Biomedical subjects

Stephen K Gray

Publications and source records attributed to Stephen K Gray.

11 recordsLinked to original sources

PubMed2006

Quantitative multispectral biosensing and 1D imaging using quasi-3D plasmonic crystals.

We developed a class of quasi-3D plasmonic crystal that consists of multilayered, regular arrays of subwavelength metal nanostructures. The complex, highly sensitive structure of the optical transmission spectra of these crystals makes them especially well suited for sensing applications. Coupled with quantitative electrodynamics modeling of their optical response, they enable full multiwavelength spectroscopic detection of molecular binding events with sensitivities that correspond to small fractions of a monolayer. The high degree of spatial uniformity of the crystals, formed by a soft nanoimprint technique, provides the ability to image binding events over large areas with micrometer spatial resolution. These features, together with compact form factors, low-cost fabrication procedures, simple readout apparatus, and ability for direct integration into microfluidic networks and arrays, suggest promise for these devices in label-free bioanalytical detection systems.

Avidin↗

PubMed2006

State-to-state reactive differential cross sections for the H+H2-->H2+H reaction on five different potential energy surfaces employing a new quantum wavepacket computer code: DIFFREALWAVE.

State-to-state differential cross sections have been calculated for the hydrogen exchange reaction, H+H2-->H2+H, using five different high quality potential energy surfaces with the objective of examining the sensitivity of these detailed cross sections to the underlying potential energy surfaces. The calculations were performed using a new parallel computer code, DIFFREALWAVE. The code is based on the real wavepacket approach of Gray and Balint-Kurti [J. Chem. Phys. 108, 950 (1998)]. The calculations are parallelized over the helicity quantum number Omega' (i.e., the quantum number for the body-fixed z component of the total angular momentum) and wavepackets for each J,Omega' set are assigned to different processors, similar in spirit to the Coriolis-coupled processors approach of Goldfield and Gray [Comput. Phys. Commun. 84, 1 (1996)]. Calculations for J=0-24 have been performed to obtain converged state-to-state differential cross sections in the energy range from 0.4 to 1.2 eV. The calculations employ five different potential energy surfaces, the BKMP2 surface and a hierarchical family of four new ab initio surfaces [S. L. Mielke, et al., J. Chem. Phys. 116, 4142 (2002)]. This family of four surfaces has been calculated using three different hierarchical sets of basis functions and also an extrapolation to the complete basis set limit, the so called CCI surface. The CCI surface is the most accurate surface for the H3 system reported to date. Our calculations of differential cross sections are the first to be reported for the A2, A3, A4, and CCI surfaces. They show that there are some small differences in the cross sections obtained from the five different surfaces, particularly at higher energies. The calculations also show that the BKMP2 performs well and gives cross sections in very good agreement with the results from the CCI surface, displaying only small divergences at higher energies.

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PubMed2006

Time dependent quantum dynamics study of the O++H2(v=0,j=0)-->OH++H ion-molecule reaction and isotopic variants (D2,HD).

The time dependent real wave packet method using the helicity decoupling approximation was used to calculate the cross section evolution with collision energy (excitation function) of the O++H2(v=0,j=0)-->OH++H reaction and its isotopic variants with D2 and HD, using the best available ab initio analytical potential energy surface. The comparison of the calculated excitation functions with exact quantum results and experimental data showed that the present quantum dynamics approach is a very useful tool for the study of the selected and related systems, in a quite wide collision energy interval (approximately 0.0-1.1 eV), involving a much lower computational cost than the quantum exact methods and without a significant loss of accuracy in the cross sections.

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PubMed2006

Quantum dynamics study of the dissociative photodetachment of HOCO-.

Six-dimensional wave packet calculations are carried out to study the behavior of HOCO subsequent to the photodetachment of an electron from the negative anion, HOCO-. It is possible to form stable and/or long-lived HOCO complexes, as well as the dissociative products OH+CO and H+CO2. A variety of observables are determined: the electron kinetic energy (eKE) distributions associated with the OH+CO and H+CO2 channels, the correlated eKE and product translational energy distribution for the OH+CO channel, and product branching ratios. Most of our results are in good accord with the experimental results of Clements, Continetti, and Francisco [J. Chem. Phys. 117, 6478 (2002)], except that the calculated eKE distribution for the H+CO2 channel is noticeably colder than experiment. Reasons for this discrepancy are suggested.

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PubMed2006

Theoretical study of the complex-forming CH + H2 --> CH2 + H reaction.

The complex-forming CH + H2 --> CH2 + H reaction is studied employing a recently developed global potential energy function. The reaction probability in the total angular momentum J = 0 limit is estimated with a four-atom quantum wave packet method and compared with classical trajectory and statistical theory results. The formation of complexes from different reactant internal states is also determined with wave packet calculations. While there is no barrier to reaction along the minimum energy path, we find that there are angular constraints to complex formation. Trajectory-based estimates of the low-pressure rate constants are made and compared with experimental results. We find that zero-point energy violation in the trajectories is a particularly severe problem for this reaction.

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PubMed2006

Quantum States of hydrogen and its isotopes confined in single-walled carbon nanotubes: dependence on interaction potential and extreme two-dimensional confinement.

Quantum mechanical energy levels are computed for the hydrogen molecule and its homonuclear isotopes confined within carbon nanotubes of various sizes and structures using three different interaction potentials. Two translational and two rotational degrees of freedom are treated explicitly. We study the dependence on the interaction potential and the size of the nanotube of several features, including zero-pressure quantum sieving selectivities, ortho-para energy splittings, and wave function characteristics. We show that large quantum sieving selectivities, as well as large deviations from gas phase ortho-para splittings, occur only under the condition of extreme two-dimensional confinement, when the characteristic length of the hydrogen-carbon interaction potential is nearly equal to the radius of the nanotube.

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PubMed2005

Near-field photochemical imaging of noble metal nanostructures.

The sub-diffraction imaging of the optical near-field in nanostructures, based on a photochemical technique, is reported. A photosensitive azobenzene-dye polymer is spin coated onto lithographic structures and is subsequently irradiated with laser light. Photoinduced mass transport creates topographic modifications at the polymer film surface that are then measured with atomic force microscopy (AFM). The AFM images correlate with rigorous theoretical calculations of the near-field intensities for a range of different nanostructures and illumination polarizations. This approach is a first step toward additional methods for resolving confined optical near fields, which can augment scanning probe methodologies for high spatial resolution of optical near fields.

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PubMed2005

Surface plasmon standing waves in large-area subwavelength hole arrays.

A flexible and parallel procedure to generate large-area, free-standing films of subwavelength hole arrays has been demonstrated. This method is materials-general, and multilayered films of different materials were constructed. The optical quality of these films was tested using a near-field scanning optical microscope, which revealed the formation of surface plasmon standing wave patterns that were consistent with numerical simulations. Because the properties of the holes and the film materials can be easily tailored, new types of plasmonic and photonic devices can be envisioned and tested.

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PubMed2004

Quantum dynamics of vibrationally activated OH-CO reactant complexes.

A six-dimensional wave packet study of the unimolecular decay of vibrationally activated OH-CO reactant channel complexes is presented. The ab initio based Lakin-Troya-Schatz-Harding potential energy functions for the A' and A" states are employed. Good agreement with the experimental product distributions and lifetimes of Pond and Lester is found. We are able to confirm that complexes with two vibrational quanta of excitation in OH, vOH=2, and no vibrational excitation in CO, vCO=0, decay through two pathways. One pathway leads to products (vOH=1, vCO=0) with relatively high OH rotational energy and the other leads to products (vOH=1, vCO=1) with relatively low OH rotational energy. We also find that the lifetime of the A" state is less than the A' state and that there is a propensity for A" products.

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PubMed2004

A new expression for the direct quantum mechanical evaluation of the thermal rate constant.

Based on the formalism of Miller, Schwartz, and Tromp [J. Chem. Phys. 79, 4889(1983)], we derive a new expression for the thermal rate constant for a chemical reaction. The expression involves an unperturbed, i.e., reactant or product channel Boltzmann operator for the imaginary time propagation, making it possible to compute efficiently the rate constant for a range of temperatures. We illustrate numerical aspects with an extensive study of the one-dimensional Eckart barrier problem, as well as a study of the three-dimensional (J = 0) D + H2 problem.

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PubMed2004

Quantum wave packet and quasiclassical trajectory studies of OH+CO: influence of the reactant channel well on thermal rate constants.

We study the OH+CO-->H+CO2 reaction with both six-dimensional quantum wave packets (QM) and quasiclassical trajectories (QCT), determining reaction probabilities and thermal rate constants (or coefficients), and studying the influence of the reactant channel hydrogen-bonded complex well on the reaction dynamics. The calculations use the recently developed Lakin-Troya-Schatz-Harding (LTSH) ground electronic state potential energy surface, along with a modified surface developed for this study (mod-LTSH), in which the reactant channel well is removed. Our results show that there can be significant differences between the QM and QCT descriptions of the reaction for ground-state reactants and for energies important to the thermal rate constants. Zero-point energy violation plays an important role in the QCT results, and as a result, the QCT reaction probability (for ground-state reactants and zero impact parameter) is much higher than its QM counterpart at moderate to low reagent translational energies. The influence of the reactant channel well in the QCT results is to enhance reactivity at moderate energies and to suppress reactivity at the very lowest collision energies. The QM results also show the enhancement at moderate energies but, while the very lowest translational energies cannot be adequately converged, they do not indicate any tendency toward suppression as energy is reduced. QCT calculations for excited rotational states of the reactants show that the suppression of reactivity associated with the reactant channel well is less important when the reactants are rotating, and as a result, the influence of the reactant channel well on the thermal rate coefficients is relatively small, being important below 200 K. Our results indicate that there still remain important discrepancies between experiment and theory in this low temperature regime and that further improvements of the potential are needed.

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