12023 research outputs found
Sort by
Regulation of Mitochondrial Division by the Drp1 Receptors
Get PDFMitochondria can remodel their membranes by fusing or dividing. These processes are required for the proper development and viability of multicellular organisms. At the cellular level, fusion is important for mitochondrial Ca2+ homeostasis, mitochondrial DNA maintenance, mitochondrial membrane potential, and respiration. Mitochondrial division, which is better known as fission, is important for apoptosis, mitophagy, and for the proper allocation of mitochondria to daughter cells during cellular division.
The functions of proteins involved in fission have been best characterized in the yeast model organism Sarccharomyces cerevisiae. Mitochondrial fission in mammals has some similarities. In both systems, a cytosolic dynamin-like protein, called Dnm1 in yeast and Drp1 in mammals, must be recruited to the mitochondrial surface and polymerized to promote membrane division. Recruitment of yeast Dnm1 requires only one mitochondrial outer membrane protein, named Fis1. Fis1 is conserved in mammals, but its importance for Drp1 recruitment is minor. In mammals, three other receptor proteins—Mff, MiD49, and MiD51—play a major role in recruiting Drp1 to mitochondria. Why mammals require three additional receptors, and whether they function together or separately, are fundamental questions for understanding the mechanism of mitochondrial fission in mammals.
We have determined that Mff, MiD49, or MiD51 can function independently of one another to recruit Drp1 to mitochondria. Fis1 plays a minor role in Drp1 recruitment, suggesting that the emergence of these additional receptors has replaced the system used by yeast. Additionally, we found that Fis1/Mff and the MiDs regulate Drp1 activity differentially. Fis1 and Mff promote constitutive mitochondrial fission, whereas the MiDs activate recruited Drp1 only during loss of respiration.
To better understand the function of the MiDs, we have determined the atomic structure of the cytoplasmic domain of MiD51, and performed a structure-function analysis of MiD49 based on its homology to MiD51. MiD51 adopts a nucleotidyl transferase fold, and binds ADP as a co-factor that is essential for its function. Both MiDs contain a loop segment that is not present in other nucleotidyl transferase proteins, and this loop is used to interact with Drp1 and to recruit it to mitochondria.</p
Cell-Targeted Regulation of Gene Expression through Synthetic RNA Devices
Get PDFThe ability to interface with and program cellular function remains a challenging research frontier in biotechnology. Although the emerging field of synthetic biology has recently generated a variety of gene-regulatory strategies based on synthetic RNA molecules, few strategies exist through which to control such regulatory effects in response to specific exogenous or endogenous molecular signals. Here, we present the development of an engineered RNA-based device platform to detect and act on endogenous protein signals, linking these signals to the regulation of genes and thus cellular function.
We describe efforts to develop an RNA-based device framework for regulating endogenous genes in human cells. Previously developed RNA control devices have demonstrated programmable ligand-responsive genetic regulation in diverse cell types, and we attempted to adapt this class of cis-acting control elements to function in trans. We divided the device into two strands that reconstitute activity upon hybridization. Device function was optimized using an in vivo model system, and we found that device sequence is not as flexible as previously reported. After verifying the in vitro activity of our optimized design, we attempted to establish gene regulation in a human cell line using additional elements to direct device stability, structure, and localization. The significant limitations of our platform prevented endogenous gene regulation.
We next describe the development of a protein-responsive RNA-based regulatory platform. Employing various design strategies, we demonstrated functional devices that both up- and downregulate gene expression in response to a heterologous protein in a human cell line. The activity of our platform exceeded that of a similar, small-molecule-responsive platform. We demonstrated the ability of our devices to respond to both cytoplasmic- and nuclear-localized protein, providing insight into the mechanism of action and distinguishing our platform from previously described devices with more restrictive ligand localization requirements. Finally, we demonstrated the versatility of our device platform by developing a regulatory device that responds to an endogenous signaling protein.
The foundational tool we present here possesses unique advantages over previously described RNA-based gene-regulatory platforms. This genetically encoded technology may find future applications in the development of more effective diagnostic tools and targeted molecular therapy strategies.</p
Self-Assembly of Brush Polymers
Get PDFThe unique structure and properties of brush polymers have led to increased interest in them within the scientific community. This thesis describes studies on the self-assembly of these brush polymers.
Chapter 2 describes a study on the rapid self-assembly of brush block copolymers into nanostructures with photonic bandgaps spanning the entire visible spectrum, from ultraviolet to near infrared. Linear relationships are observed between the peak wavelengths of reflection and polymer molecular weights. This work enables "bottom-up" fabrication of photonic crystals with application-tailored bandgaps, through synthetic control of the polymer molecular weight and the method of self-assembly.
Chapter 3 details the analysis of the self-assembly of symmetrical brush block copolymers in bulk and thin films. Highly ordered lamellae with domain spacing ranging from 20 to 240 nm are obtained by varying molecular weight of the backbone. The relationship between degree of polymerization and the domain spacing is reported, and evidence is provided for how rapidly the brush block copolymers self-assemble and achieve thermodynamic equilibrium.
Chapter 4 describes investigations into where morphology transitions take place as the volume fraction of each block is varied in asymmetrical brush block copolymers. Imaging techniques are used to observe a transition from lamellar to a cylindrical morphology as the volume fraction of one of the blocks exceeds 70%. It is also shown that the asymmetric brush block copolymers can be kinetically trapped into undulating lamellar structures by drop casting the samples.
Chapter 5 explores the capability of macromolecules to interdigitate into densely grafted molecular brush copolymers using stereocomplex formation as a driving force. The stereocomplex formation between complementary linear polymers and brush copolymers is demonstrated, while the stereocomplex formation between complementary brush copolymers is shown to be restricted.</p
The Madden-Julian Oscillation: Observation, Modeling, and Theory
Get PDFThe Madden-Julian Oscillation (MJO) is a pattern of intense rainfall and associated planetary-scale circulations in the tropical atmosphere, with a recurrence interval of 30-90 days. Although the MJO was first discovered 40 years ago, it is still a challenge to simulate the MJO in general circulation models (GCMs), and even with simple models it is difficult to agree on the basic mechanisms. This deficiency is mainly due to our poor understanding of moist convection—deep cumulus clouds and thunderstorms, which occur at scales that are smaller than the resolution elements of the GCMs. Moist convection is the most important mechanism for transporting energy from the ocean to the atmosphere. Success in simulating the MJO will improve our understanding of moist convection and thereby improve weather and climate forecasting.
We address this fundamental subject by analyzing observational datasets, constructing a hierarchy of numerical models, and developing theories. Parameters of the models are taken from observation, and the simulated MJO fits the data without further adjustments. The major findings include: 1) the MJO may be an ensemble of convection events linked together by small-scale high-frequency inertia-gravity waves; 2) the eastward propagation of the MJO is determined by the difference between the eastward and westward phase speeds of the waves; 3) the planetary scale of the MJO is the length over which temperature anomalies can be effectively smoothed by gravity waves; 4) the strength of the MJO increases with the typical strength of convection, which increases in a warming climate; 5) the horizontal scale of the MJO increases with the spatial frequency of convection; and 6) triggered convection, where potential energy accumulates until a threshold is reached, is important in simulating the MJO. Our findings challenge previous paradigms, which consider the MJO as a large-scale mode, and point to ways for improving the climate models.</p
Chelation-Enforced Metal-Arene Interactions: Insights into Substrate Binding and Catalvsis by Late Transition Metal Complexes
Get PDFUnderstanding and catalyzing chemical reactions requiring multiple electron transfers is an endeavor relevant to many outstanding challenges in the field of chemistry. To study multi-electron reactions, a terphenyl diphosphine framework was designed to support one or more metals in multiple redox states via stabilizing interactions with the central arene of the terphenyl backbone. A variety of unusual compounds and reactions and their relevance toward prominent research efforts in chemistry are the subject of this dissertation.
Chapter 2 introduces the para-terphenyl diphosphine framework and its coordination chemistry with group 10 transition metal centers. Both mononuclear and dinuclear compounds are characterized. In many cases, the metal center(s) are stabilized by the terphenyl central arene. These metal–arene interactions are characterized both statically, in the solid state, and fluxionally, in solution. As a proof-of-principle, a dinickel framework is shown to span multiple redox states, showing that multielectron chemistry can be supported by the coordinatively flexible terphenyl diphosphine.
Chapter 3 presents reactivity of the terphenyl diphosphine when bound to a metal center. Because of the dearomatizing effect of the metal center, the central arene of the ligand is susceptible to reactions that do not normally affect arenes. In particular, Ni-to-arene H-transfer and arene dihydrogenation reactions are presented. Additionally, evidence for reversibility of the Ni-to-arene H-transfer is discussed.
Chapter 4 expands beyond the chelated metal-arene interactions of the previous chapters. A dipalladium(I) terphenyl diphosphine framework is used to bind a variety of exogenous organic ligands including arenes, dienes, heteroarenes, thioethers, and anionic ligands. The compounds are structurally characterized, and many ligands exhibit unprecedented bindng modes across two metal centers. The relative binding affinities are evaluated spectroscopically, and equilibrium binding constants for the examined ligands are determined to span over 13 orders of magnitude. As an application of this framework, mild hydrogenation conditions of bound thiophene are presented.
Chapter 5 studies nickel-mediated C–O bond cleavage of aryl alkyl ethers, a transformation with emerging applications in fields such as lignin biofuels and organic methodology. Other group members have shown the mechanism of C–O bond cleavage of an aryl methyl ether incorporated into a meta-terphenyl diphosphine framework to proceed through β-H elimination of an alkoxide. First, the electronic selectivity of the model system is examined computationally and compared with catalytic systems. The lessons learned from the model system are then applied to isotopic labeling studies for catalytic aryl alkyl ether cleavage under dihydrogen. Results from selective deuteration experiments and mass spectrometry draw a clear analogy between the mechanisms of the model and catalytic systems that does not require dihydrogen for C–O bond cleavage, although dihydrogen is proposed to play a role in catalyst activation and catalytic turnover.
Appendix A presents initial efforts toward heterodinuclear complexes as models for CO dehydrogenase and Fischer Tropsch chemistry. A catechol-incorporating terphenyl diphosphine is reported, and metal complexes thereof are discussed.
Appendix B highlights some structurally characterized terphenyl diphosphine complexes that either do not thematically belong in the research chapters or proved to be difficult to reproduce. These compounds show unusual coordination modes of the terphenyl diphosphine from which other researchers may glean insights.</p
The Power of Quantum Fourier Sampling
Get PDFHow powerful are Quantum Computers? Despite the prevailing belief that Quantum Computers are more powerful than their classical counterparts, this remains a conjecture backed by little formal evidence. Shor's famous factoring algorithm [Shor97] gives an example of a problem that can be solved efficiently on a quantum computer with no known efficient classical algorithm. Factoring, however, is unlikely to be NP-Hard, meaning that few unexpected formal consequences would arise, should such a classical algorithm be discovered. Could it then be the case that any quantum algorithm can be simulated efficiently classically? Likewise, could it be the case that Quantum Computers can quickly solve problems much harder than factoring? If so, where does this power come from, and what classical computational resources do we need to solve the hardest problems for which there exist efficient quantum algorithms?
We make progress toward understanding these questions through studying the relationship between classical nondeterminism and quantum computing. In particular, is there a problem that can be solved efficiently on a Quantum Computer that cannot be efficiently solved using nondeterminism? In this thesis we address this problem from the perspective of sampling problems. Namely, we give evidence that approximately sampling the Quantum Fourier Transform of an efficiently computable function, while easy quantumly, is hard for any classical machine in the Polynomial Time Hierarchy. In particular, we prove the existence of a class of distributions that can be sampled efficiently by a Quantum Computer, that likely cannot be approximately sampled in randomized polynomial time with an oracle for the Polynomial Time Hierarchy.
Our work complements and generalizes the evidence given in Aaronson and Arkhipov's work [AA2013] where a different distribution with the same computational properties was given. Our result is more general than theirs, but requires a more powerful quantum sampler. </p
Label-free Detection of Single Molecule Using Microtoroid Optical Resonators
Get PDFBeing able to detect a single molecule without the use of labels has been a long standing goal of bioengineers and physicists. This would simplify applications ranging from single molecular binding studies to those involving public health and security, improved drug screening, medical diagnostics, and genome sequencing. One promising technique that has the potential to detect single molecules is the microtoroid optical resonator. The main obstacle to detecting single molecules, however, is decreasing the noise level of the measurements such that a single molecule can be distinguished from background. We have used laser frequency locking in combination with balanced detection and data processing techniques to reduce the noise level of these devices and report the detection of a wide range of nanoscale objects ranging from nanoparticles with radii from 100 to 2.5 nm, to exosomes, ribosomes, and single protein molecules (mouse immunoglobulin G and human interleukin-2). We further extend the exosome results towards creating a non-invasive tumor biopsy assay. Our results, covering several orders of magnitude of particle radius (100 nm to 2 nm), agree with the 'reactive' model prediction for the frequency shift of the resonator upon particle binding. In addition, we demonstrate that molecular weight may be estimated from the frequency shift through a simple formula, thus providing a basis for an ``optical mass spectrometer'' in solution. We anticipate that our results will enable many applications, including more sensitive medical diagnostics and fundamental studies of single receptor-ligand and protein-protein interactions in real time. The thesis summarizes what we have achieved thus far and shows that the goal of detecting a single molecule without the use of labels can now be realized
Density Functional Theory Embedding for Correlated Wavefunctions
Get PDFMethods that exploit the intrinsic locality of molecular interactions show significant promise in making tractable the electronic structure calculation of large-scale systems. In particular, embedded density functional theory (e-DFT) offers a formally exact approach to electronic structure calculations in which the interactions between subsystems are evaluated in terms of their electronic density. In the following dissertation, methodological advances of embedded density functional theory are described, numerically tested, and applied to real chemical systems.
First, we describe an e-DFT protocol in which the non-additive kinetic energy component of the embedding potential is treated exactly. Then, we present a general implementation of the exact calculation of the non-additive kinetic potential (NAKP) and apply it to molecular systems. We demonstrate that the implementation using the exact NAKP is in excellent agreement with reference Kohn-Sham calculations, whereas the approximate functionals lead to qualitative failures in the calculated energies and equilibrium structures.
Next, we introduce density-embedding techniques to enable the accurate and stable calculation of correlated wavefunction (CW) in complex environments. Embedding potentials calculated using e-DFT introduce the effect of the environment on a subsystem for CW calculations (WFT-in-DFT). We demonstrate that WFT-in-DFT calculations are in good agreement with CW calculations performed on the full complex.
We significantly improve the numerics of the algorithm by enforcing orthogonality between subsystems by introduction of a projection operator. Utilizing the projection-based embedding scheme, we rigorously analyze the sources of error in quantum embedding calculations in which an active subsystem is treated using CWs, and the remainder using density functional theory. We show that the embedding potential felt by the electrons in the active subsystem makes only a small contribution to the error of the method, whereas the error in the nonadditive exchange-correlation energy dominates. We develop an algorithm which corrects this term and demonstrate the accuracy of this corrected embedding scheme.</p
Dynamically Controllable Integrated Radiation and Self-Correcting Power Generation in mm-Wave Circuits and Systems
Get PDFThis thesis presents novel design methodologies for integrated radiators and power generation at mm-wave frequencies that are enabled by the continued integration of various electronic and electromagnetic (EM) structures onto the same substrate. Beginning with the observation that transistors and their connections to EM radiating structures on an integrated substrate are essentially free, the concept of multi-port driven (MPD) radiators is introduced, which opens a vast design space that has been generally ignored due to the cost structure associated with discrete components that favors fewer transistors connected to antennas through a single port.
From Maxwell's equations, a new antenna architecture, the radial MPD antennas based on the concept of MPD radiators, is analyzed to gain intuition as to the important design parameters that explain the wide-band nature of the antenna itself. The radiator is then designed and implemented at 160 GHz in a 0.13 um SiGe BiCMOS process, and the single element design has a measured effective isotropic radiated power (EIRP) of +4.6 dBm with a total radiated power of 0.63 mW.
Next, the radial MPD radiator is adapted to enable dynamic polarization control (DPC). A DPC antenna is capable of controlling its radiated polarization dynamically, and entirely electronically, with no mechanical reconfiguration required. This can be done by having multiple antennas with different polarizations, or within a single antenna that has multiple drive points, as in the case of the MPD radiator with DPC. This radiator changes its polarization by adjusting the relative phase and amplitude of its multiple ports to produce polarizations with any polarization angle, and a wide range of axial ratios. A 2x1 MPD radiator array with DPC at 105 GHz is presented whose measurements show control of the polarization angle throughout the entire 0 degree through 180 degree range while in the linear polarization mode and maintaining axial ratios above 10 dB in all cases. Control of the axial ratio is also demonstrated with a measured range from 2.4 dB through 14 dB, while maintaining a fixed polarization angle. The radiator itself has a measured maximum EIRP of +7.8 dBm, with a total radiated power of 0.9 mW, and is capable of beam steering.
MPD radiators were also applied in the domain of integrated silicon photonics. For these designs, the driver transistor circuitry was replaced with silicon optical waveguides and photodiodes to produce a 350 GHz signal. Three of these optical MPD radiator designs have been implemented as 2x2 arrays at 350 GHz. The first is a beam forming array that has a simulated gain of 12.1 dBi with a simulated EIRP of -2 dBm. The second has the same simulated performance, but includes optical phase modulators that enable two-dimensional beam steering. Finally, a third design incorporates multi-antenna DPC by combining the outputs of both left and right handed circularly polarized MPD antennas to produce a linear polarization with controllable polarization angle, and has a simulated gain of 11.9 dBi and EIRP of -3 dBm. In simulation, it can tune the polarization from 0 degrees through 180 degrees while maintaining a radiated power that has a 0.35 dB maximum deviation from the mean.
The reliability of mm-wave radiators and power amplifiers was also investigated, and two self-healing systems have been proposed. Self-healing is a global feedback method where integrated sensors detect the performance of the circuit after fabrication and report that data to a digital control algorithm. The algorithm then is capable of setting actuators that can control the performance of the mm-wave circuit and counteract any performance degradation that is observed by the sensors. The first system is for a MPD radiator array with a partially integrated self-healing system. The self-healing MPD radiator senses substrate modes through substrate mode pickup sensors and infers the far-field radiated pattern from those sensors. DC current sensors are also included to determine the DC power consumption of the system. Actuators are implemented in the form of phase and amplitude control of the multiple drive points.
The second self-healing system is a fully integrated self-healing power amplifier (PA) at 28 GHz. This system measures the output power, gain and efficiency of the PA using radio frequency (RF) power sensors, DC current sensors and junction temperature sensors. The digital block is synthesized from VHDL code on-chip and it can actuate the output power combining matching network using tunable transmission line stubs, as well as the DC operating point of the amplifying transistors through bias control. Measurements of 20 chips confirm self-healing for two different algorithms for process variation and transistor mismatch, while measurements from 10 chips show healing for load impedance mismatch, and linearity healing. Laser induced partial and total transistor failure show the benefit of self-healing in the case of catastrophic failure, with improvements of up to 3.9 dB over the default case. An exemplary yield specification shows self-healing improving the yield from 0% up through 80%.</p
Experimental Characterization of Front Propagation by Marangoni Forces in Ultrathin Liquid Films
No full textItalian physicist Carlo Marangoni published a treatise in 1865 which first described the
spontaneous flow of a liquid film caused by gradients in surface t ension at a gas/liquid
interface. Such gradients are established by variations in surface concentration of molecular
species which lower the surface tension in proportion to the interface concentration.
While the dynamics and power law behavior of the initial circular advancing front in surfactant
coated films has been studied for about two decades, there has been relatively little
work conducted on characterizing the fractal spreading patterns which develop behind this
front. In this thesis, we examine the dynamics of front propagation and subsequent fractal
evolution in ultrathin liquid films of glycerol driven to spread by concentration gradients
in Aerosol OT, an insoluble anionic surfactant. We vary only the initial deposition volume
and concentration while maintaining the initial liquid film thickness at 2.5 microns.
Contrary to theoretical analyses in the literature, our results reveal that the coefficient
and exponent characterizing the advance of both the first front as well as the following
unstable front is not a constant depending only on geometry (i.e. rectilinear vs axisymmetric
spreading) but varies with the initial surfactant concentration of the deposition
volume. Furthermore, the overall speed of the fronts is observed to increase with ambient
relative humidity, an effect we ascribe to a reduction in the viscosity of the glycerol film
clue to absorption of water from the ambient atmosphere. Only in cases of relatively high
humidity (higher than approximately 40% relative humidity) do we observe the formation
of fractal patterns in the unstable front. Measurements of the fractal dimension yield
values in the range 1.45-1.65. The largest values approximate those fractal dimensions
observed in systems undergoing diffusion driven aggregation or viscous fingering, neither
of which mechanism is pertinent to Marangoni flow