Dinakar Ramadurai

Semiconductor nanostructures in biological applications

Semiconductor nanostructures in biological applications are discussed. Results are presented on the use of colloidal semiconductor quantum dots both as biological tags and as structures that interact with and influence biomolecules. Results are presented on the use of semiconducting carbon nanotubes in biological applications.

Binding of semiconductor quantum dots to cellular integrins

There is currently a major international effort aimed at integrating semiconductor nanostructures with biological structures. This paper reports the functionalization of cadmium sulfide quantum dots with peptides that facilitate the selective binding of these quantum-dot-peptide complexes to integrins in the membranes of cancer cells of the MDA-MB-435 cell line. In addition, this paper focuses on the roles that biological environments play in altering and determining the optical and vibrational properties of these nanostructures.

Integrating and Tagging Biological Structures with Nanoscale Semiconductor Quantum dot Structures

This account has highlighted the recent progress in using semiconductor biotags based on their narrow, tunable and symmetric emission spectra as well as their temporal stability and resistance to photobleaching, especially as compared to fluorescent dyes. This progress has been possible as a result of key developments underlying the synthesis and functionalization of semiconductor nanocrystals. The advances in binding fluorescent semiconductor nanocrystals to biomolecules have facilitated the selective binding of these nanoscale fluorescent structures to specific subcellular structures. To go beyond using nanocrystals as biotags by integrating semiconductor nanocrystals directly with biological structures, it is necessary to further understand the physical properties of semiconductor nanocrystals in biological environments and in direct contact with biological structures. This review has highlighted several such interaction mechanisms, including the interaction of electrolytes with nanocrystals, the modification of the photoluminescence spectra of nanocrystals due to the environmentally-induced changes in the acoustic phonon spectra in nanocrystals, and the role of surface states on the observed intermittent blinking of quantum dots. To realize the possible uses of semiconductor nanocrystals as elements of coupled nanocrystal-biological-systems, it is necessary to study such interaction mechanisms in greater detail.

Optoelectronic Signatures of Biomolecules Including Hybrid Nanostructure-DNA Ensembles

Biological macromolecules such as DNA, proteins, and polysaccharides often display unique absorptive signatures in the THz region, useful in their identification and imaging through Raman and Fourier transform transmission spectroscopy. The optoelectronic properties of nanostructure-DNA complexes immobilized on transparent, semi-rigid substrates such as polymethyl methacrylate (PMMA) have been studied. By chemically modifying the PMMA substrates with amine terminal groups and using suitable linking agents, amine terminated DNA can be localized on these substrates. THz Fourier transform transmission spectroscopy was used to detect low-frequency vibrational modes (10-25 cm-1) within single- and double-stranded DNA molecules immobilized on PMMA attached to TiO2 nanoparticles. Additionally, DNA strands end terminated with TiO2 nanoparticles are used in this study to cleave the DNA at guanine (G) rich sites due to trapping of photo-induced charge carriers from the TiO2 at these sites. Theoretical modeling of charge transport through DNA via polaron transport is discussed in detail. By examining the vibrational modes of DNA, as well as the transport of charge in DNA this study underlies potential applications involving DNA micro-arrays, DNA-based sensors, and DNA-based THz devices.

Colloidal quantum dots as optoelectronic elements

Novel optoelectronic systems based on ensembles of semiconductor nanocrystals are addressed in this paper. Colloidal semiconductor quantum dots and related quantum-wire structures have been characterized optically; these optical measurements include those made on self-assembled monolayers of DNA molecules terminated on one end with a common substrate and on the other end with TiO2 quantum dots. The electronic properties of these structures are modeled and compared with experiment. The characterization and application of ensembles of colloidal quantum dots with molecular interconnects are considered. The chemically-directed assembly of ensembles of colloidal quantum dots with biomolecular interconnects is demonstrated with quantum dot densities in excess of 10 cm. A number of novel photodetectors have been designed based on the combined use of double-barrier quantum-well injectors, colloidal quantum dots, and conductive polymers. Optoelectronic devices including photodetectors and solar cells based on threedimensional ensembles of quantum dots are considered along with underlying phenomena such as miniband formation and the robustness of minibands to displacements of quantum dots in the ensemble.

Conductive biomolecules and their THz vibrational interactions: key aspects of bioelectronics

This paper focuses on understanding the THz-phonon mediated transport of polarons in biomolecules, with particular attention on polaron transport in DNA. In order to exploit biology-based approaches to realizing new electronic systems, it is necessary to understand the electrical transport properties and THz-phonon interactions of biomolecules that portend applications both as electrically conductive wires and as structures that facilitate the chemically-directed assembly of massively integrated ensembles of nanoscale semiconducting elements into terascale integrated networks. Special attention is given to charge transport in biomolecules using indirect-bandgap colloidal nanocrystals linked with biomolecules.

ENVIRONMENTAL EFFECTS INFLUENCING THE VIBRATIONAL MODES OF DNA: NANOSTRUCTURES COUPLED TO BIOMOLECULES

The interactions of charges in DNA with the vibrational modes in DNA depend on the spectra of these vibrational modes. Using (a) the Su-Schrieffer-Heeger (SSH) Hamiltonian approach, (b) integrated structures of DNA and manmade nanostructures, and (c) gel electrophoresis techniques,1 the interaction between charges in DNA and the vibrational modes of DNA are investigated. As is well-known, DNA has a rich spectrum of modes in the THz spectral regime. The use of manmade nanostructures integrated with DNA facilitates the engineering of nanoscale systems useful in studying the role of environmental effects on the vibrational modes of DNA as well as the interaction of these modes with charge carriers in DNA. Among the DNA-based structures considered in this account are: B-DNA and Z-DNA strands related by a conformational change; and DNA molecules bound on one terminal to indirect bandgap semiconductor quantum dots. Gel electrophoresis is used as a tool for the analysis of carrier interactions in novel integrated DNA-manmade-nanostructure complexes, and models based on the SSH Hamiltonian2 are employed as a means of analyzing the interactions between the vibrational modes of DNA and charge carriers in DNA.3-4

INTERACTIONS OF THz VIBRATIONAL MODES WITH CHARGE CARRIERS IN DNA: POLARON-PHONON INTERACTIONS

This paper presents models and experimental measurements that shed light on THz-phonon mediated transport of polarons in biomolecules. Polaron transport in DNA has been considered recently in view of the expected derealization of charge carriers on a one-dimensional wire as well as the highly charged nature of DNA.1,2 An understanding of the electrical transport properties and THz-phonon interactions of biomolecules is important in view of DNAs potential applications both as electrically conductive wires and as structures that facilitate the chemically-directed assembly of massively integrated ensembles of nanoscale semiconducting elements into terascale integrated networks. Moreover, understanding these interactions provides information of the THz spectrum of vibrational modes in DNA. A primary focus of this paper is on charge transport in biomolecules using indirect-bandgap colloidal nanocrystals linked with biomolecules.3 Through a combination of theoretical and experimental approaches,4-7 this paper focuses on understanding the electrical properties and THz-frequency interactions of DNA. Moreover, this paper presents observed charge transport phenomena in DNA and discusses how these measurements are related to carrier scattering from the THz vibrational modes in DNA. Indeed, carrier transport in DNA is analyzed in light of theoretical calculations of the effects of THz-frequency phonon emission by propagating carriers, THz-frequency phonon absorption by propagating and trapped carriers, and effective mass calculations for specific sequences of the DNA bases.1-7 These studies focus on THz-phonon-mediated processes since an extra carrier on a one-dimensional chain minimizes its energy by forming an extended polaron, and since many biomolecules, including DNA, exhibit THz vibrational spectra.8 Accordingly, these calculations focus on THz-phonon-mediated processes. These results are discussed in terms of the role of THz-phonon-mediated charge trapping and detrapping effects near guanine-rich regions of the DNA as well as on the understanding and identification of DNA with specific base sequences that promote charge transport. As in previous studies, optical excitation is used to inject carriers into DNA wires. Moreover, this paper reports on the use of gel electrophoresis to study charge-induced cleavage of DNA and the related transport of charge in DNA. Phonon absorption and emission from polarons in DNA,9 is analyzed using parameters from the well-known Su-Schrieffer-Heeger Hamiltonian.

Carrier Scattering by Optical Phonons, Two-Phonon Processes in Photon Absorption, and Spontaneous Polarization in Wurtzites

This paper focuses on the role of phonon scattering in wurtzites, emphasizes results indicating strong carrier-phonon scattering effects in these materials, and illustrates band-bending effects in wurtzite quantum dots due to spontaneous polarization.