Protein structure refinement algorithms

Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.

Difficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.

Magnetospheric access of solar particles and the configuration of the distant geomagnetic field

The access of 1.2-40 MeV protons and 0.4-1.0 MeV electrons from interplanetary space to the polar cap regions has been investigated with an experiment on board a low altitude, polar orbiting satellite (OG0-4).

A total of 333 quiet time observations of the electron polar cap boundary give a mapping of the boundary between open and closed geomagnetic field lines which is an order of magnitude more comprehensive than previously available.

Persistent features (north/south asymmetries) in the polar cap proton flux, which are established as normal during solar proton events, are shown to be associated with different flux levels on open geomagnetic field lines than on closed field lines. The pole in which these persistent features are observed is strongly correlated to the sector structure of the interplanetary magnetic field and uncorrelated to the north/south component of this field. The features were observed in the north (south) pole during a negative (positive) sector 91% of the time, while the solar field had a southward component only 54% of the time. In addition, changes in the north/south component have no observable effect on the persistent features.

Observations of events associated with co-rotating regions of enhanced proton flux in interplanetary space are used to establish the characteristics of the 1.2 - 40 MeV proton access windows: the access window for low polar latitudes is near the earth, that for one high polar latitude region is ~250 R_⊕ behind the earth, while that for the other high polar latitude region is ~1750 R_⊕ behind the earth. All of the access windows are of approximately the same extent (~120 R_⊕). The following phenomena contribute to persistent polar cap features: limited interplanetary regions of enhanced flux propagating past the earth, radial gradients in the interplanetary flux, and anisotropies in the interplanetary flux.

These results are compared to the particle access predictions of the distant geomagnetic tail configurations proposed by Michel and Dessler, Dungey, and Frank. The data are consistent with neither the model of Michel and Dessler nor that of Dungey. The model of Frank can yield a consistent access window configuration provided the following constraints are satisfied: the merging rate for open field lines at one polar neutral point must be ~5 times that at the other polar neutral point, related to the solar magnetic field configuration in a consistent fashion, the migration time for open field lines to move across the polar cap region must be the same in both poles, and the open field line merging rate at one of the polar neutral points must be at least as large as that required for almost all the open field lines to have merged in 0 (one hour). The possibility of satisfying these constraints is investigated in some detail.

The role played by interplanetary anisotropies in the observation of persistent polar cap features is discussed. Special emphasis is given to the problem of non-adiabatic particle entry through regions where the magnetic field is changing direction. The degree to which such particle entry can be assumed to be nearly adiabatic is related to the particle rigidity, the angle through which the field turns, and the rate at which the field changes direction; this relationship is established for the case of polar cap observations.

Origin of the double-peak structure in longitudinal momentum distributions for single ionization of an He atom in strong laser field

The single ionization of an He atom by intense linearly polarized laser field in the tunneling regime is studied by S- matrix theory. When only the first term of the expansion of the S matrix is considered and time, spatial distribution, and fluctuation of the laser pulse are taken into account, the obtained momentum distribution in the polarization direction of laser field is consistent with the semiclassical calculation, which only considers tunneling and the interaction between the free electron and external field. When the second term, which includes the interaction between the core and the free electron, is considered, the momentum distribution shows a complex multipeak structure with the central minimum and the positions of some peaks are independent of the intensity in some intensity regime, which is consistent with the recent experimental result. Based on our analysis, we found that the structures observed in the momentum distribution of an He atom are attributed to the " soft" collision of the tunneled electron with the core.

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.

Part I. Approximate Hartree-Fock wavefunctions one-electron properties and electronic structure of the water molecule. Part II. Perturbation-variational calculation of the nuclear spin-spin isotope coupling constant in HD

Part I

Several approximate Hartree-Fock SCF wavefunctions for the ground electronic state of the water molecule have been obtained using an increasing number of multicenter s, p, and d Slater-type atomic orbitals as basis sets. The predicted charge distribution has been extensively tested at each stage by calculating the electric dipole moment, molecular quadrupole moment, diamagnetic shielding, Hellmann-Feynman forces, and electric field gradients at both the hydrogen and the oxygen nuclei. It was found that a carefully optimized minimal basis set suffices to describe the electronic charge distribution adequately except in the vicinity of the oxygen nucleus. Our calculations indicate, for example, that the correct prediction of the field gradient at this nucleus requires a more flexible linear combination of p-orbitals centered on this nucleus than that in the minimal basis set. Theoretical values for the molecular octopole moment components are also reported.

Part II

The perturbation-variational theory of R. M. Pitzer for nuclear spin-spin coupling constants is applied to the HD molecule. The zero-order molecular orbital is described in terms of a single 1s Slater-type basis function centered on each nucleus. The first-order molecular orbital is expressed in terms of these two functions plus one singular basis function each of the types e^-r/r and e^-r ln r centered on one of the nuclei. The new kinds of molecular integrals were evaluated to high accuracy using numerical and analytical means. The value of the HD spin-spin coupling constant calculated with this near-minimal set of basis functions is J_HD = +96.6 cps. This represents an improvement over the previous calculated value of +120 cps obtained without using the logarithmic basis function but is still considerably off in magnitude compared with the experimental measurement of J_HD = +43 0 ± 0.5 cps.

A large-area photolithography technique based on surface plasmons leakage modes

An atomic force microscope (AFM) assisted surface plasmons leakage radiation photolithography technique has been numerically demonstrated by using two-dimensional finite-difference time-domain (2D-FDTD) method. With the aid of a metallic AFM tip, particular characteristic of the Kretstchmann configuration to excite surface plasmons (SPs) is utilized to achieve large-area patterns with high spatial resolution and contrast, the photoresist could be exposed with low power laser due to the remarkable local field enhancement at the metal/dielectric interface and the resonant localized SPs modes near the tip. Good tolerance on the film thickness and incident angle has been obtained, which provides a good practicability for experiments. This photolithography technique proposed here can realize large-area, high-resolution, high-contrast, nondestructive, arbitrary-structure fabrication of nanoscale devices. (c) 2007 Elsevier B.V. All rights reserved.

Analytical vectorial structure of hollow Gaussian beams in the far field

The analytical vectorial structure of HGB is investigated in the far field based on the vector plane wave spectrum and the method of stationary phase. The energy flux distributions of HGB in the far-field, which is composed of TE term and TM term, are demonstrated. The physics pictures of HGB is illustrated from the vectorial structure, which is important to understand the theoretical aspects of both scalar and vector HGB propagation. (c) 2008 Optical Society of America.

Evolution of localized blobs of swirling or buoyant fluid with and without an ambient magnetic field.

We investigate the evolution of localized blobs of swirling or buoyant fluid in an infinite, inviscid, electrically conducting fluid. We consider the three cases of a strong imposed magnetic field, a weak imposed magnetic field, and no magnetic field. For a swirling blob in the absence of a magnetic field, we find, in line with others, that the blob bursts radially outward under the action of the centrifugal force, forming a thin annular vortex sheet. A simple model of this process predicts that the vortex sheet thins exponentially fast and that it moves radially outward with constant velocity. These predictions are verified by high-resolution numerical simulations. When an intense magnetic field is applied, this phenomenon is suppressed, with the energy and angular momentum of the blob now diffusing axially along the magnetic field lines, converting the blob into a columnar structure. For modest or weak magnetic fields, there are elements of both types of behavior, with the radial bursting dominating over axial diffusion for weak fields. However, even when the magnetic field is very weak, the flow structure is quite distinct to that of the nonmagnetic case. In particular, a small but finite magnetic field places a lower bound on the thickness of the annular vortex sheet and produces an annulus of counter-rotating fluid that surrounds the vortex core. The behavior of the buoyant blob is similar. In the absence of a magnetic field, it rapidly develops the mushroomlike shape of a thermal, with a thin vortex sheet at the top and sides of the mushroom. Again, a simple model of this process predicts that the vortex sheet at the top of the thermal thins exponentially fast and rises with constant velocity. These predictions are consistent with earlier numerical simulations. Curiously, however, it is shown that the net vertical momentum associated with the blob increases linearly in time, despite the fact that the vertical velocity at the front of the thermal is constant. As with the swirling blob, an imposed magnetic field inhibits the formation of a vortex sheet. A strong magnetic field completely suppresses the phenomenon, replacing it with an axial diffusion of momentum, while a weak magnetic field allows the sheet to form, but places a lower bound on its thickness. The magnetic field does not, however, change the net vertical momentum of the blob, which always increases linearly with time.