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Biomedical subjects

Norbert F Scherer

Publications and source records attributed to Norbert F Scherer.

16 recordsLinked to original sources
PubMed2006

Coherent electronic and nuclear dynamics for charge transfer in 1-ethyl-4-(carbomethoxy)pyridinium iodide.

Although polaronic interactions and states abound in charge transfer processes and reactions, quantitative and separable determination of electronic and nuclear relaxation is still challenging. The present paper employs the amplitudes, polarizations, and phases of four-wave mixing signals to obtain unique dynamical information on relaxation processes following photoinduced charge transfer between iodide and 1-ethyl-4-(carbomethoxy)pyridinium ions. Pump-probe signal amplitudes reveal the coherent coupling of an underdamped 115 cm(-1) nuclear mode to the charge transfer excitation. Assignments of this recurrence to intramolecular vibrational modes of the acceptor and to modulation of the intermolecular donor-acceptor distance are discussed on the basis of a high-level density functional theory normal-mode analysis and previously observed wave packet dynamics of solvated molecular iodine. Nuclear relaxation of the acceptor induces sub-picosecond decay of the pump-probe polarization anisotropy from an initial value of 0.4 to an asymptotic value of -0.05. Electronic structure calculations suggest that relaxation along the torsional coordinate of the ethyl group is the origin of the anisotropy decay. Electric-field-resolved transient grating (EFR-TG) signal fields are obtained by spectral interferometry with a diffractive optic based interferometer. These measurements show that the signal phase and amplitude possess similar dynamics. Model calculations are used to demonstrate how the EFR-TG signal phase yields unique information on transient material resonances located outside the laser pulse spectrum. This effect can be rationalized in that the real and imaginary parts of the nonlinear polarization are related by the Kramers-Kronig transformation, which allows the dispersive component of the polarization response to exhibit spectral sensitivity over a larger frequency range than that defined by the absorption bandwidth.

Algorithms↗
PubMed2006

Field-resolved coherent Raman spectroscopy of high frequency vibrational resonances.

Electric fields of coherent Raman signals are resolved with sensitivity for high-frequency vibrational resonances utilizing a four-pulse, trapezoidal beam geometry in a diffractive optic-based interferometer. Our experiments show that the heterodyne detected signal phase is stabilized for particular terms in the third-order response function by the cancellation of inter-pulse phases. The C-H stretching modes of cyclohexane and benzene are studied under two polarization conditions. The temporal profiles of signal fields for cyclohexane exhibit a low-frequency recurrence due to the interference between the signals associated with the symmetric and asymmetric C-H stretching modes. In contrast, the electronically nonresonant polarizability response of benzene gives rise to a significant broadband signal component in addition to that associated with its C-H vibrational resonance. Time-frequency shapes of the Raman signal fields are strongly dependent on the properties of the liquid and the polarizations of the laser pulses.

Letter↗
PubMed2006

Single-molecule mechanics of mussel adhesion.

The glue proteins secreted by marine mussels bind strongly to virtually all inorganic and organic surfaces in aqueous environments in which most adhesives function poorly. Studies of these functionally unique proteins have revealed the presence of the unusual amino acid 3,4-dihydroxy-L-phenylalanine (dopa), which is formed by posttranslational modification of tyrosine. However, the detailed binding mechanisms of dopa remain unknown, and the chemical basis for mussels' ability to adhere to both inorganic and organic surfaces has never been fully explained. Herein, we report a single-molecule study of the substrate and oxidation-dependent adhesive properties of dopa. Atomic force microscopy (AFM) measurements of a single dopa residue contacting a wet metal oxide surface reveal a surprisingly high strength yet fully reversible, noncovalent interaction. The magnitude of the bond dissociation energy as well as the inability to observe this interaction with tyrosine suggests that dopa is critical to adhesion and that the binding mechanism is not hydrogen bond formation. Oxidation of dopa, as occurs during curing of the secreted mussel glue, dramatically reduces the strength of the interaction to metal oxide but results in high strength irreversible covalent bond formation to an organic surface. A new picture of the interfacial adhesive role of dopa emerges from these studies, in which dopa exploits a remarkable combination of high strength and chemical multifunctionality to accomplish adhesion to substrates of widely varying composition from organic to metallic.

Adhesiveness↗
PubMed2006

Resolving the emission times of solute and solvent four-wave mixing signals by spectral interferometry.

Electric field-resolved transient grating measurements are used to distinguish the four-wave mixing signal emission from a resonant solute and a non-resonant solvent. The two components of the solution (i.e., solute and solvent) emit signal fields at different times with respect to the arrival of the probe pulse to the sample. This gives rise to a recurrence in the temporal profile of the total signal field. We show that the origin of this interference is the difference in relaxation time scales of the holographic gratings associated with the solute and solvent. The grating of the resonant solute relaxes on the time scale of a few picoseconds due to depopulation of its excited electronic state, whereas the electronic polarizability response of the solvent relaxes on the femtosecond time scale. This separability of responses is a general phenomenon that is particularly useful for studying weakly absorbing solute dynamics in polarizable solvents.

Journal Article↗
PubMed2006

Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation.

The Per-Arnt-Sim (PAS) domain is a ubiquitous protein module with a common three-dimensional fold involved in a wide range of regulatory and sensory functions in all domains of life. The activation of these functions is thought to involve partial unfolding of N- or C-terminal helices attached to the PAS domain. Here we use atomic force microscopy to probe receptor activation in single molecules of photoactive yellow protein (PYP), a prototype of the PAS domain family. Mechanical unfolding of Cys-linked PYP multimers in the presence and absence of illumination reveals that, in contrast to previous studies, the PAS domain itself is extended by approximately 3 nm (at the 10-pN detection limit of the measurement) and destabilized by approximately 30% in the light-activated state of PYP. Comparative measurements and steered molecular dynamics simulations of two double-Cys PYP mutants that probe different regions of the PAS domain quantify the anisotropy in stability and changes in local structure, thereby demonstrating the partial unfolding of their PAS domain upon activation. These results establish a generally applicable single-molecule approach for mapping functional conformational changes to selected regions of a protein. In addition, the results have profound implications for the molecular mechanism of PAS domain activation and indicate that stimulus-induced partial protein unfolding can be used as a signaling mechanism.

Anisotropy↗
PubMed2006

Optical trapping and alignment of single gold nanorods by using plasmon resonances.

We demonstrate three-dimensional trapping and orientation of individual Au nanorods by using laser light slightly detuned from their longitudinal plasmon mode. Detuning to the long-wavelength side of the resonance allows stable trapping for several minutes, with an exponential dependence of trapping time on laser power (consistent with a Kramer's escape process). Detuning to the short-wavelength side causes repulsion of the rods from the laser focus. Alignment of the long axis of the rods with the trapping laser polarization is observed as a suppression of rotational diffusion about the short axis.

Journal Article↗
PubMed2006

Optical coherence and theoretical study of the excitation dynamics of a highly symmetric cyclophane-linked oligophenylenevinylene dimer.

Optoelectronic properties of a polyphenylenevinylene-based oligomer and its paracylophane-linked dimer are studied using a variety of experimental and theoretical techniques. Despite the symmetrical structure and redshifted absorption of the dimer versus the monomer, an exciton picture is not the most appropriate. Electronic structure calculations establish changes in charge density upon optical excitation and show localized excitations that cannot be accounted for by a simple Frenkel exciton model. Visible frequency pump-probe anisotropy measurements suggest that the dimer should be considered as a three-level system with a fast, approximately 130 fs, internal conversion from the higher to lower energy excited electronic state. Signatures of nuclear relaxation processes are compared for electric field-resolved transient grating and two-dimensional photon echo spectra. These measurements reveal that nuclear relaxation occurs on similar time scales for the monomer and dimer. The connection between the spectral phase of four-wave mixing signals and the time dependent width of a nuclear wave packet is discussed. Semiempirical electronic structure and metropolis Monte Carlo calculations show that the dominant line broadening mechanisms for the monomer and dimer are associated with inter-ring torsional coordinates. Together, the theoretical calculations and electric field-resolved four-wave mixing experiments suggest that while the structure of dimer is more rigid than that of monomer, the difference in their rigidities is not sufficient to slow down excited state relaxation of dimer with respect to the monomer.

Journal Article↗
PubMed2005

Generation of optical vector beams with a diffractive optical element interferometer.

We present a novel approach to generating radially and azimuthally polarized vector beams that utilize an interferometer constructed from two identical diffractive optical elements. The measured polarization properties of four vector beam states and their phase relationships are in good agreement with theoretical expectations. This interferometer is passively phase stable and robust, making it suitable for linear and nonlinear optical (superresolution) microscopy.

Journal Article↗
PubMed2005

Correlating second harmonic optical responses of single Ag nanoparticles with morphology.

Femtosecond laser excited second harmonic (SH) activity from single Ag nanoparticles is reported. A correlation of SH single-particle measurements with high-resolution imaging of particle morphology by TEM was achieved by creating position markers on an optical and electron transparent substrate (Si3N4 thin film, approximately 100 nm). We compared the SH activity of single Ag nanoparticles (nanospheres versus nanorods) and cluster structures (composed of two or multiple particles, e.g., dimers and trimers). The direct correlation of single-particle structures and SH activity, spectral and power dependence, strongly suggests one-photon resonant driven nonlinear oscillator response mechanism.

Microscopy, Electron, Transmission↗
PubMed2005

Scattered light interference from a single metal nanoparticle and its mirror image.

The spatial distribution of surface plasmon scattering from a single nanoparticle changes dramatically near a metal surface as a result of interference from the direct scattered light and indirect scattered light from the mirror reflection. The unique interference patterns have been reproduced by simulations based on Huygens-Fresnel wave propagation theory. The large spectral width of the surface plasmon scattering enables a vertical distance measurement with 10 nm resolution through this nonintrusive far field interferometry.

Letter↗
PubMed2004

Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization.

We present an efficient method of introducing fluorophore labels at selected locations in a large RNA. The method is based on specific and highly efficient hybridization between a fluorophore-containing DNA oligonucleotide and a modular hairpin loop replacing a functionally unimportant hairpin loop in the RNA. We demonstrate its feasibility using a 255-nucleotide RNA derived from the catalytic domain of RNase P from Bacillus subtilis. Hybridization of the DNA oligonucleotide to the modular hairpin loop minimally perturbs the structure and function of this RNA. This labeling scheme should be applicable in studies of RNA conformational dynamics by ensemble and single molecule fluorescence methods.

Bacillus subtilis↗
PubMed2004

Thermally-induced formation of atomic Au clusters and conversion into nanocubes.

A thermal method for converting Au colloids into atomic Au clusters and subsequent growth of Au nanocubes from clusters is reported. Mass spectral analysis shows that these clusters are Au trimers. The Au clusters show distinct optical absorption at 305 and 250 nm and have extraordinary stability under ambient conditions.

Journal Article↗
PubMed2004

Nanometer-localized multiple single-molecule fluorescence microscopy.

Fitting the image of a single molecule to the point spread function of an optical system greatly improves the precision with which single molecules can be located. Centroid localization with nanometer precision has been achieved when a sufficient number of photons are collected. However, if multiple single molecules reside within a diffraction-limited spot, this localization approach does not work. This paper demonstrates nanometer-localized multiple single-molecule (NALMS) fluorescence microscopy by using both centroid localization and photobleaching of the single fluorophores. Short duplex DNA strands are used as nanoscale "rulers" to validate the NALMS microscopy approach. Nanometer accuracy is demonstrated for two to five single molecules within a diffraction-limited area. NALMS microscopy will greatly facilitate single-molecule study of biological systems because it covers the gap between fluorescence resonance energy transfer-based (<10 nm) and diffraction-limited microscopy (>100 nm) measurements of the distance between two fluorophores. Application of NALMS microscopy to DNA mapping with <10-nm (i.e., 30-base) resolution is demonstrated.

DNA↗
PubMed2004

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme.

The equilibrium folding of the catalytic domain of Bacillus subtilis RNase P RNA is investigated by single-molecule fluorescence resonance energy transfer (FRET). Previous ensemble studies of this 255-nucleotide ribozyme described the equilibrium folding with two transitions, U-to-I(eq)-to-N, and focused on the I(eq)-to-N transition. The present study focuses on the U-to-I(eq) transition. Comparative ensemble measurements of the ribozyme construct labeled with fluorescein at the 5' end and Cy3 at the 3' end show that modifications required for labeling do not interfere with folding and help to define the Mg(2+) concentration range for the U-to-I(eq) transition. Histogram analysis of the Mg(2+)-dependent single-molecule FRET efficiency reveals two previously undetermined folding intermediates. The single-molecule FRET trajectories exhibit non-two-state and nonergodic behaviors at intermediate Mg(2+) concentrations on the time scale of seconds. The trajectories at intermediate Mg(2+) concentrations are classified into five classes based on three FRET levels and their dynamics of interconversion within the measured time range. This heterogeneity, together with the observation of "nonsudden jump" FRET transitions, indicates that the early folding steps of this ribozyme involve a series of intermediates with different degrees of kinetic isolation and that folding occurs under kinetic control and involves many "local" conformational switches. A free energy contour is constructed to illustrate the complex folding surface.

Circular Dichroism↗
PubMed2003

Finite-difference time-domain simulation of ultrashort pulse propagation incorporating quantum-mechanical response functions.

A semiclassical implementation of the finite-difference time-domain method is used to simulate coherent linear propagation of ultrashort mid-infrared pulses through optically dense samples of isotropically diluted liquid water. Bloch equations for the density matrix are used as a simple model of the O--H oscillator relaxation, and the algorithm is extended to other response functions. Sensitivity of the field to the form of the response function is demonstrated, and the results are compared with experimentally determined electric fields in the same media [Rev. Sci. Instrum. 73, 2227 (2002)].

Computer Simulation↗