Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

I. The Superstition Hills, California, earthquakes of 24 November 1987. II. Three-dimensional velocity structure of southern California.

Part 1 of this thesis is about the 24 November, 1987, Superstition Hills earthquakes. The Superstition Hills earthquakes occurred in the western Imperial Valley in southern California. The earthquakes took place on a conjugate fault system consisting of the northwest-striking right-lateral Superstition Hills fault and a previously unknown Elmore Ranch fault, a northeast-striking left-lateral structure defined by surface rupture and a lineation of hypocenters. The earthquake sequence consisted of foreshocks, the M_s 6.2 first main shock, and aftershocks on the Elmore Ranch fault followed by the M_s 6.6 second main shock and aftershocks on the Superstition Hills fault. There was dramatic surface rupture along the Superstition Hills fault in three segments: the northern segment, the southern segment, and the Wienert fault.

In Chapter 2, M_L≥4.0 earthquakes from 1945 to 1971 that have Caltech catalog locations near the 1987 sequence are relocated. It is found that none of the relocated earthquakes occur on the southern segment of the Superstition Hills fault and many occur at the intersection of the Superstition Hills and Elmore Ranch faults. Also, some other northeast-striking faults may have been active during that time.

Chapter 3 discusses the Superstition Hills earthquake sequence using data from the Caltech-U.S.G.S. southern California seismic array. The earthquakes are relocated and their distribution correlated to the type and arrangement of the basement rocks. The larger earthquakes occur only where continental crystalline basement rocks are present. The northern segment of the Superstition Hills fault has more aftershocks than the southern segment.

An inversion of long period teleseismic data of the second mainshock of the 1987 sequence, along the Superstition Hills fault, is done in Chapter 4. Most of the long period seismic energy seen teleseismically is radiated from the southern segment of the Superstition Hills fault. The fault dip is near vertical along the northern segment of the fault and steeply southwest dipping along the southern segment of the fault.

Chapter 5 is a field study of slip and afterslip measurements made along the Superstition Hills fault following the second mainshock. Slip and afterslip measurements were started only two hours after the earthquake. In some locations, afterslip more than doubled the coseismic slip. The northern and southern segments of the Superstition Hills fault differ in the proportion of coseismic and postseismic slip to the total slip.

The northern segment of the Superstition Hills fault had more aftershocks, more historic earthquakes, released less teleseismic energy, and had a smaller proportion of afterslip to total slip than the southern segment. The boundary between the two segments lies at a step in the basement that separates a deeper metasedimentary basement to the south from a shallower crystalline basement to the north.

Part 2 of the thesis deals with the three-dimensional velocity structure of southern California. In Chapter 7, an a priori three-dimensional crustal velocity model is constructed by partitioning southern California into geologic provinces, with each province having a consistent one-dimensional velocity structure. The one-dimensional velocity structures of each region were then assembled into a three-dimensional model. The three-dimension model was calibrated by forward modeling of explosion travel times.

In Chapter 8, the three-dimensional velocity model is used to locate earthquakes. For about 1000 earthquakes relocated in the Los Angeles basin, the three-dimensional model has a variance of the the travel time residuals 47 per cent less than the catalog locations found using a standard one-dimensional velocity model. Other than the 1987 Whittier earthquake sequence, little correspondence is seen between these earthquake locations and elements of a recent structural cross section of the Los Angeles basin. The Whittier sequence involved rupture of a north dipping thrust fault bounded on at least one side by a strike-slip fault. The 1988 Pasadena earthquake was deep left-lateral event on the Raymond fault. The 1989 Montebello earthquake was a thrust event on a structure similar to that on which the Whittier earthquake occurred. The 1989 Malibu earthquake was a thrust or oblique slip event adjacent to the 1979 Malibu earthquake.

At least two of the largest recent thrust earthquakes (San Fernando and Whittier) in the Los Angeles basin have had the extent of their thrust plane ruptures limited by strike-slip faults. This suggests that the buried thrust faults underlying the Los Angeles basin are segmented by strike-slip faults.

Earthquake and explosion travel times are inverted for the three-dimensional velocity structure of southern California in Chapter 9. The inversion reduced the variance of the travel time residuals by 47 per cent compared to the starting model, a reparameterized version of the forward model of Chapter 7. The Los Angeles basin is well resolved, with seismically slow sediments atop a crust of granitic velocities. Moho depth is between 26 and 32 km.

Two and Three Finger Caging of Polygons and Polyhedra

Multi-finger caging offers a rigorous and robust approach to robot grasping. This thesis provides several novel algorithms for caging polygons and polyhedra in two and three dimensions. Caging refers to a robotic grasp that does not necessarily immobilize an object, but prevents it from escaping to infinity. The first algorithm considers caging a polygon in two dimensions using two point fingers. The second algorithm extends the first to three dimensions. The third algorithm considers caging a convex polygon in two dimensions using three point fingers, and considers robustness of this cage to variations in the relative positions of the fingers.

This thesis describes an algorithm for finding all two-finger cage formations of planar polygonal objects based on a contact-space formulation. It shows that two-finger cages have several useful properties in contact space. First, the critical points of the cage representation in the hand’s configuration space appear as critical points of the inter-finger distance function in contact space. Second, these critical points can be graphically characterized directly on the object’s boundary. Third, contact space admits a natural rectangular decomposition such that all critical points lie on the rectangle boundaries, and the sublevel sets of contact space and free space are topologically equivalent. These properties lead to a caging graph that can be readily constructed in contact space. Starting from a desired immobilizing grasp of a polygonal object, the caging graph is searched for the minimal, intermediate, and maximal caging regions surrounding the immobilizing grasp. An example constructed from real-world data illustrates and validates the method.

A second algorithm is developed for finding caging formations of a 3D polyhedron for two point fingers using a lower dimensional contact-space formulation. Results from the two-dimensional algorithm are extended to three dimension. Critical points of the inter-finger distance function are shown to be identical to the critical points of the cage. A decomposition of contact space into 4D regions having useful properties is demonstrated. A geometric analysis of the critical points of the inter-finger distance function results in a catalog of grasps in which the cages change topology, leading to a simple test to classify critical points. With these properties established, the search algorithm from the two-dimensional case may be applied to the three-dimensional problem. An implemented example demonstrates the method.

This thesis also presents a study of cages of convex polygonal objects using three point fingers. It considers a three-parameter model of the relative position of the fingers, which gives complete generality for three point fingers in the plane. It analyzes robustness of caging grasps to variations in the relative position of the fingers without breaking the cage. Using a simple decomposition of free space around the polygon, we present an algorithm which gives all caging placements of the fingers and a characterization of the robustness of these cages.

In Vitro Surfactant and Perfluorocarbon Aerosol Deposition in a Neonatal Physical Model of the Upper Conducting Airways

Objective: Aerosol delivery holds potential to release surfactant or perfluorocarbon (PFC) to the lungs of neonates with respiratory distress syndrome with minimal airway manipulation. Nevertheless, lung deposition in neonates tends to be very low due to extremely low lung volumes, narrow airways and high respiratory rates. In the present study, the feasibility of enhancing lung deposition by intracorporeal delivery of aerosols was investigated using a physical model of neonatal conducting airways. Methods: The main characteristics of the surfactant and PFC aerosols produced by a nebulization system, including the distal air pressure and air flow rate, liquid flow rate and mass median aerodynamic diameter (MMAD), were measured at different driving pressures (4-7 bar). Then, a three-dimensional model of the upper conducting airways of a neonate was manufactured by rapid prototyping and a deposition study was conducted. Results: The nebulization system produced relatively large amounts of aerosol ranging between 0.3 +/- 0.0 ml/min for surfactant at a driving pressure of 4 bar, and 2.0 +/- 0.1 ml/min for distilled water (H(2)Od) at 6 bar, with MMADs between 2.61 +/- 0.1 mu m for PFD at 7 bar and 10.18 +/- 0.4 mu m for FC-75 at 6 bar. The deposition study showed that for surfactant and H(2)Od aerosols, the highest percentage of the aerosolized mass (similar to 65%) was collected beyond the third generation of branching in the airway model. The use of this delivery system in combination with continuous positive airway pressure set at 5 cmH(2)O only increased total airway pressure by 1.59 cmH(2)O at the highest driving pressure (7 bar). Conclusion: This aerosol generating system has the potential to deliver relatively large amounts of surfactant and PFC beyond the third generation of branching in a neonatal airway model with minimal alteration of pre-set respiratory support.

Status of vibrational structure in Ni62

Measurements consisting of γ-ray excitation functions and angular distributions were performed using the (n,n′γ) reaction on Ni62. The excitation function data allowed us to check the consistency of the placement of transitions in the level scheme. From γ-ray angular distributions, the lifetimes of levels up to ~3.8 MeV in excitation energy were extracted with the Doppler-shift attenuation method. The experimentally deduced values of reduced transition probabilities were compared with the predictions of the quadrupole vibrator model and with large-scale shell model calculations in the fp shell configuration space. Two-phonon states were found to exist with some notable deviation from the predictions of the quadrupole vibrator model, but no evidence for the existence of three-phonon states could be established. Z=28 proton core excitations played a major role in understanding the observed structure. © 2011 American Physical Society.

An efficient model for the dynamic behaviour of a single pile in viscoelastic soil

This paper presents a novel, three-dimensional, single-pile model, formulated in the wavenumber domain and adapted to account for boundary conditions using the superposition of loading cases. The pile is modelled as a column in axial vibration, and a Euler-Bernoulli beam in lateral vibration. The surrounding soil is treated as a viscoelastic continuum. The response of the pile is presented in terms of the stiffness and damping coefficients, and also the magnitude and phase of the pile-head frequency-response function. Comparison with existing models shows that excellent agreement is observed between this model, a boundary-element formulation, and an elastic-continuum-type formulation. This three-dimensional model has an accuracy equivalent to a 3D boundary-element model, and a runtime similar to a 2D plane-strain analytical model. Analysis of the response of the single pile illustrates a difference in axial and lateral vibration behaviour; the displacement along the pile is relatively invariant under axial loads, but in lateral vibration the pile exhibits localised deformations. This implies that a plane-strain assumption is valid for axial loadings and only at higher frequencies for lateral loadings. © 2013 Elsevier Ltd.

HTGR fuel element depletion benchmark: Stage three results

Recently, a new numerical benchmark exercise for High Temperature Gas Cooled Reactor (HTGR) fuel depletion was defined. The purpose of this benchmark is to provide a comparison basis for different codes and methods applied to the burnup analysis of HTGRs. The benchmark specifications include three different models: (1) an infinite lattice of tristructural isotropic (TRISO) fuel particles, (2) an infinite lattice of fuel pebbles, and (3) a prismatic fuel including fuel and coolant channels. In this paper, we present the results of the third stage of the benchmark obtained with MCNP based depletion code BGCore and deterministic lattice code HELIOS 1.9. The depletion calculations were performed for three-dimensional model of prismatic fuel with explicitly described TRISO particles as well as for two-dimensional model, in which double heterogeneity of the TRISO particles was eliminated using reactivity equivalent physical transformation (RPT). Generally, good agreement in the results of the calculations obtained using different methods and codes was observed.

Shell effect and capture cross sections in the synthesis of superheavy nuclei

The shell effect is included in the improved isospin dependent quantum molecular dynamics model in which the shell correction energy of the system is calculated by using the deformed two-center shell model. A switch function is introduced to connect the shell correction energy of the projectile and the target with that of the compound nucleus during the dynamical fusion process. It is found that the calculated capture cross sections reproduce the experimental data quantitatively at the energy near the Coulomb barrier. The capture cross sections for reaction (35) (80) Br + (82) (208) Pb -> (117) (288) X are also calculated and discussed.

Structure of upper-g(9/2)-shell nuclei and shape effect in the Ag-94 isomeric states

Using a shell model which is capable of describing the spectra of upper g(9/2)-shell nuclei close to the N = Z line, we study the structure of two isomeric states 7(+) and 21(+) in the odd-odd N = Z nucleus Ag-94. It is found that both isomeric states exhibit a large collectivity. The 7(+) state is oblately deformed, and is suggested to be a shape isomer in nature. The 21(+) state becomes isomeric because of level inversion of the 19(+) and 21(+) states due to core excitations across the N = Z = 50 shell gap. Calculation of spectroscopic quadrupole moment indicates clearly an enhancement in these states due to the core excitations. However, the present shell model calculation that produces the 19(+)-21(+) level inversion cannot accept the large-deformation picture of Mukha et al.

A multicomponent model of phytoplankton size structure

Size-fractionated filtration (SFF) is a direct method for estimating pigment concentration in various size classes. It is also common practice to infer the size structure of phytoplankton communities from diagnostic pigments estimated by high-performance liquid chromatography (HPLC). In this paper, the three-component model of Brewin et al. (2010) was fitted to coincident data from HPLC and from SFF collected along Atlantic Meridional Transect cruises. The model accounted for the variability in each data set, but the fitted model parameters differed for the two data sets. Both HPLC and SFF data supported the conceptual framework of the three-component model, which assumes that the chlorophyll concentration in small cells increases to an asymptotic maximum, beyond which further increase in chlorophyll is achieved by the addition of larger celled phytoplankton. The three-component model was extended to a multicomponent model of size structure using observed relationships between model parameters and assuming that the asymptotic concentration that can be reached by cells increased linearly with increase in the upper bound on the cell size. The multicomponent model was verified using independent SFF data for a variety of size fractions and found to perform well (0.628 ≤ r ≤ 0.989) lending support for the underlying assumptions. An advantage of the multicomponent model over the three-component model is that, for the same number of parameters, it can be applied to any size range in a continuous fashion. The multicomponent model provides a useful tool for studying the distribution of phytoplankton size structure at large scales.

Temporal changes in total and size-fractioned chlorophyll-a in surface waters of three provinces in the Atlantic Ocean (September to November) between 2003 and 2010

Phytoplankton total chlorophyll concentration (TCHLa) and phytoplankton size structure are two important ecological indicators in biological oceanography. Using high performance liquid chromatography (HPLC) pigment data, collected from surface waters along the Atlantic Meridional Transect (AMT), we examine temporal changes in TCHLa and phytoplankton size class (PSC: micro-, nano- and pico-phytoplankton) between 2003 and 2010 (September to November cruises only), in three ecological provinces of the Atlantic Ocean. The HPLC data indicate no significant change in TCHLa in northern and equatorial provinces, and an increase in the southern province. These changes were not significantly different to changes in TCHLa derived using satellite ocean-colour data over the same study period. Despite no change in AMT TCHLa in northern and equatorial provinces, significant differences in PSC were observed, related to changes in key diagnostic pigments (fucoxanthin, peridinin, 19′-hexanoyloxyfucoxanthin and zeaxanthin), with an increase in small cells (nano- and pico-phytoplankton) and a decrease in larger cells (micro-phytoplankton). When fitting a three-component model of phytoplankton size structure — designed to quantify the relationship between PSC and TCHLa to each AMT cruise, model parameters varied over the study period. Changes in the relationship between PSC and TCHLa have wide implications in ecology and marine biogeochemistry, and provide key information for the development and use of empirical ocean-colour algorithms. Results illustrate the importance of maintaining a time-series of in-situ observations in remote regions of the ocean, such as that acquired in the AMT programme.

A 3-D well-differentiated model of pediatric bronchial epithelium demonstrates unstimulated morphological differences between asthmatic and nonasthmatic cells

There is a need for reproducible and effective models of pediatric bronchial epithelium to study disease states such as asthma. We aimed to develop, characterize, and differentiate an effective, an efficient, and a reliable three-dimensional model of pediatric bronchial epithelium to test the hypothesis that children with asthma differ in their epithelial morphologic phenotype when compared with nonasthmatic children. Primary cell cultures from both asthmatic and nonasthmatic children were grown and differentiated at the air-liquid interface for 28 d. Tight junction formation, MUC5AC secretion, IL-8, IL-6, prostaglandin E2 production, and the percentage of goblet and ciliated cells in culture were assessed. Well-differentiated, multilayered, columnar epithelium containing both ciliated and goblet cells from asthmatic and nonasthmatic subjects were generated. All cultures demonstrated tight junction formation at the apical surface and exhibited mucus production and secretion. Asthmatic and nonasthmatic cultures secreted similar quantities of IL-8, IL-6, and prostaglandin E2. Cultures developed from asthmatic children contained considerably more goblet cells and fewer ciliated cells compared with those from nonasthmatic children. A well-differentiated model of pediatric epithelium has been developed that will be useful for more in vivo like study of the mechanisms at play during asthma.

On the use of OpenFOAM to model Oscillating wave surge converters

The Computational Fluid Dynamic (CFD) toolbox OpenFOAM is used to assess the applicability of Reynolds-Averaged Navier-Stokes (RANS) solvers to the simulation of Oscillating Wave Surge Converters (OWSC) in significant waves. Simulation of these flap type devices requires the solution of the equations of motion and the representation of the OWSC’s motion in a moving mesh. A new way to simulate the sea floor inside a section of the moving mesh with a moving dissipation zone is presented. To assess the accuracy of the new solver, experiments are conducted in regular and irregular wave traces for a full three dimensional model. Results of acceleration and flow features are presented for numerical and experimental data. It is found that the new numerical model reproduces experimental results within the bounds of experimental accuracy.

Heating Mechanisms for Intermittent Loops in Active Region Cores from AIA/SDO EUV Observations

We investigate intensity variations and energy deposition in five coronal loops in active region cores. These were selected for their strong variability in the AIA/SDO 94 Å intensity channel. We isolate the hot Fe XVIII and Fe XXI components of the 94 Å and 131 Å by modeling and subtracting the "warm" contributions to the emission. HMI/SDO data allow us to focus on "inter-moss" regions in the loops. The detailed evolution of the inter-moss intensity time series reveals loops that are impulsively heated in a mode compatible with a nanoflare storm, with a spike in the hot 131 Å signals leading and the other five EUV emission channels following in progressive cooling order. A sharp increase in electron temperature tends to follow closely after the hot 131 Å signal confirming the impulsive nature of the process. A cooler process of growing emission measure follows more slowly. The Fourier power spectra of the hot 131 Å signals, when averaged over the five loops, present three scaling regimes with break frequencies near 0.1 min–1 and 0.7 min–1. The low frequency regime corresponds to 1/f noise; the intermediate indicates a persistent scaling process and the high frequencies show white noise. Very similar results are found for the energy dissipation in a 2D "hybrid" shell model of loop magneto-turbulence, based on reduced magnetohydrodynamics, that is compatible with nanoflare statistics. We suggest that such turbulent dissipation is the energy source for our loops

Deposition of charged inhaled aerosols with transient airflow in sequential lung airway model

Transport and deposition of charged inhaled aerosols in double planar bifurcation representing generation three to five of human respiratory system has been studied under a light activity breathing condition. Both steady and oscillatory laminar inhalation airflow is considered. Particle trajectories are calculated using a Lagrangian reference frame, which is dominated by the fluid force driven by airflow, gravity force and electrostatic forces (both of space and image charge forces). The particle-mesh method is selected to calculate the space charge force. This numerical study investigates the deposition efficiency in the three-dimensional model under various particle sizes, charge values, and inlet particle distribution. Numerical results indicate that particles carrying an adequate level of charge can improve deposition efficiency in the airway model.