Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface.

Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi.OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi.OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76-5.05 Mbps, and contained "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi.OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology.

Multiresonant Multidimensional Spectroscopy of Surface-Trapped Excitons in PbSe Quantum Dots.

Recent work spectrally isolated and measured the quantum states associated with ultrafast relaxation from an initially excited 1S excitonic state to a lower energy state that is present in an inadequately capped PbSe quantum dot sample. The relaxed state was attributed to a surface-trapped exciton (STE). This letter reports the line-narrowed, multiresonant, two-dimensional spectrum of this sample. The multidimensional spectrum is unusual because diagonal peaks are absent, but there is a strong cross-peak between the 1S and STE transitions. Theoretical modeling provided values for the coherent and incoherent dynamics, the relative exciton and biexciton transition moments, the Coulombic coupling, and the homogeneous and inhomogeneous broadening. This work demonstrates the feasibility of using multiresonant methods to probe the quantum state dynamics of interface states in nanostructures.

Fully and partially coherent pathways in multiply enhanced odd-order wave-mixing spectroscopy.

Nuclear magnetic resonance spectroscopy relies on using multiple excitation pulses to create multiple quantum coherences that provide great specificity for chemical measurements. Coherent multidimensional spectroscopy (CMDS) is the optical analogue of NMR. Current CMDS methods use three excitation pulses and phase matching to create zero, single, and double quantum coherences. In order to create higher order multiple quantum coherences, the number of interactions must be increased by raising the excitation intensities high enough to create Rabi frequencies that are comparable to the dephasing rates of vibrational coherences. The higher Rabi frequencies create multiple, odd-order coherence pathways. The coherence pathways that involve intermediate populations are partially coherent and are sensitive to population relaxation effects. Pathways that are fully coherent involve only coherences and measure the direct coupling between excited quantum states. The fully coherent pathways are related to the multiple quantum coherences created in multiple pulse NMR methods such as heteronuclear multiple quantum coherence (HMQC) spectroscopy with the important difference that HMQC NMR methods have a defined number of interactions and avoid dynamic Stark effects whereas the multiply enhanced odd-order wave-mixing pathways do not. The difference arises because CMDS methods use phase matching to define the interactions and at high intensities, multiple pathways obey the same phase matching conditions. The multiple pathways correspond to the pathways created by dynamic Stark effects. This paper uses rhodium dicarbonyl chelate (RDC) as a model to demonstrate the characteristics of multiply enhanced odd-order wave-mixing (MEOW) methods. Dynamic Stark effects excite vibrational ladders on the symmetric and asymmetric CO stretch modes and create a series of multiple quantum coherences and populations using partially and fully coherent pathways. Vibrational quantum states up to v = 6 are excited. A series of spectra provides different two-dimensional cross sections through the multidimensional parameter space involving two excitation frequencies, the frequency of the output coherence, and the excitation pulse time delays. The spectra allow the identification of 18 different overtone and combination band states. Comparison with a local mode model with two anharmonic Morse oscillators with interbond coupling shows excellent agreement.

Multiply enhanced odd-order wave-mixing spectroscopy.

Extending current coherent multidimensional spectroscopy (CMDS) methods to higher order multiwave mixing requires excitation intensities where dynamic Stark effects become important. This paper examines the dynamic Stark effects that occur in mixed frequency/time domain CMDS methods at high excitation intensities in a model system with an isolated vibrational state. The phase-matching restrictions in CMDS define the excitation beams that interact by nonlinear mixing while the dynamic Stark effects create vibrational ladders of increasingly more energetic overtone and combination band states. The excited quantum states form coherences that reemit the output beams. This paper uses the phase-matching conditions k(out) = k(1) - k(2) + k(2') and k(out) =- k(1) + k(2) + k(2'), where the subscripts denote the excitation frequencies of each excitation pulse and the output pulse. The phase-matching condition constrains each pulse to have an odd number of interactions so the overall mixing process that creates the output coherence must also involve an odd number of interactions. Tuning the excitation frequencies and spectrally resolving the output intensity creates three-dimensional spectra that resolve the individual overtone states. Changing the excitation pulse time delays measures the dynamics of the coherences and populations created by the multiple excitations. The multidimensional spectra probe the highly excited states of a molecular potential energy surface. This paper uses tungsten hexacarbonyl (W(CO)(6)) as a model for observing how dynamic Stark effects change the multidimensional spectra of a simple system. The simplicity of the W(CO)(6) system provides the experimental data required to develop the nonperturbative theoretical methods that will be necessary to model this new approach to CMDS.

Coherent multidimensional vibrational spectroscopy of representative N-alkanes.

Mixed frequency/time domain, two color triply vibrationally enhanced (TRIVE) four wave mixing (FWM) spectroscopy is used to study the methyl and methylene modes in octane and dotriacontane. The experiments involve scanning different combinations of the two excitation frequencies, the monochromator frequency, and the two time delays between the three excitation pulses while the remaining variables are fixed. Two dimensional spectra of the methyl and methylene stretching region have weak, asymmetrical diagonal- and cross-peaks when the excitation pulses are temporally overlapped. As the time delays change, the spectra change as new peaks appear and their peak intensity and position change. Combined two-dimensional scans of the excitation frequency and time delay show the changes are caused by relaxation of the initially excited populations to other states that are coupled to the methyl and methylene stretching modes. Two dimensional time delay scans show that the coherence dephasing rates are very fast so fully coherent TRIVE FWM pathways involving multiple quantum coherences are not possible without shorter excitation pulses. Similar experiments involving the methyl and methylene bend and stretching modes identify cross-peaks between these modes and population transfer processes that create cross-peaks. The asymmetric methylene stretch/Fermi resonance band is observed to contain unresolved states that couple differently with the symmetric methylene stretching and scissor modes as well as with lower lying quantum states that are fed by population transfer. The TRIVE FWM data show that the multidimensional spectra are dominated by rapid population transfer within the methyl and methylene stretching modes and to lower quantum states that are coupled to the stretching modes.

Multiple quantum coherence spectroscopy.

Multiple quantum coherences provide a powerful approach for studies of complex systems because increasing the number of quantum states in a quantum mechanical superposition state increases the selectivity of a spectroscopic measurement. We show that frequency domain multiple quantum coherence multidimensional spectroscopy can create these superposition states using different frequency excitation pulses. The superposition state is created using two excitation frequencies to excite the symmetric and asymmetric stretch modes in a rhodium dicarbonyl chelate and the dynamic Stark effect to climb the vibrational ladders involving different overtone and combination band states. A monochromator resolves the free induction decay of different coherences comprising the superposition state. The three spectral dimensions provide the selectivity required to observe 19 different spectral features associated with fully coherent nonlinear processes involving up to 11 interactions with the excitation fields. The different features act as spectroscopic probes of the diagonal and off-diagonal parts of the molecular potential energy hypersurface. This approach can be considered as a coherent pump-probe spectroscopy where the pump is a series of excitation pulses that prepares a multiple quantum coherence and the probe is another series of pulses that creates the output coherence.

Mixed frequency-/time-domain coherent multidimensional spectroscopy: research tool or potential analytical method?

Coherent multidimensional spectroscopy (CMDS) is now the optical analogue of nuclear magnetic resonance (NMR). Just as NMR heteronuclear multiple-quantum coherence (HMQC) methods rely on multiple quantum coherences, achieving widespread application requires that CMDS also excites multiple quantum coherences over a wide range of quantum state energies. This Account focuses on frequency-domain CMDS because these methods tune the excitation frequencies to resonance with the desired quantum states and can form multiple quantum coherences between states with very different energies. CMDS methods use multiple excitation pulses to excite multiple quantum states within their dephasing time, so their quantum mechanical phase is maintained. Coherences formed from pairs of the excited states emit coherent beams of light. The temporal ordering of the excitation pulses defines a sequence of coherences that can result in zero, single, double, or higher order coherences as required for multiple quantum coherence CMDS. Defining the temporal ordering and the excitation frequencies and spectrally resolving the output frequency also defines a particular temporal pathway for the coherences, just as an NMR pulse sequence defines an NMR method. Two dimensional contour plots through this multidimensional parameter space allow visualization of the state energies and dynamics. This Account uses nickel and rhodium chelates as models for understanding mixed frequency-/time-domain CMDS. Mixed frequency-/time-domain methods use excitation pulse widths that are comparable to the dephasing times, so multidimensional spectra are obtained by scanning the excitation frequencies, while the coherence and population dynamics are obtained by scanning the time delays. Changing the time delays changes the peaks in the 2D excitation spectra depending upon whether the pulse sequence excites zero, single, or double quantum coherences. In addition, peaks split as a result of the frequency-domain manifestation of quantum beating. Similarly, changing the excitation and monochromator frequencies changes the dependence on the excitation delay times depending upon whether the frequencies match the resonances involved in the different time-ordered pathways. Contour plots that change a time delay and frequency visualize the temporal changes of specific spectral features. Frequency-domain methods are resonant with specific states, so the sequence of coherences and populations is defined. Coherence transfer, however, can cause output beams at unexpected frequencies. Coherence transfer occurs when the thermal bath induces a coherence between two states (a and g) to evolve to a new coherence (b and g). Since the two coherences have different frequencies and since there are different time orderings for the occurrence of coherence transfer, the delay time dependence develops modulations that depend on the coherences' frequency difference. Higher order coherences can also be generated by raising the excitation intensities. New features appear in the 2D spectra and dynamic Stark splittings occur. These effects will form the basis for the higher order multiple quantum coherence methods and also provide a method for probing molecular potential energy surfaces.