33 resultados para Coupled channel calculations
Resumo:
A set of coupled-channel differential equations based on a rotationally distorted optical potential is used to calculate the wave functions required to evaluate the gamma ray transition rate from the first excited state to the ground state in ^(13)C and ^(13)N. The bremsstrahlung differential cross section of low energy protons is also calculated and compared with existing data. The marked similarity between the potentials determined at each resonance level in both nuclei supports the hypothesis of the charge symmetry of nuclear forces by explaining the deviation of the ratios of the experimental E1 transition strengths from unity.
Resumo:
The problem of two channels NN and NN*, coupled through unitarity, is studied to see whether sizable peaks can be produced in elastic nucleon-nucleon scattering due to the opening of a strongly coupled inelastic channel. One-pion-exchange (OPE) interactions are calculated to estimate the NN*→NN* and NN→NN* amplitudes. The OPE production amplitudes are used as the sole dynamical input to drive the multichannel ND-1 equations in the determinental approximation, and the effect on the J = 2+ (1D2) elastic NN scattering amplitude is studied as the width of the unstable N* and strength of coupling to the inelastic channel are varied. A cusp-type enhancement appears in the NN channel near the NN* threshold but for the known value of the N* width the cusp is so “wooly” that any resulting elastic peak is likely to be too broad and diminished in height to be experimentally prominent. A brief survey of current experimental knowledge of the real part of the 1D2 NN phase shift near the NN* threshold is given, and the values are found to be much smaller than the nearly “resonant” phase shifts predicted by the coupled channel model.
Resumo:
Signal recognition particle (SRP) and signal recognition particle receptor (SR) are evolutionarily conserved GTPases that deliver secretory and membrane proteins to the protein-conducting channel Sec61 complex in the lipid bilayer of the endoplasmic reticulum in eukaryotes or the SecYEG complex in the inner membrane of bacteria. Unlike the canonical Ras-type GTPases, SRP and SR are activated via nucleotide-dependent heterodimerization. Upon formation of the SR•SRP targeting complex, SRP and SR undergo a series of discrete conformational changes that culminate in their reciprocal activation and hydrolysis of GTP. How the SR•SRP GTPase cycle is regulated and coupled to the delivery of the cargo protein to the protein-conducting channel at the target membrane is not well-understood. Here we examine the role of the lipid bilayer and SecYEG in regulation of the SRP-mediated protein targeting pathway and show that they serve as important biological cues that spatially control the targeting reaction.
In the first chapter, we show that anionic phospholipids of the inner membrane activate the bacterial SR, FtsY, and favor the late conformational states of the targeting complex conducive to efficient unloading of the cargo. The results of our studies suggest that the lipid bilayer acts as a spatial cue that weakens the interaction of the cargo protein with SRP and primes the complex for unloading its cargo onto SecYEG.
In the second chapter, we focus on the effect of SecYEG on the conformational states and activity of the targeting complex. While phospholipids prime the complex for unloading its cargo, they are insufficient to trigger hydrolysis of GTP and the release of the cargo from the complex. SecYEG modulates the conformation of the targeting complex and triggers the GTP hydrolysis from the complex, thus driving the targeting reaction to completion. The results of this study suggest that SecYEG is not a passive recipient of the cargo protein; rather, it actively releases the cargo from the targeting complex. Together, anionic phospholipids and SecYEG serve distinct yet complementary roles. They spatially control the targeting reaction in a sequential manner, ensuring efficient delivery and unloading of the cargo protein.
In the third chapter, we reconstitute the transfer reaction in vitro and visualize it in real time. We show that the ribosome-nascent chain complex is transferred to SecYEG via a stepwise mechanism with gradual dissolution and formation of the contacts with SRP and SecYEG, respectively, explaining how the cargo is kept tethered to the membrane during the transfer and how its loss to the cytosol is avoided.
In the fourth chapter, we examine interaction of SecYEG with secretory and membrane proteins and attempt to address the role of a novel insertase YidC in this interaction. We show that detergent-solubilized SecYEG is capable of discriminating between the nascent chains of various lengths and engages a signal sequence in a well-defined conformation in the absence of accessory factors. Further, YidC alters the conformation of the signal peptide bound to SecYEG. The results described in this chapter show that YidC affects the SecYEG-nascent chain interaction at early stages of translocation/insertion and suggest a YidC-facilitated mechanism for lateral exit of transmembrane domains from SecYEG into the lipid bilayer.
Resumo:
An analytic technique is developed that couples to finite difference calculations to extend the results to arbitrary distance. Finite differences and the analytic result, a boundary integral called two-dimensional Kirchhoff, are applied to simple models and three seismological problems dealing with data. The simple models include a thorough investigation of the seismologic effects of a deep continental basin. The first problem is explosions at Yucca Flat, in the Nevada test site. By modeling both near-field strong-motion records and teleseismic P-waves simultaneously, it is shown that scattered surface waves are responsible for teleseismic complexity. The second problem deals with explosions at Amchitka Island, Alaska. The near-field seismograms are investigated using a variety of complex structures and sources. The third problem involves regional seismograms of Imperial Valley, California earthquakes recorded at Pasadena, California. The data are shown to contain evidence of deterministic structure, but lack of more direct measurements of the structure and possible three-dimensional effects make two-dimensional modeling of these data difficult.
Resumo:
The thesis is divided into two parts. Part I generalizes a self-consistent calculation of residue shifts from SU3 symmetry, originally performed by Dashen, Dothan, Frautschi, and Sharp, to include the effects of non-linear terms. Residue factorizability is used to transform an overdetermined set of equations into a variational problem, which is designed to take advantage of the redundancy of the mathematical system. The solution of this problem automatically satisfies the requirement of factorizability and comes close to satisfying all the original equations.
Part II investigates some consequences of direct channel Regge poles and treats the problem of relating Reggeized partial wave expansions made in different reaction channels. An analytic method is introduced which can be used to determine the crossed-channel discontinuity for a large class of direct-channel Regge representations, and this method is applied to some specific representations.
It is demonstrated that the multi-sheeted analytic structure of the Regge trajectory function can be used to resolve apparent difficulties arising from infinitely rising Regge trajectories. Also discussed are the implications of large collections of "daughter trajectories."
Two things are of particular interest: first, the threshold behavior in direct and crossed channels; second, the potentialities of Reggeized representations for us in self-consistent calculations. A new representation is introduced which surpasses previous formulations in these two areas, automatically satisfying direct-channel threshold constraints while being capable of reproducing a reasonable crossed channel discontinuity. A scalar model is investigated for low energies, and a relation is obtained between the mass of the lowest bound state and the slope of the Regge trajectory.
Resumo:
Part 1. Many interesting visual and mechanical phenomena occur in the critical region of fluids, both for the gas-liquid and liquid-liquid transitions. The precise thermodynamic and transport behavior here has some broad consequences for the molecular theory of liquids. Previous studies in this laboratory on a liquid-liquid critical mixture via ultrasonics supported a basically classical analysis of fluid behavior by M. Fixman (e. g., the free energy is assumed analytic in intensive variables in the thermodynamics)--at least when the fluid is not too close to critical. A breakdown in classical concepts is evidenced close to critical, in some well-defined ways. We have studied herein a liquid-liquid critical system of complementary nature (possessing a lower critical mixing or consolute temperature) to all previous mixtures, to look for new qualitative critical behavior. We did not find such new behavior in the ultrasonic absorption ascribable to the critical fluctuations, but we did find extra absorption due to chemical processes (yet these are related to the mixing behavior generating the lower consolute point). We rederived, corrected, and extended Fixman's analysis to interpret our experimental results in these more complex circumstances. The entire account of theory and experiment is prefaced by an extensive introduction recounting the general status of liquid state theory. The introduction provides a context for our present work, and also points out problems deserving attention. Interest in these problems was stimulated by this work but also by work in Part 3.
Part 2. Among variational theories of electronic structure, the Hartree-Fock theory has proved particularly valuable for a practical understanding of such properties as chemical binding, electric multipole moments, and X-ray scattering intensity. It also provides the most tractable method of calculating first-order properties under external or internal one-electron perturbations, either developed explicitly in orders of perturbation theory or in the fully self-consistent method. The accuracy and consistency of first-order properties are poorer than those of zero-order properties, but this is most often due to the use of explicit approximations in solving the perturbed equations, or to inadequacy of the variational basis in size or composition. We have calculated the electric polarizabilities of H2, He, Li, Be, LiH, and N2 by Hartree-Fock theory, using exact perturbation theory or the fully self-consistent method, as dictated by convenience. By careful studies on total basis set composition, we obtained good approximations to limiting Hartree-Fock values of polarizabilities with bases of reasonable size. The values for all species, and for each direction in the molecular cases, are within 8% of experiment, or of best theoretical values in the absence of the former. Our results support the use of unadorned Hartree-Pock theory for static polarizabilities needed in interpreting electron-molecule scattering data, collision-induced light scattering experiments, and other phenomena involving experimentally inaccessible polarizabilities.
Part 3. Numerical integration of the close-coupled scattering equations has been carried out to obtain vibrational transition probabilities for some models of the electronically adiabatic H2-H2 collision. All the models use a Lennard-Jones interaction potential between nearest atoms in the collision partners. We have analyzed the results for some insight into the vibrational excitation process in its dependence on the energy of collision, the nature of the vibrational binding potential, and other factors. We conclude also that replacement of earlier, simpler models of the interaction potential by the Lennard-Jones form adds very little realism for all the complication it introduces. A brief introduction precedes the presentation of our work and places it in the context of attempts to understand the collisional activation process in chemical reactions as well as some other chemical dynamics.
Resumo:
Measuring electrical activity in large numbers of cells with high spatial and temporal resolution is a fundamental problem for the study of neural development and information processing. To address this problem, we have constructed FlaSh: a novel, genetically-encoded probe that can be used to measure trans-membrane voltage in single cells. We fused a modified green fluorescent protein (GFP) into a voltage-sensitive potassium channel so that voltage dependent rearrangements in the potassium channel induce changes in the fluorescence of GFP. A voltage sensor encoded into DNA has the advantage that it may be introduced into an organism non-invasively and targeted to specific developmental stages, brain regions, cell types, and sub-cellular compartments.
We also describe modifications to FlaSh that shift its color, kinetics, and dynamic range. We used multiple green fluorescent proteins to produce variants of the FlaSh sensor that generate ratiometric signal output via fluorescence resonance energy transfer (FRET). Finally, we describe initial work toward FlaSh variants that are sensitive to G-protein coupled receptor (GPCR) activation. These sensors can be used to design functional assays for receptor activation in living cells.
Resumo:
Hartree-Fock (HF) calculations have had remarkable success in describing large nuclei at high spin, temperature and deformation. To allow full range of possible deformations, the Skyrme HF equations can be discretized on a three-dimensional mesh. However, such calculations are currently limited by the computational resources provided by traditional supercomputers. To take advantage of recent developments in massively parallel computing technology, we have implemented the LLNL Skyrme-force static and rotational HF codes on Intel's DELTA and GAMMA systems at Caltech.
We decomposed the HF code by assigning a portion of the mesh to each node, with nearest neighbor meshes assigned to nodes connected by communication· channels. This kind of decomposition is well-suited for the DELTA and the GAMMA architecture because the only non-local operations are wave function orthogonalization and the boundary conditions of the Poisson equation for the Coulomb field.
Our first application of the HF code on parallel computers has been the study of identical superdeformed (SD) rotational bands in the Hg region. In the last ten years, many SD rotational bands have been found experimentally. One very surprising feature found in these SD rotational bands is that many pairs of bands in nuclei that differ by one or two mass units have nearly identical deexcitation gamma-ray energies. Our calculations of the five rotational bands in ^(192)Hg and ^(194)Pb show that the filling of specific orbitals can lead to bands with deexcitation gamma-ray energies differing by at most 2 keV in nuclei differing by two mass units and over a range of angular momenta comparable to that observed experimentally. Our calculations of SD rotational bands in the Dy region also show that twinning can be achieved by filling or emptying some specific orbitals.
The interpretation of future precise experiments on atomic parity nonconservation (PNC) in terms of parameters of the Standard Model could be hampered by uncertainties in the atomic and nuclear structure. As a further application of the massively parallel HF calculations, we calculated the proton and neutron densities of the Cesium isotopes from A = 125 to A = 139. Based on our good agreement with experimental charge radii, binding energies, and ground state spins, we conclude that the uncertainties in the ratios of weak charges are less than 10^(-3), comfortably smaller than the anticipated experimental error.
Resumo:
The condensation of phenanthroline-5,6-dione (phendione) with polyamines is a versatile synthetic route to a wide variety of chelating ligands. Condensation with 2,3- napthalene diamine gives benzo[i]dipyrido[3,2-a:2',3'-c]phenazine (bdppz) a ligand containing weakly-coupled orbitals of benzophenazine (bpz) and 2,2' -bipyridinde(bpy) character. The bpy character gives Re and Ru complexes excited-state redox properties; intramolecular electron transfer (ET) takes place to the bpz portion of the ligand. The charge-separated state so produced has an extraordinarily-long 50 µs lifetime. The slow rate of charge recombination arises from a combination of extremely weak coupling between the metal center and the bpz acceptor orbital and Marcus "inverted region" behavior. Molecular orbital calculations show that only 3% the electron density in the lowest unoccupied molecular orbital lies on the bpy atoms of bdppz, effectively trapping the transferred electron on the bpz portion. The rate of charge recombination decreases with increasing driving force, showing that these rates lie in the inverted region. Comparison of forward and back ET rates shows that donor-acceptor coupling is four orders of magnitude greater for photoinduced electron transfer than it is for thermal charge recombination.
Condensation of phendione with itself or tetramines gives a series of binucleating tetrapyridophenazine ligands of incrementally-varying coordination-site separation. When a photoredox-active metal center is attached, excited-state energy and electron transfer to an acceptor metal center at the other coordination site can be studied as a function of distance. A variety of monometallic and homo- and heterodimetallic tetrapyridophenazine complexes has been synthesized. Electro- and magnetochemistry show that no ground-state interaction exists between the metals in bimetallic complexes. Excited-state energy and electron transfer, however, takes place at rates which are invariant with increasing donor-acceptor separation, indicating that a very efficient coupling mechanism is at work. Theory and experiment have suggested that such behavior might exist in extended π-systems like those presented by these ligands.
Condensation of three equivalents of 4,5-dimethyl-1,2-phenylenediamine with hexaketocyclohexane gives the trinucleating ligand hexaazahexamethyltrinapthalene (hhtn). Attaching two photredox-active metal centers and a third catalytic center to hhtn provides means by which multielectron photocatalyzed reactions might be carried out. The coordination properties of hhtn have been examined; X-ray crystallographic structure determination shows that the ligand's constricted coordination pocket leads to distorted geometries in its mono- and dimetallic derivatives.
Resumo:
A search for dielectron decays of heavy neutral resonances has been performed using proton-proton collision data collected at √s = 7 TeV by the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) in 2011. The data sample corresponds to an integrated luminosity of 5 fb−1. The dielectron mass distribution is consistent with Standard Model (SM) predictions. An upper limit on the ratio of the cross section times branching fraction of new bosons, normalized to the cross section times branching fraction of the Z boson, is set at the 95 % confidence level. This result is translated into limits on the mass of new neutral particles at the level of 2120 GeV for the Z′ in the Sequential Standard Model, 1810 GeV for the superstring-inspired Z′ψ resonance, and 1940 (1640) GeV for Kaluza-Klein gravitons with the coupling parameter k/MPl of 0.10 (0.05).
Resumo:
With the size of transistors approaching the sub-nanometer scale and Si-based photonics pinned at the micrometer scale due to the diffraction limit of light, we are unable to easily integrate the high transfer speeds of this comparably bulky technology with the increasingly smaller architecture of state-of-the-art processors. However, we find that we can bridge the gap between these two technologies by directly coupling electrons to photons through the use of dispersive metals in optics. Doing so allows us to access the surface electromagnetic wave excitations that arise at a metal/dielectric interface, a feature which both confines and enhances light in subwavelength dimensions - two promising characteristics for the development of integrated chip technology. This platform is known as plasmonics, and it allows us to design a broad range of complex metal/dielectric systems, all having different nanophotonic responses, but all originating from our ability to engineer the system surface plasmon resonances and interactions. In this thesis, we demonstrate how plasmonics can be used to develop coupled metal-dielectric systems to function as tunable plasmonic hole array color filters for CMOS image sensing, visible metamaterials composed of coupled negative-index plasmonic coaxial waveguides, and programmable plasmonic waveguide network systems to serve as color routers and logic devices at telecommunication wavelengths.
Resumo:
Lipid bilayer membranes are models for cell membranes--the structure that helps regulate cell function. Cell membranes are heterogeneous, and the coupling between composition and shape gives rise to complex behaviors that are important to regulation. This thesis seeks to systematically build and analyze complete models to understand the behavior of multi-component membranes.
We propose a model and use it to derive the equilibrium and stability conditions for a general class of closed multi-component biological membranes. Our analysis shows that the critical modes of these membranes have high frequencies, unlike single-component vesicles, and their stability depends on system size, unlike in systems undergoing spinodal decomposition in flat space. An important implication is that small perturbations may nucleate localized but very large deformations. We compare these results with experimental observations.
We also study open membranes to gain insight into long tubular membranes that arise for example in nerve cells. We derive a complete system of equations for open membranes by using the principle of virtual work. Our linear stability analysis predicts that the tubular membranes tend to have coiling shapes if the tension is small, cylindrical shapes if the tension is moderate, and beading shapes if the tension is large. This is consistent with experimental observations reported in the literature in nerve fibers. Further, we provide numerical solutions to the fully nonlinear equilibrium equations in some problems, and show that the observed mode shapes are consistent with those suggested by linear stability. Our work also proves that beadings of nerve fibers can appear purely as a mechanical response of the membrane.
Resumo:
This dissertation describes studies of G protein-coupled receptors (GPCRs) and ligand-gated ion channels (LGICs) using unnatural amino acid mutagenesis to gain high precision insights into the function of these important membrane proteins.
Chapter 2 considers the functional role of highly conserved proline residues within the transmembrane helices of the D2 dopamine GPCR. Through mutagenesis employing unnatural α-hydroxy acids, proline analogs, and N-methyl amino acids, we find that lack of backbone hydrogen bond donor ability is important to proline function. At one proline site we additionally find that a substituent on the proline backbone N is important to receptor function.
In Chapter 3, side chain conformation is probed by mutagenesis of GPCRs and the muscle-type nAChR. Specific side chain rearrangements of highly conserved residues have been proposed to accompany activation of these receptors. These rearrangements were probed using conformationally-biased β-substituted analogs of Trp and Phe and unnatural stereoisomers of Thr and Ile. We also modeled the conformational bias of the unnatural Trp and Phe analogs employed.
Chapters 4 and 5 examine details of ligand binding to nAChRs. Chapter 4 describes a study investigating the importance of hydrogen bonds between ligands and the complementary face of muscle-type and α4β4 nAChRs. A hydrogen bond involving the agonist appears to be important for ligand binding in the muscle-type receptor but not the α4β4 receptor.
Chapter 5 describes a study characterizing the binding of varenicline, an actively prescribed smoking cessation therapeutic, to the α7 nAChR. Additionally, binding interactions to the complementary face of the α7 binding site were examined for a small panel of agonists. We identified side chains important for binding large agonists such as varenicline, but dispensable for binding the small agonist ACh.
Chapter 6 describes efforts to image nAChRs site-specifically modified with a fluorophore by unnatural amino acid mutagenesis. While progress was hampered by high levels of fluorescent background, improvements to sample preparation and alternative strategies for fluorophore incorporation are described.
Chapter 7 describes efforts toward a fluorescence assay for G protein association with a GPCR, with the ultimate goal of probing key protein-protein interactions along the G protein/receptor interface. A wide range of fluorescent protein fusions were generated, expressed in Xenopus oocytes, and evaluated for their ability to associate with each other.
Resumo:
Studies in turbulence often focus on two flow conditions, both of which occur frequently in real-world flows and are sought-after for their value in advancing turbulence theory. These are the high Reynolds number regime and the effect of wall surface roughness. In this dissertation, a Large-Eddy Simulation (LES) recreates both conditions over a wide range of Reynolds numbers Reτ = O(102)-O(108) and accounts for roughness by locally modeling the statistical effects of near-wall anisotropic fine scales in a thin layer immediately above the rough surface. A subgrid, roughness-corrected wall model is introduced to dynamically transmit this modeled information from the wall to the outer LES, which uses a stretched-vortex subgrid-scale model operating in the bulk of the flow. Of primary interest is the Reynolds number and roughness dependence of these flows in terms of first and second order statistics. The LES is first applied to a fully turbulent uniformly-smooth/rough channel flow to capture the flow dynamics over smooth, transitionally rough and fully rough regimes. Results include a Moody-like diagram for the wall averaged friction factor, believed to be the first of its kind obtained from LES. Confirmation is found for experimentally observed logarithmic behavior in the normalized stream-wise turbulent intensities. Tight logarithmic collapse, scaled on the wall friction velocity, is found for smooth-wall flows when Reτ ≥ O(106) and in fully rough cases. Since the wall model operates locally and dynamically, the framework is used to investigate non-uniform roughness distribution cases in a channel, where the flow adjustments to sudden surface changes are investigated. Recovery of mean quantities and turbulent statistics after transitions are discussed qualitatively and quantitatively at various roughness and Reynolds number levels. The internal boundary layer, which is defined as the border between the flow affected by the new surface condition and the unaffected part, is computed, and a collapse of the profiles on a length scale containing the logarithm of friction Reynolds number is presented. Finally, we turn to the possibility of expanding the present framework to accommodate more general geometries. As a first step, the whole LES framework is modified for use in the curvilinear geometry of a fully-developed turbulent pipe flow, with implementation carried out in a spectral element solver capable of handling complex wall profiles. The friction factors have shown favorable agreement with the superpipe data, and the LES estimates of the Karman constant and additive constant of the log-law closely match values obtained from experiment.
Resumo:
Cancellation of interfering frequency-modulated (FM) signals is investigated with emphasis towards applications on the cellular telephone channel as an important example of a multiple access communications system. In order to fairly evaluate analog FM multiaccess systems with respect to more complex digital multiaccess systems, a serious attempt to mitigate interference in the FM systems must be made. Information-theoretic results in the field of interference channels are shown to motivate the estimation and subtraction of undesired interfering signals. This thesis briefly examines the relative optimality of the current FM techniques in known interference channels, before pursuing the estimation and subtracting of interfering FM signals.
The capture-effect phenomenon of FM reception is exploited to produce simple interference-cancelling receivers with a cross-coupled topology. The use of phase-locked loop receivers cross-coupled with amplitude-tracking loops to estimate the FM signals is explored. The theory and function of these cross-coupled phase-locked loop (CCPLL) interference cancellers are examined. New interference cancellers inspired by optimal estimation and the CCPLL topology are developed, resulting in simpler receivers than those in prior art. Signal acquisition and capture effects in these complex dynamical systems are explained using the relationship of the dynamical systems to adaptive noise cancellers.
FM interference-cancelling receivers are considered for increasing the frequency reuse in a cellular telephone system. Interference mitigation in the cellular environment is seen to require tracking of the desired signal during time intervals when it is not the strongest signal present. Use of interference cancelling in conjunction with dynamic frequency-allocation algorithms is viewed as a way of improving spectrum efficiency. Performance of interference cancellers indicates possibilities for greatly increased frequency reuse. The economics of receiver improvements in the cellular system is considered, including both the mobile subscriber equipment and the provider's tower (base station) equipment.
The thesis is divided into four major parts and a summary: the introduction, motivations for the use of interference cancellation, examination of the CCPLL interference canceller, and applications to the cellular channel. The parts are dependent on each other and are meant to be read as a whole.