On Ultrafast Time-Domain TeraHertz Spectroscopy in the Condensed Phase: Linear Spectroscopic Measurements of Hydrogen-Bond Dynamics of Astrochemical Ice Analogs and Nonlinear TeraHertz Kerr Effect Measurements of Vibrational Quantum Beats

Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz (THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz, 3 cm^-1 to 300 cm^-1, or 3000 μm to 30 μm) has been shown to provide unique possibilities in the study of condensed-phase processes. The goal of this work is to expand the possibilities available in the THz region and undertake new investigations of fundamental interest to chemistry. Since we are fundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz spectroscopy can provide new understanding: astrochemistry and solvation science. To advance these fields, we had to develop new instrumentation that would enable the experiments necessary to answer new questions in either astrochemistry or solvation science. We first developed a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz (THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm^-1) and the mid-IR (400 - 4000 cm^-1). The importance of astrochemical ices lies in their key role in the formation of complex organic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of performing variety of spectroscopic studies that can provide especially relevant laboratory data to support astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric Observatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array (ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm plasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz (~0.3 cm^-1) resolution.

Using the above instrumentation, experimental spectra of astrochemical ice analogs of water and carbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high vacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a new feature in both amorphous solid water and crystalline water at 33 cm^-1 (1 THz). In addition, our studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide as it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz spectra of mixed and layered ices are further analyzed by fitting their spectra features to those of pure amorphous solid water and crystalline water ice to quantify the effects of temperature changes on structure. From the results of this work, it appears that THz spectroscopy is potentially well suited to study thermal transformations within the ice.

To advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear THz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy. We implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased THz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS), and high numerical aperture optics which generates THz electric field in excess of 300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz (THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar interaction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument improves on both the frequency coverage, and sensitivity previously reported; it also ensures a backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we observe a quantum beat at 3.66 THz (122 cm^-1), in exact agreement with the fundamental transition frequency of the υ4 vibration of the molecule. This result provides new insight into dipolar vs. Raman selection rules at terahertz frequencies.

To conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab. We report the first results from an experiment using a plasma-based THz source for nonlinear spectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal resolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping. Finally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz data and how such a scheme could be implemented in the Blake lab. The instruments developed herein will hopefully remain a part of the groups core competencies and serve as building blocks for the next generation of THz instrumentation that pushes the frontiers of both chemistry and the scientific enterprise as a whole.

Investigating the relationships between user capabilities and product demands for older and disabled users

This paper presents the results of a study that specifically looks at the relationships between measured user capabilities and product demands in a sample of older and disabled users. An empirical study was conducted with 19 users performing tasks with four consumer products (a clock-radio, a mobile phone, a blender and a vacuum cleaner). The sensory, cognitive and motor capabilities of each user were measured using objective capability tests. The study yielded a rich dataset comprising capability measures, product demands, outcome measures (task times and errors), and subjective ratings of difficulty. Scatter plots were produced showing quantified product demands on user capabilities, together with subjective ratings of difficulty. The results are analysed in terms of the strength of correlations observed taking into account the limitations of the study sample. Directions for future research are also outlined. © 2011 Springer-Verlag.

Effect of electric stimulation on heart beat and body muscle in fish

The effect of AC and DC electric stimulations on the heart-rate and the entire body of Heteropneustis fossillis, Tilapia mossambica and Macrobrachium rosenbergii were studied and presented in kymograph tracings. The reaction of spinal cord in Puntius ticto, Heteropneustis fossilis and Tilapia mossambica to D. C. field was observed to find out its role in electric shocks. A test-check of the electrical resistance of a few species was also conducted. The effect of D. C. and A.C. on the body muscle was found to be the same as that in the case of frog. Different degrees of cardiac slowing were observed in AC and DC. Unbalanced galvanotropic movements were also noticed in spinal fishes.

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

Molecular phylogeny of the specialized schizothoracine fishes (Teleostei : Cyprinidae), with their implications for the uplift of the Qinghai-Tibetan Plateau

Molecular phylogeny of three genera containing nine species and subspecies of the specialized schizothoracine fishes are investigated based on the complete nucleotide sequence of mitochondrial cytochrome b gene. Meantime relationships between the main cladogenetic events of the specialized schizothoracine fishes and the stepwise uplift of the Qinghai-Tibetan Plateau are also conducted using the molecular clock, which is calibrated by geological isolated events between the upper reaches of the Yellow River and the Qinghai Lake. Results indicated that the specialized schizothoracine fishes are not a monophyly. Five species and subspecies of Ptychobarbus form a monophyly. But three species of Gymnodiptychus do not form a monophyly. Gd. integrigymnatus is a sister taxon of the highly specialized schizothoracine fishes while Gd. pachycheilus has a close relation with Gd. dybowskii, and both of them are as a sister group of Diptychus maculatus. The specialized schizothoracines fishes might have originated during the Miocene (about 10 MaBP), and then the divergence of three genera happened during late Miocene (about 8 MaBP). Their main specialization occurred during the late Pliocene and Pleistocene (3.54-0.42 MaBP). The main cladogenetic events of the specialized schizothoracine fishes are mostly correlated with the geological tectonic events and intensive climate shift happened at 8, 3.6, 2.5 and 1.7 MaBP of the late Cenozoic. Molecular clock data do not support the hypothesis that the Qinghai-Tibetan Plateau uplifted to near present or even higher elevations during the Oligocene or Miocene, and neither in agreement with the view that the plateau uplifting reached only to an altitude of 2000 in during the late Pliocene (about 2.6 MaBP).

Speciation and Phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: Analysis of the Cytochrome b Gene of mtDNA from Diverse Populations

Gao-Yan Li, Xu-Zhen Wang, Ya-Hui Zhao, Jie Zhang, Chun-Guang Zhang, and Shun-Ping He (2009) Speciation and phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: analysis of the cytochrome b gene of mtDNA from diverse populations. Zoological Studies 48(4): 569-583. The cyprinid fish Opsariichthys bidens Gunther is distributed in all major river systems of continental East Asia, and represents an attractive model for phylogeographic studies among cyprinid species or within a given species. In this study, we investigated the phylogeographic and demographic history of this species, using partial sequences of the cytochrome (cyt) b gene in mitochondrial (mt)DNA. Fish samples were collected from almost all major river systems where O. bidens is distributed in China. Sequence analysis showed remarkably high polymorphism, with 125 haplotypes in the 234 specimens examined, and with 89.8% of haplotypes occurring in only 1 specimen. A neutrality test indicated that some groups were not at mutation-drift equilibrium, suggesting a past population expansion. These results were supported by a mismatch distribution analysis. Based on our analysis, O. bidens consists of 4 groups belonging to 2 clades. The divergence time of the 2 clades was estimated to be 11.06-8.04 my. This value corresponds to the time of the 2nd uplift of the Qinghai-Tibet Plateau, the emergence of the East Asian monsoon, and the Epoch-6 Event. A two species scheme is proposed. http://zoolstud.sinica.edu.tw/Journals/48.4/569.pdf

How polluted is the Yangtze River? Water quality downstream from the Three Gorges Dam

The concentrations of major anions and cations, nitrogen and phosphorus, dissolved and particulate trace elements, and organic pollutants were determined for the middle and lower reaches of the Yangtze River (Changjiang) from below the Three Gorges Dam (TGD) to the mouth at Shanghai in November 2006. The concentration of dissolved inorganic phosphate (DIP) was constant at a low level of 6-8 mu gP/L, but the concentration of nitrate (NO3-) approximately doubled downstream and was closely correlated with K+. This translated to a daily load of well over 1000 It of dissolved inorganic nitrogen (DIN) at Datong. The average concentrations of dissolved Pb (0.078 +/- 0.023 mu g/L), Cd (0.024 +/- 0.009 mu g/L), Cr(0.57 +/- 0.09 mu g/L), Cu (1.9 +/- 0.7 mu g/L), and Ni (0.50 +/- 0.49 mu g/L) were comparable with those in other major world rivers, while As (3.3 +/- 1.3 mu g/L) and Zn (1.5 +/- 0.6 mu g/L) were higher by factors of 5.5 and 2.5, respectively. The trace element contents of suspended particles of As (31 +/- 28 mu g/g), Pb (83 +/- 34 mu g/g), and Ni (52 +/- 16 mu g/g) were close to maximum concentrations recommended for rivers by the European Community (EC). The average concentrations of Cd (2.6 +/- 1.6 mu g/g), Cr (185 +/- 102 mu g/g), Cu (115 +/- 106 mu g/g), and Zn (500 +/- 300 mu g/g) exceeded the EC standards by a factor of two, and Hg (4.4 +/- 4.7 mu g/g) by a factor of 4 to 5. Locally occurring peak concentrations exceed these values up to fourfold, among them the notorious elements As, Hg, and Tl. All dissolved and particulate trace element concentrations were higher than estimates made twenty years ago [Zhang, J., Geochemistry of trace metals from Chinese river/estuary systems: an overview. Estuar Coast Shelf Sci 1995; 41: 631-658.]. The enormous loads of anthropogenic pollutants disposed to the river were diluted by the large water discharge of the Yangtze even during the lowest flow resulting in the relatively low concentration levels of trace elements and organic pollutants observed. We estimated loads of e.g. As, Pb and Ni to the East China Sea to be about 4600 kg As d(-1), 3000 kg Pb d(-1), and 2000 kg Ni d(-1). About 6000 t d(-1) of dissolved organic carbon (DOC) was delivered into the sea at the time of our cruise. We tested for 236 organic pollutants, and only the most infamous were found to be barely above detection limits. We estimated that the load of chlorinated compounds, aromatic hydrocarbons, phenols, and PAHs were between 500 and 3500 kg d(-1). We also detected eight herbicides entering the estuary with loads of 5-350 kg d(-1). The pollutant load, even when at low concentrations, are considerable and pose an increasing threat to the health of the East China Sea ecosystem. (c) 2008 Elsevier B.V. All rights reserved.

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8.89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4.78 mya from the Chinese group. The northern-southern clades of S. nigripinnis began to diverge c. 2.12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0.34 mya. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isles.

Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces : Teleostei): A new insight

The Otocephala, a clade including ostariophysan and clupeomorph telcosts, represents about a quarter of total fish species diversity, with about 1000 gencra and more than 7000 species. A series of recent papers have defended that the origin of this clade and of its major groups may be significantly older than the oldest fossils of each of these groups suggest. Some of these recent papers explicitly defend a Pangean origin for some otocephalan groups Such as the Siluriformes or Cypriniformes. To know whether or not the otocephalans as a whole, and particularly the mainly freshwater, cosmopolitan otophysans could have originated before the splitting of the Pangean Supercontinent is of extreme importance, since otophysan fishes are among the most useful animal groups for the determination of historical continental relationships. In the present work we examined divergence times for each major otocephalan group by an analysis of complete mtDNA sequences, in order to investigate if these divergence times support the hypotheses advanced in recent studies. The complete mtDNA sequences of nine representative non-otocephalan fish species and of twenty-one representative otocephalan species was compared. The present study is thus, among the studies dealing with molecular divergence times of telcosts, the one in which a greater number of otocephalan species are included. The divergence times obtained support that the major otocephalan groups had a much older origin than the oldest fossil records available for these groups suggest. The origin of the Otocephala is estimated as having occurred about 282 Mya, with the origin of the Otophysi being estimated at about 251 Mya. (c) 2005 Elsevier B.V. All rights reserved.

Molecular phylogeny of the specialized schizothoracine fishes (Teleostei : Cyprinidae), with their implications for the uplift of the Qinghai-Tibetan Plateau

Molecular phylogeny of three genera containing nine species and subspecies of the specialized schizothoracine fishes are investigated based on the complete nucleotide sequence of mitochondrial cytochrome b gene. Meantime relationships between the main cladogenetic events of the specialized schizothoracine fishes and the stepwise uplift of the Qinghai-Tibetan Plateau are also conducted using the molecular clock, which is calibrated by geological isolated events between the upper reaches of the Yellow River and the Qinghai Lake. Results indicated that the specialized schizothoracine fishes are not a monophyly. Five species and subspecies of Ptychobarbus form a monophyly. But three species of Gymnodiptychus do not form a monophyly. Gd. integrigymnatus is a sister taxon of the highly specialized schizothoracine fishes while Gd. pachycheilus has a close relation with Gd. dybowskii, and both of them are as a sister group of Diptychus maculatus. The specialized schizothoracines fishes might have originated during the Miocene (about 10 MaBP), and then the divergence of three genera happened during late Miocene (about 8 MaBP). Their main specialization occurred during the late Pliocene and Pleistocene (3.54-0.42 MaBP). The main cladogenetic events of the specialized schizothoracine fishes are mostly correlated with the geological tectonic events and intensive climate shift happened at 8, 3.6, 2.5 and 1.7 MaBP of the late Cenozoic. Molecular clock data do not support the hypothesis that the Qinghai-Tibetan Plateau uplifted to near present or even higher elevations during the Oligocene or Miocene, and neither in agreement with the view that the plateau uplifting reached only to an altitude of 2000 in during the late Pliocene (about 2.6 MaBP).

All-optical clock recovery using a ridge width varied two-section partly gain-coupled DFB self-pulsation laser

A 1.55 mu m InGaAsP-InP partly gain-coupled two-section DFB self-pulsation laser (SPL) with a varied ridge width has been fabricated. The laser produces self-pulsations with a frequency tuning range of more than 135 GHz. All-optical clock recovery from 40 Gb/s degraded data streams has been demonstrated. Successful lockings of the device at frequencies of 30 GHz, 40 GHz, 50 GHz, and 60 GHz to a 10 GHz sidemode injection are also conducted, which demonstrates the capability of the device for all-optical clock recovery at different frequencies. This flexibility of the device is highly desired for practical uses. Crown Copyright

Observation of quantum beat in Rb by parametric four-wave mixing

Two coupled parametric four-wave-mixing processed in Rb atoms are studied using perturbation theory, which reveals clear evidence of the appearance of quantum beat at 608 cm(-1), corresponding to the energy difference of the 7s - 5d states of Rb atoms, in the parametric four-wave-mixing signals. A pump-probe technique is utilized to observe the quantum beat. Time-varying characteristics of the quantum beat are investigated using time-dependent Fourier transform. The results show that the time-varying characteristics of the quantum beat potential tool for monitoring the dissociation of molecules.

Effect of heat treatment on the parameters of crystal structure and degree of crystallinity of poly(aryl-ether-ether-ketone)

The variations of unit cell parameters and crystallite size of nine PEEK samples treated at various temperatures have been studied by using Wide-Angle X-ray Diffraction (WAXD), The results indicate a decrease in unit cell parameter a,b and c but an increase in crystallite size L(hkl) With the increase beat treatment temperature. Based on X-ray scattering intensity theory and using the graphic multipeak resolution method, the formula of degree of crystallinity (W-c,W-X) for PEEK is derived. The results calculated are compatible with the density measurement and calorimetry.

Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau

The Ligularia-Cremanthodium-Parasenecio (L-C-P) complex of the Tussilagininae (Asteraceae: Senecioneae) contains more than 200 species that are endemic to the Qinghai-Tibetan Plateau in eastern Asia. These species are morphologically distinct; however, their relationships appear complex. A phylogenetic analysis of members of the complex and selected taxa, of the tribe Senecioneae was conducted using chloroplast (ndhF and trnL-F) and nuclear (ITS) sequences. Phylogenetic trees were constructed from individual and combined datasets of the three different sequences. All analyses suggested that Doronicum, a genus that has been included in the Tussilagininae, should be excluded from this subtribe and placed at the base of the tribe Senecioneae. In addition, the Tussilagininae should be broadly circumscribed to include the Tephroseridinae. Within the expanded Tussilagininae containing all 13 genera occurring in eastern Asia, Tussilago and NSPetasites diverged early as a separate lineage, while the remaining I I genera comprise an expanded L-C-P complex clade. We suggest that the L-C-P clade, which is largely unresolved, most likely originated as a consequence of an explosive radiation. The few monophyletic subclades identified in the L-C-P clade with robust support further suggest that some genera of Tussilagininae from eastern Asia require generic re-circumscriptions given the occurrence of subclades containing species of the same genus in different parts of the phylogentic tree due to homoplasy of important morphological characters used to delimit them. Molecular-clock analyses suggest that the explosive radiation of the L-C-P complex occurred mostly within the last 20 million years, which falls well within the period of recent major uplifts of the Qinghai-Tibetan Plateau between the early Miocene to the Pleistocene. It is proposed that significant increases in geological and ecological diversity that accompanied such uplifting, most likely promoted rapid and continuous allopatric speciation in small and isolated populations, and allowed fixation or acquisition of similar morphological characters within unrelated lineages. This phenomenon, possibly combined with interspecific diploid hybridization because of secondary sympatry during relatively stable stages between different uplifts, could be a major cause of high species diversity in the Qinghai-Tibetan Plateau and adjacent areas of eastern Asia. (c) 2005 Elsevier Inc. All rights reserved.