Conformationally Controlled Electron Delocalization in n-Type Rods: Synthesis, Structure, and Optical, Electrochemical, and Spectroelectrochemical Properties of Dicyanocyclophanes

A series of dicyanobiphenyl-cyclophanes 1-6 with various pi-backbone conformations and characteristic n-type semiconductor properties is presented. Their synthesis, optical, structural, electrochemical, spectroelectrochemical, and packing properties are investigated. The X-ray crystal structures of all n-type rods allow the systematic correlation of structural features with physical properties. In addition, the results are supported by quantum mechanical calculations based on density functional theory. A two-step reduction process is observed for all n-type rods, in which the first step is reversible. The potential gap between the reduction processes depends linearly on the cos(2) value of the torsion angle phi between the pi-systems. Similarly, optical absorption spectroscopy shows that the vertical excitation energy of the conjugation band correlates with the cos(2) value of the torsion angle phi. These correlations demonstrate that the fixed intramolecular torsion angle phi is the dominant factor determining the extent of electron delocalization in these model compounds, and that the angle phi measured in the solid-state structure is a good proxy for the molecular conformation in solution. Spectroelectrochemical investigations demonstrate that conformational rigidity is maintained even in the radical anion form. In particular, the absorption bands corresponding to the SOMO-LUMO+i transitions are shifted bathochromically, whereas the absorption bands corresponding to the HOMO-SOMO transition are shifted hypsochromically with increasing torsion angle phi.

Theoretical estimation of optical absorption and photoluminescence in nanostructured silicon; an approach to improve efficiency in nanostructured solar cells

Renewable energy is growing in demand, and thus the the manufacture of solar cells and photovoltaic arrays has advanced dramatically in recent years. This is proved by the fact that the photovoltaic production has doubled every 2 years, increasing by an average of 48% each year since 2002. Covering the general overview of solar cell working, and its model, this thesis will start with the three generations of photovoltaic solar cell technology, and move to the motivation of dedicating research to nanostructured solar cell. For the current generation solar cells, among several factors, like photon capture, photon reflection, carrier generation by photons, carrier transport and collection, the efficiency also depends on the absorption of photons. The absorption coefficient,α, and its dependence on the wavelength, λ, is of major concern to improve the efficiency. Nano-silicon structures (quantum wells and quantum dots) have a unique advantage compared to bulk and thin film crystalline silicon that multiple direct and indirect band gaps can be realized by appropriate size control of the quantum wells. This enables multiple wavelength photons of the solar spectrum to be absorbed efficiently. There is limited research on the calculation of absorption coefficient in nano structures of silicon. We present a theoretical approach to calculate the absorption coefficient using quantum mechanical calculations on the interaction of photons with the electrons of the valence band. One model is that the oscillator strength of the direct optical transitions is enhanced by the quantumconfinement effect in Si nanocrystallites. These kinds of quantum wells can be realized in practice in porous silicon. The absorption coefficient shows a peak of 64638.2 cm-1 at = 343 nm at photon energy of ξ = 3.49 eV ( = 355.532 nm). I have shown that a large value of absorption coefficient α comparable to that of bulk silicon is possible in silicon QDs because of carrier confinement. Our results have shown that we can enhance the absorption coefficient by an order of 10, and at the same time a nearly constant absorption coefficient curve over the visible spectrum. The validity of plots is verified by the correlation with experimental photoluminescence plots. A very generic comparison for the efficiency of p-i-n junction solar cell is given for a cell incorporating QDs and sans QDs. The design and fabrication technique is discussed in brief. I have shown that by using QDs in the intrinsic region of a cell, we can improve the efficiency by a factor of 1.865 times. Thus for a solar cell of efficiency of 26% for first generation solar cell, we can improve the efficiency to nearly 48.5% on using QDs.

Mechanical modeling of Intraneural Ganglion Cyst

Intraneural Ganglion Cyst is a 200 year old mystery related to nerve injury which is yet to be solved. Current treatments for the above problem are relatively simple procedures related to removal of cystic contents from the nerve. However, these treatments may result into neuropathic pain and recurrence of the cyst. The articular theory proposed by Spinner et al., (Spinner et al. 2003) takes into consideration the neurological deficit in Common Peroneal Nerve (CPN) branch of the sciatic nerve and affirms that in addition to the above treatments, ligation of articular branch results into foolproof eradication of the deficit. Mechanical Modeling of the Affected Nerve Cross Section will reinforce the articular theory (Spinner et al. 2003). As the cyst propagates, it compresses the neighboring fascicles and the nerve cross section appears like a signet ring. Hence, in order to mechanically model the affected nerve cross section; computational methods capable of modeling excessively large deformations are required. Traditional FEM produces distorted elements while modeling such deformations, resulting into inaccuracies and premature termination of the analysis. The methods described in this Master’s Thesis are effective enough to be able to simulate such deformations. The results obtained from the model adequately resemble the MRI image obtained at the same location and shows an appearance of a signet ring. This Master’s Thesis describes the neurological deficit in brief followed by detail explanation of the advanced computational methods used to simulate this problem. Finally, qualitative results show the resemblance of mechanical model to MRI images of the Nerve Cross Section at the same location validating the capability of these methods to study this neurological deficit.

Immobilizing bacteriorhodopsin on a single electron transistor

As awareness of potential human and environmental impacts from toxins has increased, so has the development of innovative sensors. Bacteriorhodopsin (bR) is a light activated proton pump contained in the purple membrane (PM) of the bacteria Halobacterium salinarum. Bacteriorhodopsin is a robust protein which can function in both wet and dry states and can withstand extreme environmental conditions. A single electron transistor(SET) is a nano-scale device that exploits the quantum mechanical properties of electrons to switch on and off. SETs have tremendous potential in practical applications due to their size, ultra low power requirements, and electrometer-like sensitivity. The main goal of this research was to create a bionanohybrid device by integrating bR with a SET device. This was achieved by a multidisciplinary approach. The SET devices were created by a combination of sputtering, photolithography, and focused ion beam machining. The bionanomaterial bacteriorhodopsin was created through oxidative fermentation and a series of transmembrane purification processes. The bR was then integrated with the SET by electrophoretic deposition, creating a bionanohybrid device. The bionanohybrid device was then characterized using a semiconductor parametric analyzer. Characterization demonstrated that the bR modulated the operational characteristics of the SET when bR was activated with light within its absorbance spectrum. To effectively integrate bacteriorhodopsin with microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS), it is critical to know the electrical properties of the material and to understand how it will affect the functionality of the device. Tests were performed on dried films of bR to determine if there is a relationship between inductance, capacitance, and resistance (LCR) measurements and orientation, light-on/off, frequency, and time. The results indicated that the LCR measurements of the bR depended on the thickness and area of the film, but not on the orientation, as with other biological materials such as muscle. However, there was a transient LCR response for both oriented and unoriented bR which depended on light intensity. From the impedance measurements an empirical model was suggested for the bionanohybrid device. The empirical model is based on the dominant electrical characteristics of the bR which were the parallel capacitance and resistance. The empirical model suggests that it is possible to integrate bR with a SET without influencing its functional characteristics.

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

MULTISCALE EXAMINATION AND MODELING OF ELECTRON TRANSPORT IN NANOSCALE MATERIALS AND DEVICES

For half a century the integrated circuits (ICs) that make up the heart of electronic devices have been steadily improving by shrinking at an exponential rate. However, as the current crop of ICs get smaller and the insulating layers involved become thinner, electrons leak through due to quantum mechanical tunneling. This is one of several issues which will bring an end to this incredible streak of exponential improvement of this type of transistor device, after which future improvements will have to come from employing fundamentally different transistor architecture rather than fine tuning and miniaturizing the metal-oxide-semiconductor field effect transistors (MOSFETs) in use today. Several new transistor designs, some designed and built here at Michigan Tech, involve electrons tunneling their way through arrays of nanoparticles. We use a multi-scale approach to model these devices and study their behavior. For investigating the tunneling characteristics of the individual junctions, we use a first-principles approach to model conduction between sub-nanometer gold particles. To estimate the change in energy due to the movement of individual electrons, we use the finite element method to calculate electrostatic capacitances. The kinetic Monte Carlo method allows us to use our knowledge of these details to simulate the dynamics of an entire device— sometimes consisting of hundreds of individual particles—and watch as a device ‘turns on’ and starts conducting an electric current. Scanning tunneling microscopy (STM) and the closely related scanning tunneling spectroscopy (STS) are a family of powerful experimental techniques that allow for the probing and imaging of surfaces and molecules at atomic resolution. However, interpretation of the results often requires comparison with theoretical and computational models. We have developed a new method for calculating STM topographs and STS spectra. This method combines an established method for approximating the geometric variation of the electronic density of states, with a modern method for calculating spin-dependent tunneling currents, offering a unique balance between accuracy and accessibility.

Quantum and classical criticality in a dimerized quantum antiferromagnet

A quantum critical point (QCP) is a singularity in the phase diagram arising because of quantum mechanical fluctuations. The exotic properties of some of the most enigmatic physical systems, including unconventional metals and superconductors, quantum magnets and ultracold atomic condensates, have been related to the importance of critical quantum and thermal fluctuations near such a point. However, direct and continuous control of these fluctuations has been difficult to realize, and complete thermodynamic and spectroscopic information is required to disentangle the effects of quantum and classical physics around a QCP. Here we achieve this control in a high-pressure, high-resolution neutron scattering experiment on the quantum dimer material TlCuCl3. By measuring the magnetic excitation spectrum across the entire quantum critical phase diagram, we illustrate the similarities between quantum and thermal melting of magnetic order. We prove the critical nature of the unconventional longitudinal (Higgs) mode of the ordered phase by damping it thermally. We demonstrate the development of two types of criticality, quantum and classical, and use their static and dynamic scaling properties to conclude that quantum and thermal fluctuations can behave largely independently near a QCP.

Measuring the mechanical properties of plant cells by combining micro-indentation with osmotic treatments

Growth in plants results from the interaction between genetic and signalling networks and the mechanical properties of cells and tissues. There has been a recent resurgence in research directed at understanding the mechanical aspects of growth, and their feedback on genetic regulation. This has been driven in part by the development of new micro-indentation techniques to measure the mechanical properties of plant cells in vivo. However, the interpretation of indentation experiments remains a challenge, since the force measures results from a combination of turgor pressure, cell wall stiffness, and cell and indenter geometry. In order to interpret the measurements, an accurate mechanical model of the experiment is required. Here, we used a plant cell system with a simple geometry, Nicotiana tabacum Bright Yellow-2 (BY-2) cells, to examine the sensitivity of micro-indentation to a variety of mechanical and experimental parameters. Using a finite-element mechanical model, we found that, for indentations of a few microns on turgid cells, the measurements were mostly sensitive to turgor pressure and the radius of the cell, and not to the exact indenter shape or elastic properties of the cell wall. By complementing indentation experiments with osmotic experiments to measure the elastic strain in turgid cells, we could fit the model to both turgor pressure and cell wall elasticity. This allowed us to interpret apparent stiffness values in terms of meaningful physical parameters that are relevant for morphogenesis.

Fluid-structure interaction of an elastic pipe immersed inside a coaxial rigid pipe: a model for the Tullio phenomenon

An axisymmetric, elastic pipe is filled with an incompressible fluid and is immersed in a second, coaxial rigid pipe which contains the same fluid. A pressure pulse in the outer fluid annulus deforms the elastic pipe which invokes a fluid motion in the fluid core. It is the aim of this study to investigate streaming phenomena in the core which may originate from such a fluid-structure interaction. This work presents a numerical solver for such a configuration. It was developed in the OpenFOAM software environment and is based on the Arbitrary Lagrangian Eulerian (ALE) approach for moving meshes. The solver features a monolithic integration of the one-dimensional, coupled system between the elastic structure and the outer fluid annulus into a dynamic boundary condition for the moving surface of the fluid core. Results indicate that our configuration may serve as a mechanical model of the Tullio Phenomenon (sound-induced vertigo).

The Harmonic Oscillator, a Review of Classical and Elementary Quantum Mechanics

The classical harmonic oscillator and an elementary discussion of the quantum mechanical solutions for the harmonic oscillator are discussed.

A three-dimensional dynamical model of Amundsenisen icefield, Svalbard.

Amundsenisen is an ice field, 80 km2 in area, located in Southern Spitsbergen, Svalbard. Radio-echo sounding measurements at 20 MHz show high intensity returns from a nearly flat basal reflector at four zones, all of them with ice thickness larger than 500m. These reflections suggest possible subglacial lakes. To determine whether basal liquid water is compatible with current pressure and temperature conditions, we aim at applying a thermo mechanical model with a free boundary at the bed defined as solution of a Stefan problem for the interface ice-subglaciallake. The complexity of the problem suggests the use of a bi-dimensional model, but this requires that well-defined flowlines across the zones with suspected subglacial lakes are available. We define these flow lines from the solution of a three-dimensional dynamical model, and this is the main goal of the present contribution. We apply a three-dimensional full-Stokes model of glacier dynamics to Amundsenisen icefield. We are mostly interested in the plateau zone of the icefield, so we introduce artificial vertical boundaries at the heads of the main outlet glaciers draining Amundsenisen. At these boundaries we set velocity boundary conditions. Velocities near the centres of the heads of the outlets are known from experimental measurements. The velocities at depth are calculated according to a SIA velocity-depth profile, and those at the rest of the transverse section are computed following Nye’s (1952) model. We select as southeastern boundary of the model domain an ice divide, where we set boundary conditions of zero horizontal velocities and zero vertical shear stresses. The upper boundary is a traction-free boundary. For the basal boundary conditions, on the zones of suspected subglacial lakes we set free-slip boundary conditions, while for the rest of the basal boundary we use a friction law linking the sliding velocity to the basal shear stress,in such a way that, contrary to the shallow ice approximation, the basal shear stress is not equal to the basal driving stress but rather part of the solution.

Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading

With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, function of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells has only very recently been proposed (Jerusalem et al., 2013). In this paper, we present the implementation details of Neurite: the finite difference parallel program used in this reference. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite-explicit and implicit-were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between lectrophysiology and mechanics (Jerusalem et al., 2013). This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted.

Waves, analytical signals, and some postulates of quantum theory

In this paper we apply the formalism of the analytical signal theory to the Schrödinger wavefunction. Making use exclusively of the wave-particle duality and the rinciple of relativistic covariance, we actually derive the form of the quantum energy and momentum operators for a single nonrelativistic particle. Without using any more quantum postulates, and employing the formalism of the characteristic function, we also derive the quantum-mechanical prescription for the measurement probability in such cases.

Convex polytopes and quantization of symplectic manifolds

Quantum mechanics associate to some symplectic manifolds M a quantum model Q(M), which is a Hilbert space. The space Q(M) is the quantum mechanical analogue of the classical phase space M. We discuss here relations between the volume of M and the dimension of the vector space Q(M). Analogues for convex polyhedra are considered.