Charge and spin transport in nanoscale junction from first principles

Recently nanoscale junctions consisting of 0-D nanostructures (single molecule) or 1-D nanostructures (semiconducting nanowire) sandwiched between two metal electrodes are successfully fabricated and characterized. What lacks in the recent developments is the understanding of the mechanism behind the observed phenomena at the level of atoms and electrons. For example, the origin of observed switching effect in a semiconducting nanowire due to the influence of an external gate bias is not yet understood at the electronic structure level. On the same context, different experimental groups have reported different signs in tunneling magneto-resistance for the same organic spin valve structure, which has baffled researchers working in this field. In this thesis, we present the answers to some of these subtle questions by investigating the charge and spin transport in different nanoscale junctions. A parameter-free, single particle Green’s function approach in conjunction with a posteriori density functional theory (DFT) involving a hybrid orbital dependent functional is used to calculate the tunneling current in the coherent transport limit. The effect of spin polarization is explicitly incorporated to investigate spin transport in a nanoscale junction. Through the electron transport studies in PbS nanowire junction, a new orbital controlled mechanism behind the switching of the current is proposed. It can explain the switching behavior, not only in PbS nanowire, but in other lead-chalcogenide nanowires as well. Beside this, the electronic structure properties of this nanowire are studied using periodic DFT. The quantum confinement effect was investigated by calculating the bandgap of PbS nanowires with different diameters. Subsequently, we explain an observed semiconducting to metallic phase transition of this nanowire by calculating the bandgap of the nanowire under uniform radial strain. The compressive radial strain on the nanowire was found to be responsible for the metallic to semiconducting phase transition. Apart from studying one dimensional nanostructure, we also present transport properties in zero dimensional single molecular junctions. We proposed a new codoping approach in a single molecular carborane junction, where a cation and an anion are simultaneously doped to find the role of a single atom in the device. The main purpose was to build a molecular junction where a single atom can dictate the flow of electrons in a circuit. Recent observations of both positive and negative sign in tunneling magnetoresistance (TMR) the using same organic spin-valve structure hasmystified researchers. From our spin dependent transport studies in a prototypical organic molecular tunneling device, we found that a 3% change in metal-molecule interfacial distance can alter the sign of TMR. Changing the interfacial distance by 3%, the number of participating eigenstates as well as their orbital characteristic changes for anti-parallel configuration of the magnetization at the two electrodes, leading to the sign reversal of the TMR. Apart from this, the magnetic proximity effect under applied bias is investigated quantitatively, which can be used to understand the observed unexpectedmagnetismin carbon basedmaterials when they are in close proximity with magnetic substrates.

Bacteriorhodopsin protein hybrids for chemical and biological sensing

Bacteriorhodopsin (bR), an optoelectric protein found in Halobacterium salinarum, has the potential for use in protein hybrid sensing systems. Bacteriorhodopsin has no intrinsic sensing properties, however molecular and chemical tools permit production of bR protein hybrids with transducing and sensing properties. As a proof of concept, a maltose binding protein-bacteriorhodopsin ([MBP]-bR) hybrid was developed. It was proposed that the energy associated with target molecule binding, maltose, to the hybrid sensor protein would provide a means to directly modulate the electrical output from the MBP-bR bio-nanosensor platform. The bR protein hybrid is produced by linkage between bR (principal component of purified purple membrane [PM]) and MBP, which was produced by use of a plasmid expression vector system in Escherichia coli and purified utilizing an amylose affinity column. These proteins were chemically linked using 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS), which facilitates formation of an amide bond between a primary carboxylic acid and a primary amine. The presence of novel protein hybrids after chemical linkage was analyzed by SDSPAGE. Soluble proteins (MBP-only derivatives and unlinked MBP) were separated from insoluble proteins (PM derivatives and unlinked PM) using size exclusion chromatography. The putatively identified MBP-bR protein hybrid, in addition to unlinked bR, was collected. This sample was normalized for bR concentration to native PM and both were deposited onto indium tin oxide (ITO) coated glass slides by electrophoretic sedimentation. The photoresponse of both samples, activated using 100 Watt tungsten lamp at 10 cm distance, were equal at 175 mV. Testing of deposited PM with 1 mM sucrose or 1 mM maltose showed no change in the photoresponse of the xiv material, however addition of 1 mM maltose to the deposited MBP-bR linked hybrid material elicited a 57% decrease in photoresponse indicating a positive response for targeting of maltose. This chemically linked MBP-bR hybrid protein, with bacteriorhodopsin, as a photoresponsive transducing substrate, shows promise for creation of a universal sensing array by attachment of other pertinent sensing materials, in lieu of the maltose binding protein utilized. This strategy would allow significant reduction in sensor size, while increasing responsiveness and sensitivity at nano and picomolar levels.

A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.