performed on BRCs which undergo charge separation. Through comparison of the coherences in the BRC with a monomer of one of its main constituent pigments, Bacteriochlorophyll a (BChla), we assign multiple coherence origins, including those due to excited vibrational modes and those due to vibronic coupling between molecules inside of the BRC. The results presented in this thesis serve as the first direct comparison of monomeric BChla and BRC coherences. The coherence analysis detailed in this thesis presents several novel results. We significantly observe many prominent coherence modes in monomeric BChla; previous studies of coherence in this system have yielded conflicting reports of few or no coherences. We assign the observed BChla coherences to both excited and ground electronic state vibrational origins. We similarly observe a large number of coherence modes in two BRC mutants. These signals show strong signatures of vibrational coherence, similarly to in BChla, and additionally show signatures which are not explained by either purely vibrational or purely electronic origins. These signatures can be described by a mixed vibrational-electronic, or vibronic, model which has recently been used to describe coherences in a variety of photosynthetic proteins, including the BRC. We assign several of the signatures to the upper excitonic state of the strongly-coupled special pair, which has historically been difficult to resolve directly due to its low oscillator strength and proximity to other broad, strong transitions. The upper excitonic state is better resolved in this work due to vibronic coupling of the special pair states to neighboring monomeric BChla molecules. This vibronic coupling implies a stronger degree of coupling between these molecules than previously thought, providing a new perspective of the BRC as a system in which excitonic states are strongly delocalized over the special pair and monomeric BChla pigments. Accurate modeling of these signatures additionally requires inclusion of special pair charge transfer states. The results presented in this thesis should inform future efforts to model both Bacteriochlorophyll a and BRC electronic structures and the charge separation process in the BRC.PHDApplied PhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/145822/1/vpolicht_1.pd

Time-domain observation of interlayer exciton formation and thermalization in a MoSe2/WSe2 heterostructure

: Vertical heterostructures of transition metal dichalcogenides (TMDs) host interlayer excitons with electrons and holes residing in different layers. With respect to their intralayer counterparts, interlayer excitons feature longer lifetimes and diffusion lengths, paving the way for room temperature excitonic optoelectronic devices. The interlayer exciton formation process and its underlying physical mechanisms are largely unexplored. Here we use ultrafast transient absorption spectroscopy with a broadband white-light probe to simultaneously resolve interlayer charge transfer and interlayer exciton formation dynamics in a MoSe2/WSe2 heterostructure. We observe an interlayer exciton formation timescale nearly an order of magnitude (~1 ps) longer than the interlayer charge transfer time (~100 fs). Microscopic calculations attribute this relative delay to an interplay of a phonon-assisted interlayer exciton cascade and thermalization, and excitonic wave-function overlap. Our results may explain the efficient photocurrent generation observed in optoelectronic devices based on TMD heterostructures, as the interlayer excitons are able to dissociate during thermalization

Measuring individual identity information in animal signals: Overview and performance of available identity metrics

Identity signals have been studied for over 50 years but, and somewhat remarkably, there is no consensus as to how to quantify individuality in animal signals. While there is a variety of different metrics to quantify individuality, these methods remain un‐validated and the relationships between them unclear. We contrasted three univariate and four multivariate identity metrics (and their different computational variants) and evaluated their performance on simulated and empirical datasets. Of the metrics examined, Beecher's information statistic (HS) performed closest to theoretical expectations and requirements for an ideal identity metric. It could be also easily and reliably converted into the commonly used discrimination score (and vice versa). Although Beecher's information statistic is not entirely independent of study sampling, this problem can be considerably lessened by reducing the number of parameters or by increasing the number of individuals in the analysis. Because it is easily calculated, has superior performance, can be used to quantify identity information in single variable or in a complete signal and because it indicates the number of individuals who can be discriminated given a set of measurements, we recommend that individuality should be quantified using Beecher's information statistic in future studies. Consistent use of Beecher's information statistic could enable meaningful comparisons and integration of results across different studies of individual identity signals.Grant NCN 2015/19/P/NZ8/0250

Analysis of genetic copy number changes in cervical disease progression

<p>Abstract</p> <p>Background</p> <p>Cervical dysplasia and tumorigenesis have been linked with numerous chromosomal aberrations. The goal of this study was to evaluate 35 genomic regions associated with cervical disease and to select those which were found to have the highest frequency of aberration for use as probes in fluorescent in-situ hybridization.</p> <p>Methods</p> <p>The frequency of gains and losses using fluorescence in-situ hybridization were assessed in these 35 regions on 30 paraffin-embedded cervical biopsy specimens. Based on this assessment, 6 candidate fluorescently labeled probes (8q24, Xp22, 20q13, 3p14, 3q26, CEP15) were selected for additional testing on a set of 106 cervical biopsy specimens diagnosed as Normal, CIN1, CIN2, CIN3, and SCC. The data were analyzed on the basis of signal mean, % change of signal mean between histological categories, and % positivity.</p> <p>Results</p> <p>The study revealed that the chromosomal regions with the highest frequency of copy number gains and highest combined sensitivity and specificity in high-grade cervical disease were 8q24 and 3q26. The cytological application of these two probes was then evaluated on 118 ThinPrep™ samples diagnosed as Normal, ASCUS, LSIL, HSIL and Cancer to determine utility as a tool for less invasive screening. Using gains of either 8q24 or 3q26 as a positivity criterion yielded specificity (Normal +LSIL+ASCUS) of 81.0% and sensitivity (HSIL+Cancer) of 92.3% based on a threshold of 4 positive cells.</p> <p>Conclusions</p> <p>The application of a FISH assay comprised of chromosomal probes 8q24 and 3q26 to cervical cytology specimens confirms the positive correlation between increasing dysplasia and copy gains and shows promise as a marker in cervical disease progression.</p

Assemblages of microfauna and depositional environment of the Cretaceous-Paleogene sediments of the Hucisko Jawornickie region (Outer Carpathians, Skole Nappe)

Rejon Huciska Jawornickiego znajduje się w obrębie jednostki skolskiej, położonej we wschodniej części Karpat Zewnętrznych. W jednostce odsłaniają się utwory formacji z Ropianki (znane też jako warstwy inoceramowe). Z obszaru pobrano do badań mikropaleontologicznych 26 próbek. Materiał pobierany był z odsłaniających się w potoku Brzezinka osadów turbidytowych. Z próbek wybrano i oznaczono 40 taksonów otwornic aglutynujących, wapiennych bentonicznych i planktonicznych. Na podstawie gatunków wskaźnikowych wyróżniono biozony: Globotruncana elevata, Globotruncana ventricosa, Radotruncana calcarata, Globotruncanella havanensis, Globotruncana aegyptiaca, Gansserina gansseri w zakresie standardowych poziomów biostratygraficznych oraz określono wiek badanych utworów na kampan-mastrycht. Paleobiogeograficznie badane zespoły otwornic wykazują podobieństwo do zespołów strefy przejściowej.Twenty six samples have been collected from the Ropianka Formation of the area of Huciska Jawornickie, from the Skole Nappe of the Outer Carpathians. Samples were collected from the turbiditic sediments cropping out in the Brzezinka river. 40 taxa of agglutinated, calcareous benthic and planktonic foraminiferids have been identified. Globotruncana elevata, Globotruncana ventricosa, Radotruncana calcarata, Globotruncanella havanensis, Globotruncana aegyptiaca, Gansserina gansseri standard biozeones of the Campanian-Maastrichtian were recognized based on presence of the index species. Paleobiogeographical affinity to the transitional biogeoprovince has been suggested

Assessment of water inflowing, stored and flowing away from Mściwojów reservoir

The hydrochemical analyses of water inflowing, stored and flowing away from Mściwojów water reservoir were conducted from April to November 2012. Measured were 27 physico-chemical indices of surface water sampled at 8 dates from four measurement-control points. Analysis of results revealed that water inflowing into Kałużnik river was the best quality - corresponded to class III, but only due to nitrate nitrogen. In the water Wierzbiak from the river, only two from among 16 indices exceeded class II (nitrate nitrogen and phosphates). Water in the reservoir was classified to quality class III because of the temperature and BOD5 similar as water flowing away from the reservoir. Moreover, the paper assessed usable values of inflowing water, stored in the reservoir and flowing away from it. On the basis of the analysis, it was stated that water cannot be supplied to people since it does not meet the requirements stated in the Minister's regulations concerning the conditions of the natural habitat of cyprinids and salmonids