Carbon/molecule/Cu/Au molecular junctions were fabricated on 4-inch silicon wafers using microfabrication techniques common in commercial semiconductor manufacturing. Electron-beam deposited carbon films are introduced as substrates, and the junctions exhibited high yield and excellent reproducibility. Current density-voltage characteristics of the devices were area scaling, weakly dependent on temperature and exponentially on molecular film thickness, and quantitatively similar to those of devices made with other techniques reported previously in our group, which contained pyrolyzed photoresist films as substrates. Furthermore, the test of cycle life and thermal stability reveals that the devices can survive at least under several millions of potential cycles at room temperature in air, and elevated temperature up to 150 C in vacuum for >40 hours. Parallel fabrication, thermal stability, and high yield are required for practical applications of molecular electronics, and the reported results provide important steps toward integration of molecular electronic devices with commercial processes and devices.

In skeletal muscle acetylcholinesterase AChE is highly expressed at sites of nerve-muscle contact where it is regulated at both the transcriptional and post-transcriptional levels. Scientists have elucidated many aspects of synaptic AChE structure, function, and localization during the past 80 years. However our understanding of the molecular mechanisms underlying its regulation is incomplete, but it appears to involve both translational and post-translational events as well. We found that Pumilio-2 (PUM2), an RNA binding translational repressor, is highly localized at the neuromuscular junction where AChE mRNA concentrates and that PUM2 binds to the AChE transcripts when immoprecipitation studies were performed. A direct binding between a recombinant PUM2-HD and the Pumilio Binding Site (PBE) in a segment of the AChE 3’UTR was demonstrated by Gel shift assays. Transfecting skeletal muscle cells with shRNAs specific for PUM2 upregulated AChE expression, whereas overexpression of PUM2 decreased AChE activity. We conclude that PUM2 binds to AChE mRNA and regulates AChE expression translationally at the neuromuscular synapse. We found that PUM2 is regulated by the motor nerve suggesting a trans-synaptic mechanism for locally regulating translation of specific synaptic proteins involved in modulating synaptic transmission, analogous to CNS synapses. PUM2 expression is critically important in many cell types, virtually nothing is known about the regulation of PUM2 expression itself. Analyzing the PUM2 mRNA 3’UTR we found fifteen possible PBEs in the 3 Kb 3’ UTR. We show that PUM2 binds in vivo to its own mRNA. Overexpression of PUM2 in several cell types transfected with a green fluorescent protein (GFP) reporter construct linked to the full length PUM2 3’UTR (GFP-PUM2-3’UTRFL) suppresses GFP expression suggesting that PUM2 downregulates its own expression by binding to its own 3’UTR. Mutations of the first five PBEs yield the expression of the reporter gene indicating that at least one PBE is functional in the autoregulation of PUM2. These observations suggest a novel model for the localized regulation of protein translation through a negative feedback loop. Much is known about PUM2 as a translational regulative protein but little is known about PUM2 cell localization and possible mechanism of translational regulation. In this work we found PUM2 to be highly localized to the cell rough endoplasmic reticulum and that PUM2 is associated with ribosomal RNA. In addition, we found that the GFP protein itself, together with its mRNA and ribosomal RNA (rRNA), were localized in the PUM2 positive complexes when GFP-PUM2-3’UTRFL was transfected into muscle cells. These observations further suggest a mechanism of regulation where translation of the protein occurs but the protein remains associated with the ribonucleoprotein complex, possibly to be transported together with its mRNA to specific domains inside the cell. Thus when needed, more protein is produced in those specific cell regions.

Traditionally, the design of continuous time active filters usually has a trade offbetween low-voltage and high dynamic range. One way to solve this problem is companding technology. There are two methods for companding filters. The first method utilizes the exponential I-V characteristics of BJT in the saturation region. In order to reduce the cost andintegrate the analog and digital circuits, the other method was exploited using CMOS process. In this project, a new first-order low pass log-domain filter based on CMOS parasitic vertical BJTwill be proposed. This filter has higher frequency response than previous circuits. We will first employ Hspice to simulate the log-domain filter to ensure the correctness of the circuit and make it a reliable reference with the circuit layout. After summarizing all the simulations and analyses, the chip will be fabricated with 0.35um CMOS technology.

Non-parametric belief propagation (NBP) is a well-known message passing method for cooperative localization in wireless networks. However, due to the over-counting problem in the networks with loops, NBP’s convergence is not guaranteed, and its estimates are typically less accurate. One solution for this problem is non-parametric generalized belief propagation based on junction tree. However, this method is intractable in large-scale networks due to the high-complexity of the junction tree formation, and the high-dimensionality of the particles. Therefore, in this article, we propose the non-parametric generalized belief propagation based on pseudo-junction tree (NGBP-PJT). The main difference comparing with the standard method is the formation of pseudo-junction tree, which represents the approximated junction tree based on thin graph. In addition, in order to decrease the number of high-dimensional particles, we use more informative importance density function, and reduce the dimensionality of the messages. As by-product, we also propose NBP based on thin graph (NBP-TG), a cheaper variant of NBP, which runs on the same graph as NGBP-PJT. According to our simulation and experimental results, NGBP-PJT method outperforms NBP and NBP-TG in terms of accuracy, computational, and communication cost in reasonably sized networks. / COOPLOC / FP7-ICT WHERE2

Noise is a major environmental pollutant, which can inict physical and psychologicalinjury. An important noise contribution stems from aeroacousticsources, which are found in e.g., ventilation ducts, engine exhaust systems andairplane engines.In this thesis, research methods for low Mach number aeroacoustic sourcesin ducts are developed. The basis of the methods is the ability to describe theintrinsic linear properties of the source as an N-port (multiport), where theoutput sound eld is related to the input sound eld and the generated soundeld, all consisting of plane waves. The methods presented are both numericaland experimental. The numerical method treats the passive properties, i.e.,scattering, attenuation and amplication of incident sound, while the experimentalmethod treats the active part (intrinsic sound generation) as well. Themethods are applied in the study of noise generation by a vortex mixer plate,placed in an airow of Mach 0.2, and in the study of acoustic-hydrodynamicinteraction in a T-junction of rectangular ducts.It is found that the accuracy of the experimental methods is signicantly increasedwhen the equations are over-determined, which is achieved by addingadditional microphones to the test rig. In the frequency range studied, themixer plate is found to generate less sound when made exible, without disturbingthe mixing quality.For the numerical method { based on the linearized Navier-Stokes equations,a model of the oscillation of the Reynolds stress (\turbulent damping")due to the acoustic eld is introduced. By comparing with experimental results,it is found that not using this model results in an over-prediction of theamplication at higher frequencies with several factors in magnitude, whileimplementing the model results in a much better agreement. / <p>QC 20121123</p>

The specialized myocytes of the ventricular conduction system (VCS) coordinate ventricular contraction and are critical for efficient pumping by the heart. Impaired VCS conduction is characteristic of inherited forms of cardiac conduction disorders. Here we show that the Iroquois homeobox 3 (Irx3) transcription factor is preferentially expressed in the developing and mature VCS. Loss of Irx3 in mice results in slowed VCS conduction and prolonged QRS duration with right bundle branch block, caused by reduction (42%) in VCS-specific connexin 40 (Cx40) expression and VCS fiber hypoplasia, absent in littermate controls. Therefore, we show that the role of Irx3 in the heart is two-fold, whereby Irx3 (1) indirectly regulates Cx40 gene expression, by repressing a repressor of Cx40 transcript, and (2) controls VCS maturation, possibly in an Nkx2-5-dependent manner. To our knowledge, this is the first report of a role for Irx3 in regulating the development and function of the VCS.

The specialized myocytes of the ventricular conduction system (VCS) coordinate ventricular contraction and are critical for efficient pumping by the heart. Impaired VCS conduction is characteristic of inherited forms of cardiac conduction disorders. Here we show that the Iroquois homeobox 3 (Irx3) transcription factor is preferentially expressed in the developing and mature VCS. Loss of Irx3 in mice results in slowed VCS conduction and prolonged QRS duration with right bundle branch block, caused by reduction (42%) in VCS-specific connexin 40 (Cx40) expression and VCS fiber hypoplasia, absent in littermate controls. Therefore, we show that the role of Irx3 in the heart is two-fold, whereby Irx3 (1) indirectly regulates Cx40 gene expression, by repressing a repressor of Cx40 transcript, and (2) controls VCS maturation, possibly in an Nkx2-5-dependent manner. To our knowledge, this is the first report of a role for Irx3 in regulating the development and function of the VCS.

No description available.

Calcium and calmodulin are implicated in mediating the Ca2+-dependent regulation of gap junctions that are essential for the intercellular transmission of molecules such as nutrients, metabolites, metal ions and signal messengers (< 1000 Da) through its specialized cell membrane channels and communication to extracellular environment. To understand the key determinants for calcium and calmodulin regulation of gap junction, in this study, we identified a calmodulin binding domain in the second half of the intracellular loop of Cxonnexin50 (the major gap junction protein found in an eye lens) using peptide fragments that encompass predicted CaM binding sites and various biophysical methods. Our study provides the first direct evidence that CaM binds to a specific region of the ubiquitous gap junction protein Cx50 in a Ca2+-dependent manner. Furthermore, two novel CaM binding regions in cytosolic loop and C-termini of Connexin43 (the most ubiquitous connexin) have been shown to interact with CaM with different binding modes in the presence of Ca2+ using high resolution NMR. Our results also elucidate the molecular determinants of regulation of gap junction by multiple CaM targeting regions and provide insight into the molecular basis of gap junction gating mechanism and the binding of CaM to the cytoslic region Cx43-3p as the major regulation site. Upon response to the cytosolic calcium increase, CaM binds to the cytosolic loop to result in the conformational change of gap junction and close the channel. It is possible for CaM to use an adjacent region as an anchor close to the regulation site to allow for fast response. Since a large number of residues in the Cxs mutated in human diseases reside at the highly identified CaM binding sites in Cxs, our studies provide insights into define the critical cellular changes and molecular mechanisms contributing to human disease pathogenesis as part of an integrated molecular model for the calcium regulation of GJs. In addition, we have applied the grafting approach to probe the metal binding capability of predicted EF-hand motifs within the streptococcal hemoprotein receptor (Shr) of Streptococcus pyrogenes as well as the nonstructural protein 1 (nsP1) of Sindbis virus and Poxvirus. This fast and robust method allows us to analyze putative EF-hand proteins at genome-wide scale and to further visualize the evolutionary scenario of the EF-hand protein family. Further, mass spectrometry has also been applied to probe modification of proteins such as CaM labeling by florescence dye and 7E15 by PEG.

In this thesis, I will present the experimental results of the dynamics of superconducting single electron transistors (sSETs), under the influence of tunable dissipation. The sSET, consisting of two dc SQUIDs in series and the third gate electrode, is deposited onto a GaAs/AlGaAs heterostructure which contains a two dimensional electron gas plane 100nm beneath the substrate surface. The Josephson coupling energy, charging energy and dissipation related Hamiltonian can all be tuned in situ, while keeping others unchanged. We measured the switching current statistics and the transport properties, as a function of the dissipation and gate charge at different temperatures. If the sSET is in the classical regime where phase is a good quantum variable, we found that the switching current and corresponding Josephson energy decrease as dissipation increases. Our observation agrees qualitatively with the theoretical calculation of a single Josephson junction with dominant Josephson energy, in a frequency dependent dissipative environment where energy barrier decreases as dissipation increases in thermally activated escape regime. This dissipation dependence result can be understood as the consequence of a reduced quantum fluctuations in the charge numbers. Whereas in the charging regime, the switching current shows a 1e periodicity with respect to gate charge, indicating a pronounced charging effect. At a specific gate charge number, quantum fluctuations of the phase variable are compressed as dissipation increases, resulting in an enhanced switching current and Josephson energy. This result matches the theory of a sSET capacitively coupled to a dissipative environment qualitatively. The temperature dependence of the switching current histogram indicates the existence of both quantum and classical thermal phase diffusion. Moreover, quantum charge fluctuations are minimized at the degeneracy point, causing a sharp dip on the width of the switching current histogram. For a sSET with comparable Josephson energy and charging energy, quantum fluctuations of both phase and charge variables are significant. The influence of dissipation on the dynamics of the device is distinct in the classical and charging regimes. Dissipation compresses quantum phase fluctuations in the charging regime, whereas reduces the quantum charge fluctuations in the classical regime. The transition between these two regimes is found to be determined by the tunnel resistance of the SQUID. The competition between Josephson and charging energies, however, is not the intrinsic parameter of this transition. Our results imply that a detailed theoretical calculation of a sSET with comparable Josephson coupling energy and charging energy under the influence of dissipation is needed.