R-3 Repository :: Browsing by Author "Nordlander, Peter J."

Browsing by Author "Nordlander, Peter J."

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A density-functional study of ammonia chemisorption on the gallium(5) arsenic(5) cluster: Single and double adsorptions
(1995) Mackey, Jeffrey Laurence; Nordlander, Peter J.
I present a computational study of the reactivity between NH$\sb3$ and the $\rm Ga\sb5As\sb5$ cluster. A single NH$\sb3$ molecule approaches several sites on the cluster and the system is relaxed to its local lowest energy configuration. In this study, gallium sites are found to lead to lower total energies, due to greater contributions to densities of states near the Fermi level. Two ammonia molecule are then allowed to react with the cluster in sequence, each approaching different sites. Interaction at one site is seen to reduce the reactivity at other sites. These results are discussed in light of experimental studies performed on these clusters.
A first principles approach to describing novel plasmonic phenomena
(2015-04-09) Kulkarni, Vikram; Nordlander, Peter J.; Hafner, Jason; Halas, Naomi
Plasmonic phenomena are described using first principles approaches such as time-dependent density functional theory (TDDFT) and molecular dynamics. These techniques are used to study hot electron generation via plasmon decay, charge transfer plasmons, plasmons in doped semiconductor nanocrystals, and heat dissipation around nanostructures. The theory presented is fully developed for spherical nanoparticles yet the physics is qualitatively the same for nanostructures of arbitrary complexity. The quantum nature of the electron gas is present in all investigations. Effects of size quantization, electronic lifetimes, resonant tunneling, exchange and correlation, Friedel oscillations and Kapitza resistance are all incorporated. Non-radiative plasmon decay into electron-hole pairs is shown to be dependent on the size of the nanoparticle and the lifetime of the electronic levels. Small nanoparticles and systems with long lifetimes are more efficient at generating high energy carriers. Charge transfer plasmons are demonstrated in dimer systems with quantized conducting junctions. An energy level of the junction must be resonant with the Fermi energy of the nanoparticles to facilitate the charge transfer. Thus the optical properties of the dimer are dictated by the electronic structure of the junction. The plasmon energies of semiconductor nanocrystals are tuned via doping. Plasmons consisting of a few hundred charge carriers are observed in the mid and far infrared regions of the electromagnetic spectrum. Many body effects are shown to correct the calculated plasmon energies when compared to classical theory. Heated nanoparticles are shown to distort the density of the surrounding solvent when illuminated at high intensities on resonance. The distortion of water around a nanoparticle leads to a significant interfacial resistance and a nonlinearity of the steady state temperature of the nanoparticle. However the nanoparticle does not produce a well-defined bubble in its immediate surroundings. This work is important for applications such as plasmon-enhanced catalysis, photocurrent generation, molecular electronics, steam generation and nanoscale heating.
A Novel Statistical Potential for Protein Beta-Sheets Prediction
(2014-04-25) Yu, Linglin; Ma, Jianpeng; Nordlander, Peter J.; Raphael, Robert M.
One of the most long-term challenging problems in biophysics studies for both computational scientists and experimentalists is protein structure prediction, whose goal is to obtain three-dimensional native protein structure from one-dimensional sequence. In protein structure prediction problems, a fundamental problem is Beta-sheets structure prediction. Though more than 85% of experimentally solved proteins contain Beta-sheet structures, limited methods have been found to rapidly and accurately predict the folded conformations. In this study, we proposed a novel statistical potential, named NP-Beta, to predict the protein Beta-sheet structure only based on the sequence information. We included three kinds of potential terms in NP-Beta, i.e. the self-packing term, the pair interacting term and the lattice term. The number of hydrogen bonds in Beta-sheets is also considered as a potential component, corresponding to a global penalty of the potential function. Computational tests show that the new statistical potential has an outstanding performance on native structure recognition from decoys comparing to the Beta-sheet specific potentials in literature. We will apply the potential to improve the prediction of Beta-strand arrangement and registration for beta proteins.
A study of the effect of surface bandwidth and other many-body effects in atom-surface collisions using a non-equilibrium Green's function technique
(1995) Steuber, Sarah Jane; Nordlander, Peter J.
We are studying the charge transfer in atom-surface scattering using a recently developed many-body theory. The final population of the atom is studied as a function of the surface workfunction, which has a strong effect on the final population. The effects caused by degeneracy, surface bandwidth and velocity are investigated. The formation of the Kondo peak, strongly controls both the initial population and the rate of charge transfer, and consequently the final population. The results show a strong degeneracy and velocity dependence for both the positive and negative ion. For the negative ion we also find a significant bandwidth dependence.
A theoretical study of cluster reactivity and the effects of electric field on adatom-surface bond
(1996) Akpati, Hilary Chukwuma; Nordlander, Peter J.
We have used the density functional ab initio method to study the reactivity of small clusters (ammonia reacting with GaAs clusters), and the effects of electric field on adatom-surface interactions (H and Al adsorbed on Si(111) surface). In the case of NH$\sb3$ reactivity at various sites of a Ga$\rm\sb5As\sb5$ cluster, a strong correlation is found between the adsorbate-cluster binding energy and charge transfer. Ionizing the bare cluster to a cationic charge state enables multiple chemisorption of ammonia, which is much less favored on a neutral cluster and can be prohibited on a negatively charged cluster. In the case H and Al adsorbed on a Si(111) surface, the influence of an external electric field, such as that present in a scanning tunnelling microscope (STM), on the chemisorption bond is investigated. The changes in charge distributions, vibrational frequencies and adsorbate desorption barriers are calculated as a function of the strength and direction of the electric field. We find that the characteristics of the chemisorption bond can, to a large extent, be controlled through the externally applied field.
A theoretical study of cyanide on alkali-halide and alkali-metal surfaces using density functional theory
(1995) Modisette, Jason Perry; Nordlander, Peter J.
Many interesting physical phenomena have been observed in electron-stimulated desorption studies of the cyanide molecule on alkali halide and alkali metal surfaces. We have performed a theoretical investigation of the nature of the cyanide-surface bond and of the desorption process using an ab initio density functional theoretic method of calculating electronic structure in the local density and Born-Oppenheimer approximations. We compare our results with experiment, and offer an explanation for an anomalous non-Boltzmann, temperature-independent rotational distribution experimentally observed in cyanide desorbed from these surfaces. As a verification of the method, we have performed extensive calculations on different bare alkali halide and alkali metal clusters and compared them with experimental results.
A theoretical study of the effects of an external electric field on adsorbate-surface systems
(1997) Akpati, Hilary Chukwuma; Nordlander, Peter J.
We have used the density functional ab initio method to conduct investigations on the effects of an applied electric field on the chemisorption bonds of adsorbate-surface systems, and on the reactivity of a gas phase semiconductor cluster. In STM current-induced excitation of adsorbates, lateral energy transfer among adsorbates tend to delocalize the excitation, and reduce resolution. We show that the strength of chemical bonds can be increased or decreased depending on the strength and direction of the applied electric field. By shifting the excitation energy of an adsorbate below the tip, energy transfer away from the site can be inhibited, and thereby lead to adsorbate excitation localization. The details of the field-induced shifts of an adsorbate-surface bonding features are shown to depend on their dipolar polarization. In the case of the reactivity of GaAs clusters with ammonia, recent experiments indicate that NH$\sb3$ adsorption rate depends strongly on cluster size, Ga/As composition ratio, and cluster charge state. We characterize the reactivity of NH$\sb3$ at various sites of a $\rm Ga\sb5As\sb5$ cluster in terms of the adsorbate binding energy and charge transfer, showing a strong correlation between the two. The dependence of the cluster reactivity on its charge state is deduced.
Advanced Computational Methods for Macromolecular Modeling and Structure Determination
(2013-12-05) Zhang, Chong; Ma, Jianpeng; Nordlander, Peter J.; Kiang, Ching-Hwa; Raphael, Robert M.
As volume and complexity of macromolecules increase, theories and algorithms that deal with structure determination at low X-ray resolution are of particular importance. With limited diffraction data in hand, experimentalists rely on advanced computational tools to extract and utilize useful information, seeking to determinate a three dimensional model that best fits the experiment data. Success of further studies on the property and function of a specific molecule - the key to practical applications - is therefore heavily dependent on the validity and accuracy of the solved structure. In this thesis I propose Deformable Complex Network (DCN) and introduce Normal Mode Analysis (NMA), which are designed to model the average coordinates of atoms and associated fluctuations, respectively. Their applications on structure determination target two major branches ? the positional refinement and temperature factor refinement. I demonstrate their remarkable performance in structure improvements based on several criteria, such as the free R value, overfitting effect and Ramachandran Statistics, with tests carried out across a broad range of real systems for generality and consistency.
Angle- and Spectral-Dependent Light Scattering from Plasmonic Nanocups
(2013-06-05) Li, Yang; Nordlander, Peter J.; Halas, Naomi J.; Link, Stephan
The interaction of light with small designed particles and structures gives rise to an increasing number of phenomena of potentially dramatic technological importance, such as metamaterials, superlens focusing, and enhanced spectroscopy. Metallic nanostructures with their geometry-dependent optical resonances are a topic of intense current interest due to their ability to manipulate light in ways not possible with conventional optical materials. A particularly fascinating aspect of these systems is the recently realized possibility of creating optical frequency “magnetic plasmon” responses of comparable magnitude to the “electric plasmon” response. Au nanocups at their magnetoinductive resonance have the unique ability to redirect scattered light in a direction dependent on cup orientation, as a true three-dimensional nanoantenna. As optical frequency nanoantennas, reduced-symmetry plasmonic nanoparticles have light-scattering properties that depend strongly on geometry, orientation, and variations in dielectric environment. Here we investigate how these factors influence the spectral and angular dependence of light scattered by Au nanocups. A simple dielectric substrate causes the axial, electric dipole mode of the nanocup to deviate substantially from its characteristic cos square free space scattering profile, while the transverse, magnetic dipole mode remains remarkably insensitive to the presence of the substrate. Nanoscale irregularities of the nanocup rim and the local substrate permittivity have a surprisingly large effect on the spectral- and angle-dependent light-scattering properties of these structures. The different angular scattering and wavelength response from the axial and transverse nanocup modes make the nanocup an interesting particle for the nanoscale manipulation of light in three dimensions. The sensitivity of this system to geometric and environmental factors may present opportunities for active, substrate-mediated control of light scattering.
Coarse-grained Direct Phasing Method for Protein X-ray Crystallography
(2013-11-04) Chen, Dong; Ma, Jianpeng; Nordlander, Peter J.; Raphael, Robert M.
X-ray crystallography is the most powerful method to obtain the structural of biological molecules if the “phase problem” can be solved for the molecules under study. The phase problem arises from the loss of phase information in diffraction experiment. In all the solutions of the phase problem, the direct method is the only one that does not require additional experimental data or knowledge of homologous structures. It can determine the phase information directly from the observed structure factor magnitudes or intensities. However, the direct phasing method has limitations when applying to macromolecule. It is only applicable in molecules with up to about 1000 non-H atoms and requires ultra-high resolution (the Sheldrick's 1.2 Å rule) diffraction data that is not available in most protein crystallography experiments. To overcome the two limitations, here we propose a coarse-grained direct phasing method. This thesis will focus on how to break the 1.2 Å resolution requirement.
Cross antennas for surface-enhanced infrared absorption (SEIRA) spectroscopy of chemical moieties
(2016-06-21) Brown, Lisa V.; Zhao, Ke; Halas, Nancy J.; Nordlander, Peter J.; Rice University; United States Patent and Trademark Office
A device for Surface Enhanced Infrared Absorption (SEIRA) that includes at least one pair of metallic antennas deposited on a substrate, wherein the pair of metallic antennas are collinear. The length, width, and height of the metallic antenna determines an infrared absorption of the pair of metallic antennas. The device also includes a gap located between the pair of metallic antennas. A chemical moiety is disposed on at least a portion of the metallic antennas such that the infrared absorption of the chemical moiety is enhanced by the at least one pair of metallic antennas.
Electron Energy Loss Spectroscopy and Optical Properties of Plasmonic Nanostructure
(2015-04-15) Cao, Yang; Nordlander, Peter J.; Geurts, Frank; Halas, Naomi
Plasmon is considered to be the incompressible self-oscillation of conducting electrons in small nanoparticles. A classical spring model could be used to describe plasmon’s behavior. Many different techniques have been applied to understand nanostructure’s plasmonic properties. Electron energy loss spectroscopy (EELS) is one of these tools, which is helpful for us to understand the interaction between fast moving electrons and nanomaterials. It could achieve very high spatial and energy resolution. Here, we develop a new finite-difference time-domain method to calculate EELS spectra and maps, which is based on a commercial software package “Lumerical”. The calculated results for different cases are compared with the well-known boundary element method (BEM) and show an excellent agreement. Our finite-difference time-domain (FDTD) method to calculate EELS spectra has further been proven really helpful by high-density plasmonic dimers’ experimental results. There are basically two different numerical techniques. One is based on finite difference method (FEM) and another is according to finite-difference time-domain method (FDTD). Both of them are very important to perform optical calculations in nanophotonics and plasmonics area. In general, they will try to solve Maxwell equations with many different boundary conditions numerically. Optical properties of nanomaterials are also very tremendous for us to understand plasmonics behavior in the external electromagnetic fields. We systematically performed FEM simulations for different dimensions’ split ring structure and identified each plasmon mode via induced charge plot. Later we also studied hollow Au Nanoshells: hollow Au-Ag Nanoshell and hollow Au-Co Nanoshell. The former showed the surprising in vivo instability in the near infrared region while the later has potential application in hot electron generation.
Electron tunneling rates between an atom and a corrugated surface
(2001) Taylor, Matthew Frederick; Nordlander, Peter J.
We introduce a new method for calculating the broadening of atomic levels as a function of the atom's position outside the surface. The surface is studied using a cluster model, and the adsorbate-cluster eigenproblem is solved using quantum chemistry codes. The resulting density of states is projected on the adsorbate orbitals, revealing the broadening of adsorbate energy levels into resonances. We extract the width of these resonances from the projected density of states to calculate the broadening. Arbitrary lateral adsorbate positions and surface geometries can be explored by specifying different atom-cluster configurations.
Energies and lifetimes of xenon Rydberg atoms near a metal surface
(2000) Braun, Jochen; Nordlander, Peter J.
We present calculations of the broadening and the shifts of the Rydberg electron levels of a Xenon atom near a metal surface. The Xenon atom is described using a pseudopotenial. The energies and widths of the Xenon states, computed from the Schrodinger equation using the complex scaling method, exhibit a complicated distance dependence. We show that some of the orbitals hybridize, when the atom approaches the surface. This effect even causes the widths of some states to decrease with decreasing atom-surface separation.
Engineered Plasmonic Nanostructures: Fano Resonance Response, Magnetic Plasmon Resonance for Waveguiding and Hot Electron Induced Photochemistry
(2013-08-05) Mukherjee, Shaunak; Halas, Naomi J.; Nordlander, Peter J.; Hafner, Jason H.
Surface plasmons are collective and coherent oscillations of conduction band electrons in metal nanostructure which enable coupling of photons to electrons at a metal dielectric interface. Plasmonic nanostructures have gained much attention due to their ability to confine, tune and manipulate light for specific applications simply by varying their geometries and local dielectric environment. This thesis will focus on designing and studying fundamental plasmonic properties of Au nanostructures for applications in photothermal cancer therapy, chemical sensing, optical waveguiding, and room temperature gas phase photocatalysis. First, this thesis focuses on spherically concentric nanoparticles, a rudimentary “nanomatryushka”, composed of a silica-coated gold nanosphere surrounded by a gold shell layer. These nanoparticles were synthesized using wet chemistry technique and were found to possess exceptional geometrically tunable optical resonances in a compact, sub-100 nm size. Changing the internal geometry of the nanoparticle not only shifts its resonance frequencies, but can also strongly modifies the relative magnitudes of the absorption and scattering cross sections, independent of nanoparticle size. In addition the inherent asymmetry of each individual Au/SiO2/Au nanomatryushka generate multiple Fano resonances due to the overlapping bright superradiant and dark subradiant plasmon modes. Fano resonances have immense potential for single particle localized surface plasmon sensing applications. Next, this thesis investigates a new class of waveguiding consisting of chains of fused heptamer nanodiscs. This novel waveguiding structure transports electromagnetic energy via magnetic plasmon resonance mode. In this new geometry, heptamer structure serves as a benzene-like subdiffraction limit building blocks which support antiphase magnetic plasmons with “antiferromagnetic” behavior in multiple repeated structures. By repeating the heptamer units, this waveguide enables low-loss magnetic plasmon propagation along linear chains, steering over large-angle bends and splitting. It has numerous potential uses in energy transport, data storage, near-field microscopy, and other nanophotonic applications. Finally, this thesis explores the use of Au-photocatalysts as multifunctional catalysts for enhanced reactivity and efficiency. Au-photocatalysts were used for room temperature dissociation of H2 on Au nanoparticle surface using visible light. Surface plasmons excited in the Au nanoparticle decay into hot electrons which can be transferred into an antibonding resonance of an H2 molecule adsorbed on the Au nanoparticle surface, triggering dissociation. This process is probed by detecting the formation of HD molecules from the dissociations of H2 and D2. The rate of dissociation was also profoundly dependent on of intensity and wavelength of excitation light. This work demonstrates an important application of plasmonics in the field of heterogeneous photocatalysis opening up a new pathway for all optical control of chemical reactions on metallic catalysts.
Experimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem
(2013-06-05) Frey, Eric; Kiang, Ching-Hwa; Deem, Michael W.; Nordlander, Peter J.
Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.
Finite-difference time-domain studies of the optical properties of metallodielectric nanostructures
(2005) Oubre, Christopher D.; Nordlander, Peter J.
The optical properties of metallic nanoshell systems are investigated using the Finite Difference Time Domain (FDTD) method. The method provides a convenient and systematic approach for calculating several physical properties of nanostructures, including the optical absorption and scattering cross sections as well as the local electromagnetic fields and induced charge densities near and on the surfaces of the nanoparticles. The method is applied to single uniform nanoshells as well as nanoshells with surface defects and structural distortions. The results show that, while defects can significantly affect local electric field enhancements, far field results such as extinction spectra can be remarkably insensitive to defects and distortions. Calculations are also presented for both homodimers and heterodimers. The results show that retardation effects must be taken into account for an accurate description of realistic size nanoparticle dimers. The optical properties of the nanoshell dimer are found to be strongly polarization dependent. Maximal coupling between the nanoshells in a dimer occurs when the electric field of the incident pulse is aligned parallel to the dimer axis. The wavelengths of the peaks in the extinction cross section of the dimer are shown to vary by more than 100 nm depending on the incident electric field polarization. The calculations show that electric field enhancements in the dimer junctions depend strongly on dimer separation. The maximum field enhancements occur in the dimer junction and at the expense of a reduced electric field enhancement in other regions of space. We investigate the usefulness of nanoshell dimers as substrates for surface enhanced Raman spectroscopy (SERS) by integrating the fourth power of the electric field enhancements around the surfaces of the nanoparticles as a function of dimer separation and wavelength. The SERS efficiency is shown to depend strongly on dimer separation but much weaker than the fourth power of the maximum electric field enhancement at a particular point. The SERS efficiency is also found to depend strongly on the wavelength of the incident light. Maximum SERS efficiency occurs for resonant excitation of the dimer plasmons. Specific implementation details as well as issues of numerical convergence are also discussed.
Fully Integrated CMOS-Compatible Photodetector with Intrinsic Gain and Red-Green-Blue Color Selectivity
(2014-04-21) Zheng, Bob; Halas, Naomi J.; Nordlander, Peter J.; Link, Stephan
Currently, image sensors are hybrid devices, combining semiconductor photodiodes with off-chip color filters of different materials to convert wavelength-selected light into useful photocurrent. Here we demonstrate a fully integrated, metal-semiconductor-metal (MSM) photodetector and plasmonic color filter fabricated entirely from Aluminum and silicon designed to detect light in selected wavelength bands across the visible spectrum. The device produces photocurrent gain by carrier accumulation, while exploiting the evanescent field of the surface plasmon for both wavelength selectivity and photocurrent enhancement. With a maximum responsivity of 12.54 A/W and a full-width-half-maximum (FWHM) spectral selectivity of ~100nm, this high performance photodetector has potential for immediate applications in color-selective low-light imaging and high pixel density imaging sensors.
Hot electron dynamics and impurity scattering on gold nanoshell surfaces
(2000) Wolfgang, John A.; Nordlander, Peter J.
Recent ultrafast pump-probe experiments studying the relaxation rate of an optically excited hot electron distribution on Au/Au2S gold nanoshells indicate that this relaxation rate can be modified by the chemical environment surrounding the shell. This work will begin a theoretical investigation of the effect of chemical adsorbates---solvents and impurities---upon nanoshell hot electron dynamics. The effects of water, polyvinyl alcohol (PVA), sulfur, p-aminobenzoic acid, p-mercaptobenzoic acid and propylamine adsorbates are examined for their electronic interaction with a noble metal surface. p-Aminobenzoic acid is found to have a very large dipole moment when adsorbed to the metal surface, in contrast to p-mercaptobenzoic acid, propylamine and water. This correlates well to the experimentally observed results where nanoshells dispersed in an aqueous soulution with p-aminobenzoic acid display a faster relaxation rate compared to nanoshells dispersed in a pure water, aqueous propylamine or aqueous p-mercaptobenzoic acid environments. This thesis will also introduce a non-equilibrium Green's function approach, based on the formalism developed by Baym and Kadanoff, to model the dynamics of a hot electron distribution. The model will be discussed in terms of a simple potential scattering mechanism, which may in later work be expanded to include more complex electron-electron and electron-phonon interactions. Lastly acoustic oscillation modes are calculated for solid gold spheres and gold-silicon nanoshells. These modes describe an effect of electron-phonon coupling between the hot electron distribution and the nanoshell lattice, whereby the electronic energy is converted into mechanical energy.
Implementation of Hot Electrons in Hybrid Antenna-Graphene Structures
(2013-09-16) Wang, Yumin; Nordlander, Peter J.; Halas, Naomi; Link, Stephan
Graphene, a one-atom-thick sheet of hexagonally packed carbon atoms, is a novel material with high electron mobility due to its unique linear and gapless electronic band structure. Its broadband absorption and unusual doping properties, along with superb mechanical flexibility make graphene of promising application in optoeletronic devices such as solar cell, ultrafast photodetectors, and terahertz modulators. How- ever, the current performance of graphene-based devices is quite unacceptable owning to serious limitations by its inherently small absorption cross section and low quan- tum efficiency. Fortunately, nanoscale optical antennas, consisting of closely spaced, coupled metallic nanoparticles, have fascinating optical response since the collective oscillation of electrons in them, namely surface plasmons, can concentrate light into a subwavelength regime close to the antennas and enhance the corresponding field considerably. Given that optical antenna have been applied in various areas such as subwavelength optics, surface enhanced spectroscopies, and sensing, they are also able to assist graphene to harvest visible and near-infrared light with high efficiency. Moreover, the efficient production of hot electrons due to the decay of the surface plasmons can be further implemented to modulate the properties of graphene. Here we choose plasmonic oligomers to serve as optical antenna since they pos- sess tunable Fano resonances, consisting of a transparency window where scattering is strongly suppressed but absorption is greatly enhanced. By placing them in di- rect contact with graphene sheet, we find the internal quantum efficiency of hybrid antenna-graphene devices achieves up to 20%. Meanwhile, doping effect due to hot electron is also observed in this device, which can be used to optically tune the elec- tronic properties of graphene.

Browsing by Author "Nordlander, Peter J."

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