Incorporating diverse data to improve genetic network alignment with IsoRank

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 26).To more accurately predict which genes from different species have the same function (orthologs), I extend the network-alignment algorithm IsoRank to simultaneously align multiple unrelated networks over the same set of nodes. In addition to the original protein-interaction networks, I align genetic-interaction networks, gene-expression correlations, and chromosome localization data to improve the functional similarity of aligned genes. Alignments are evaluated with consistency measurements of protein function within ortholog clusters, and with an information-retrieval statistic from a small set of known orthologs. Integrating these additional types of data is shown to improve IsoRank's predictions of classes of genes that have sparse coverage in the original protein-interaction networks.by Eric David Eisner.M.Eng

Thermal Conductivity of Chirality-Sorted Carbon Nanotube Networks

The thermal properties of single-walled carbon nanotubes (SWNTs) are of significant interest, yet their dependence on SWNT chirality has been, until now, not explored experimentally. Here, we used electrical heating and infrared thermal imaging to simultaneously study thermal and electrical transport in chirality-sorted SWNT networks. We examined solution processed 90% semiconducting, 90% metallic, purified unsorted (66% semiconducting), and as-grown HiPco SWNT films. The thermal conductivities of these films range from 80 to 370 W m-1 K-1 but are not controlled by chirality, instead being dependent on the morphology (i.e., mass and junction density, quasi-alignment) of the networks. The upper range of the thermal conductivities measured is comparable to that of the best metals (Cu and Ag), but with over an order of magnitude lower mass density. This study reveals important factors controlling the thermal properties of light-weight chirality-sorted SWNT films, for potential thermal and thermoelectric applications

Electrical Properties of Single-Walled Carbon Nanotube Networks Produced by Langmuir-Blodgett Deposition

This thesis investigates the use of the Langmuir-Blodgett (LB) deposition technique as a means for building up ultra-thin networks of single-walled carbon nanotubes (SWCNTs) on various substrates. Transfer from a water subphase is successfully demonstrated for a range of SWCNTs and the electrical properties of the networks are discussed in detail. In contrast to the majority of literature on LB networks of SWCNTs, transfer is completed without the addition of surfactants to the nanotube material. However, and as expected, improved deposition is achieved when SWCNTs are functionalised (through thermal oxidation) with carboxylic acid groups, decreasing their hydrophobicity. In-plane electrical data reveal preferential alignment of the nanotubes along the direction of dipping. Comprehensive studies of the current dependence on temperature and the field dependence of conductivity are presented for sorted metallic and semiconducting nanotubes in an attempt to reveal the dominant conduction mechanisms. For metallic nanotubes, typical metallic conductivity is observed with an increasing resistance with increasing temperature. The metallic nanotube temperature coefficient of resistance is 0.001/K. At high electricfield strengths (>10^6 V/m), conduction in semiconducting SWCNT networks is dominated by the Poole-Frenkel effect. Transistor structures are presented with SWCNTs as the active semiconducting layer. The best device shows p-type depletion mode behaviour with an on/offratio of around 8 and a carrier mobility of 0.3 cm^2/Vs

100 GHz electrically tunable planar Bragg grating via nematic liquid crystal overlay towards reconfigurable WDM networks

Novel liquid crystal-based integrated optical devices with >140GHz electrical tuning are presented for application towards reconfigurable wavelength division multiplexing (WDM) networks. Initial results with Bragg wavelength tuning covering five 25GHz WDM channel spacing have been achieved with 170V (peak-to-peak) sinusoidal voltages applied across electro-patterned ITO-covered glass electrodes placed 60µm apart. These prototype devices were fabricated using direct UV grating writing, with an evanescent field coupling into a liquid crystal overlay through an etched window. Electrically controlled liquid crystal birefringence modifies the waveguide effective index, resulting in Bragg wavelength shift. Merck 18523 nematic liquid crystals are used, exhibiting compatible refractive index values to that of silica (no=1.44, ne=1.49 at lambda=1550nm). Homeotropic alignment of the liquid crystal is provided by application of a surfactant layer.The inherent refractive index sensitivity of our etched direct-UV-written structures allows observation of previously unreported liquid crystal surface-behaviour, such as multi-threshold points during variation of the applied field. Continued optimisation based on evanescent field penetration, electrode layout, and surface interaction will allow implementation towards a variety of novel liquid crystal applications and devices. For example, a cascaded architecture of these integrated liquid crystal devices operating at different Bragg wavelengths would pave the way towards true colorless add/drop modules for dense optical networks

Simulations and electrical conductivity of percolated networks of finite rods with various degrees of axial alignment

We present a three-dimensional simulation and calculation of electrical conductivity above the filler percolation threshold for networks containing finite, conductive cylinders as a function of axial orientation (S) and aspect ratio (L/D). At a fixed volume fraction and L/D, the simulations exhibit a critical degree of orientation, S-c, above which the electrical conductivity decreases dramatically. With increasing filler concentration and aspect ratio, this critical orientation shifts to higher degrees of alignment. Additionally, at a fixed volume fraction and L/D, the simulated electrical conductivity displays a maximum at slight uniaxial orientation, which is less pronounced at higher volume fractions and aspect ratios. Our approach can be used as a predictive tool to design the optimal filler concentration and degree of orientation required to maximize electrical conductivity in polymer nanocomposites with conductive cylindrical fillers of finite dimension

Computation in Multicast Networks: Function Alignment and Converse Theorems

The classical problem in network coding theory considers communication over multicast networks. Multiple transmitters send independent messages to multiple receivers which decode the same set of messages. In this work, computation over multicast networks is considered: each receiver decodes an identical function of the original messages. For a countably infinite class of two-transmitter two-receiver single-hop linear deterministic networks, the computing capacity is characterized for a linear function (modulo-2 sum) of Bernoulli sources. Inspired by the geometric concept of interference alignment in networks, a new achievable coding scheme called function alignment is introduced. A new converse theorem is established that is tighter than cut-set based and genie-aided bounds. Computation (vs. communication) over multicast networks requires additional analysis to account for multiple receivers sharing a network's computational resources. We also develop a network decomposition theorem which identifies elementary parallel subnetworks that can constitute an original network without loss of optimality. The decomposition theorem provides a conceptually-simpler algebraic proof of achievability that generalizes to $L$-transmitter $L$-receiver networks.Comment: to appear in the IEEE Transactions on Information Theor

The Ergodic Capacity of Phase-Fading Interference Networks

We identify the role of equal strength interference links as bottlenecks on the ergodic sum capacity of a $K$ user phase-fading interference network, i.e., an interference network where the fading process is restricted primarily to independent and uniform phase variations while the channel magnitudes are held fixed across time. It is shown that even though there are $K(K-1)$ cross-links, only about $K/2$ disjoint and equal strength interference links suffice to determine the capacity of the network regardless of the strengths of the rest of the cross channels. This scenario is called a \emph{minimal bottleneck state}. It is shown that ergodic interference alignment is capacity optimal for a network in a minimal bottleneck state. The results are applied to large networks. It is shown that large networks are close to bottleneck states with a high probability, so that ergodic interference alignment is close to optimal for large networks. Limitations of the notion of bottleneck states are also highlighted for channels where both the phase and the magnitudes vary with time. It is shown through an example that for these channels, joint coding across different bottleneck states makes it possible to circumvent the capacity bottlenecks.Comment: 19 page

Topological transitions in carbon nanotube networks via nanoscale confinement

Efforts aimed at large-scale integration of nanoelectronic devices that exploit the superior electronic and mechanical properties of single-walled carbon nanotubes (SWCNTs) remain limited by the difficulties associated with manipulation and packaging of individual SWNTs. Alternative approaches based on ultra-thin carbon nanotube networks (CNNs) have enjoyed success of late with the realization of several scalable device applications. However, precise control over the network electronic transport is challenging due to i) an often uncontrollable interplay between network coverage and its topology and ii) the inherent electrical heterogeneity of the constituent SWNTs. In this letter, we use template-assisted fluidic assembly of SWCNT networks to explore the effect of geometric confinement on the network topology. Heterogeneous SWCNT networks dip-coated onto sub-micron wide ultra-thin polymer channels exhibit a topology that becomes increasingly aligned with decreasing channel width and thickness. Experimental scale coarse-grained computations of interacting SWCNTs show that the effect is a reflection of an aligned topology that is no longer dependent on the network density, which in turn emerges as a robust knob that can induce semiconductor-to-metallic transitions in the network response. Our study demonstrates the effectiveness of directed assembly on channels with varying degrees of confinement as a simple tool to tailor the conductance of the otherwise heterogeneous network, opening up the possibility of robust large-scale CNN-based devices.Comment: 4 pages, 3 figure