Matching Items (17)

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System Size Dependence in Fermionic Superfluids at Unitarity

Description

While the use of super-cooled gasses as a tool for the study of macroscopic quantum effects has only become experimentally viable in recent years, theories involing such gasses have existed

While the use of super-cooled gasses as a tool for the study of macroscopic quantum effects has only become experimentally viable in recent years, theories involing such gasses have existed almost as long as quantum theory itself. Albert Einstein first proposed the concept of what is known today as a Bose-Einstein condensate; the driving principle behind his theory was a deliberate exploitation of the symmetric property of multiparticle bosonic wavefunctions. Specifically, since the Bose-Einstein statistics of bosons dic- tate that any arbitrary number of particles can occupy the same state, it is possible in an extremely low energy environment for particles on the order of Avagadro's number to all condense into the ground state. This state of matter is now called a Bose-Einstein condensate (hereafter referred to as a BEC). This state of matter is interesting because having such a large number of particles in the same state allows for the observation of macroscopic quantum effects.

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Date Created
  • 2012-12

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Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

Description

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1),

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.

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Date Created
  • 2014-08-20

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Data collection strategies for time-resolved X-ray free-electron laser diffraction, and 2-color methods

Description

We compare three schemes for time-resolved X-ray diffraction from protein nanocrystals using an X-ray free-electron laser. We find expressions for the errors in structure factor measurement using the Monte Carlo

We compare three schemes for time-resolved X-ray diffraction from protein nanocrystals using an X-ray free-electron laser. We find expressions for the errors in structure factor measurement using the Monte Carlo pump-probe method of data analysis with a liquid jet, the fixed sample pump-probe (goniometer) method (both diffract-and-destroy, and below the safe damage dose), and a proposed two-color method. Here, an optical pump pulse arrives between X-ray pulses of slightly different energies which hit the same nanocrystal, using a weak first X-ray pulse which does not damage the sample. (Radiation damage is outrun in the other cases.) This two-color method, in which separated Bragg spots are impressed on the same detector readout, eliminates stochastic fluctuations in crystal size, shape, and orientation and is found to require two orders of magnitude fewer diffraction patterns than the currently used Monte Carlo liquid jet method, for 1% accuracy. Expressions are given for errors in structure factor measurement for the four approaches, and detailed simulations provided for cathepsin B and IC3 crystals. While the error is independent of the number of shots for the dose-limited goniometer method, it falls off inversely as the square root of the number of shots for the two-color and Monte Carlo methods, with a much smaller pre-factor for the two-color mode, when the first shot is below the damage threshold.

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Date Created
  • 2015-06-12

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From the lightest nuclei to the equation of state of asymmetric nuclear matter with realistic nuclear interactions

Description

We present microscopic calculations of light and medium mass nuclei and the equation of state of symmetric and asymmetric nuclear matter using different nucleon-nucleon interactions, including a new Argonne version

We present microscopic calculations of light and medium mass nuclei and the equation of state of symmetric and asymmetric nuclear matter using different nucleon-nucleon interactions, including a new Argonne version that has the same spin-isospin structure as local chiral forces at next-to-next-to-leading order. The calculations are performed using auxiliary field diffusion Monte Carlo (AFDMC) combined with an improved variational wave function and sampling technique. The AFDMC method can now be used to successfully calculate the energies of very light to medium mass nuclei as well as the energy of isospin-asymmetric nuclear matter, demonstrating microscopically the quadratic dependence of the energy on the symmetry energy.

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Date Created
  • 2014-12-29

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Injection methods and instrumentation for serial X-ray free electron laser experiments

Description

Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These

Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These new methods include serial femtosecond crystallography, single particle imaging, solution scattering, and time resolved techniques.

The XFEL is characterized by high intensity pulses, which are only about 50 femtoseconds in duration. The intensity allows for scattering from microscopic particles, while the short pulses offer a way to outrun radiation damage. XFELs are powerful enough to obliterate most samples in a single pulse. While this allows for a “diffract and destroy” methodology, it also requires instrumentation that can position microscopic particles into the X-ray beam (which may also be microscopic), continuously renew the sample after each pulse, and maintain sample viability during data collection.

Typically these experiments have used liquid microjets to continuously renew sample. The high flow rate associated with liquid microjets requires large amounts of sample, most of which runs to waste between pulses. An injector designed to stream a viscous gel-like material called lipidic cubic phase (LCP) was developed to address this problem. LCP, commonly used as a growth medium for membrane protein crystals, lends itself to low flow rate jetting and so reduces the amount of sample wasted significantly.

This work discusses sample delivery and injection for XFEL experiments. It reviews the liquid microjet method extensively, and presents the LCP injector as a novel device for serial crystallography, including detailed protocols for the LCP injector and anti-settler operation.

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Date Created
  • 2015

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Nanofluidics for single molecule DNA sequencing

Description

After a decade of efforts, accurate and affordable DNA sequencing continues to remain an important goal in current research landscape. This thesis starts with a brief overview of the recent

After a decade of efforts, accurate and affordable DNA sequencing continues to remain an important goal in current research landscape. This thesis starts with a brief overview of the recent updates in the field of DNA sequencing technologies followed by description of the nanofluidics route to single molecule DNA detection. Chapter 2 presents discusses carbon nanotube(CNT) based nanofluidics. The fabrication and DNA sensing measurements of CNT forest membrane devices are presented. Chapter 3 gives the background for functionalization and recognition aspects of reader molecules. Chapter 4 marks the transition to solid state nanopore nanofluidics. The fabrication of Imidazole functionalized nanopores is discussed. The Single Molecule detection results of DNA from Palladium nanopore devices are presented next. Combining chemical recognition to nanopore technology, it has been possible to prolong the duration of single molecule events from the order of a few micro seconds to upto a few milliseconds. Overall, the work presented in this thesis promises longer single molecule detection time in a nanofludic set up and paves way for novel nanopore- tunnel junction devices that combine recognition chemistry, tunneling device and nanopore approach.

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Created

Date Created
  • 2013

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Serial crystallography: beyond Monte Carlo data analysis

Description

The superior brightness and ultra short pulse duration of X-ray free electron laser

(XFEL) allows it to outrun radiation damage in coherent diffractive imaging since elastic scattering terminates before photoelectron cascades

The superior brightness and ultra short pulse duration of X-ray free electron laser

(XFEL) allows it to outrun radiation damage in coherent diffractive imaging since elastic scattering terminates before photoelectron cascades commences. This “diffract-before-destroy” feature of XFEL opened up new opportunities for biological macromolecule imaging and structure studies by breaking the limit to spatial resolution imposed by the maximum dose that is allowed before radiation damage. However, data collection in serial femto-second crystallography (SFX) using XFEL is affected by a bunch of stochastic factors, which pose great challenges to the data analysis in SFX. These stochastic factors include crystal size, shape, random orientation, X-ray photon flux, position and energy spectrum. Monte-Carlo integration proves effective and successful in extracting the structure factors by merging all diffraction patterns given that the data set is sufficiently large to average out all stochastic factors. However, this approach typically requires hundreds of thousands of patterns collected from experiments. This dissertation explores both experimental and algorithmic methods to eliminate or reduce the effect of stochastic factors in data acquisition and analysis. Coherent convergent X-ray beam diffraction (CCB) is discussed for possibilities of obtaining single-shot angular-integrated rocking curves. It is also shown the interference between Bragg disks helps ab-initio phasing. Two-color diffraction scheme is proposed for time-resolved studies and general data collection strategies are discussed based on error metrics. A new auto-indexing algorithm for sparse patterns is developed and demonstrated for both simulated and experimental data. Statistics show that indexing rate is increased by 3 times for I3C data set collected from beam time LJ69 at Linac coherent light source (LCLS). Finally, dynamical inversion from electron diffraction is explored as an alternative approach for structure determination.

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Created

Date Created
  • 2016

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FDTD Simulation Techniques for Simulation of Very Large 2D and 3D Domains Applied to Radar Propagation over the Ocean

Description

A domain decomposition method for analyzing very large FDTD domains, hundreds of thousands of wavelengths long, is demonstrated by application to the problem of radar scattering in the maritime environment.

A domain decomposition method for analyzing very large FDTD domains, hundreds of thousands of wavelengths long, is demonstrated by application to the problem of radar scattering in the maritime environment. Success depends on the elimination of artificial scattering from the “sky” boundary and is ensured by an ultra-high-performance absorbing termination which eliminates this reflection at angles of incidence as shallow as 0.03 degrees off grazing. The two-dimensional (2D) problem is used to detail the features of the method. The results are cross-validated by comparison to a parabolic equation (PE) method and surface integral equation method on a 1.7km sea surface problem, and to a PE method on propagation through an inhomogeneous atmosphere in a 4km-long space, both at X-band. Additional comparisons are made against boundary integral equation and PE methods from the literature in a 3.6km space containing an inhomogeneous atmosphere above a flat sea at S-band. The applicability of the method to the three-dimensional (3D) problem is shown via comparison of a 2D solution to the 3D solution of a corridor of sea. As a technical proof of the scalability of the problem with computational power, a 5m-wide, 2m-tall, 1050m-long 3D corridor containing 321.8 billion FDTD cells has been simulated at X-band. A plane wave spectrum analysis of the (X-band) scattered fields produced by a 5m-wide, 225m-long realistic 3D sea surface, and the 2D analog surface obtained by extruding a 2D sea along the width of the corridor, reveals the existence of out-of-plane 3D phenomena missed by the traditional 2D analysis. The realistic sea introduces random strong flashes and nulls in addition to a significant amount of cross-polarized field. Spatial integration using a dispersion-corrected Green function is used to reconstruct the scattered fields outside of the computational FDTD space which would impinge on a 3D target at the end of the corridor. The proposed final approach is a hybrid method where 2D FDTD carries the signal for the first tens of kilometers and the last kilometer is analyzed in 3D.

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Created

Date Created
  • 2018

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Two-flavor color superconductivity in magnetic field

Description

Quark matter at sufficiently high density and low temperature is expected to be a color superconductor, and may exist in the interior of neutron stars. The properties of two simplest

Quark matter at sufficiently high density and low temperature is expected to be a color superconductor, and may exist in the interior of neutron stars. The properties of two simplest possible color-superconducting phases, i.e., the color-flavor-locked (CFL) and two-flavor superconducting (2SC) phases, are reviewed. The effect of a magnetic field on the pairing dynamics in two-flavor color-superconducting dense quark matter is investigated. A universal form of the gap equation for an arbitrary magnetic field is derived in the weakly coupled regime of QCD at asymptotically high density, using the framework of Schwinger-Dyson equation in the improved rainbow approximation. The results for the gap in two limiting cases, weak and strong magnetic fields, are obtained and discussed. It is shown that the superconducting gap function in the weak magnetic field limit develops a directional dependence in momentum space. This property of the gap parameter is argued to be a consequence of a long-range interaction in QCD.

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Date Created
  • 2012

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Phasing two-dimensional crystal diffraction pattern with iterative projection algorithms

Description

Phase problem has been long-standing in x-ray diffractive imaging. It is originated from the fact that only the amplitude of the scattered wave can be recorded by the detector, losing

Phase problem has been long-standing in x-ray diffractive imaging. It is originated from the fact that only the amplitude of the scattered wave can be recorded by the detector, losing the phase information. The measurement of amplitude alone is insufficient to solve the structure. Therefore, phase retrieval is essential to structure determination with X-ray diffractive imaging. So far, many experimental as well as algorithmic approaches have been developed to address the phase problem. The experimental phasing methods, such as MAD, SAD etc, exploit the phase relation in vector space. They usually demand a lot of efforts to prepare the samples and require much more data. On the other hand, iterative phasing algorithms make use of the prior knowledge and various constraints in real and reciprocal space. In this thesis, new approaches to the problem of direct digital phasing of X-ray diffraction patterns from two-dimensional organic crystals were presented. The phase problem for Bragg diffraction from two-dimensional (2D) crystalline monolayer in transmission may be solved by imposing a compact support that sets the density to zero outside the monolayer. By iterating between the measured stucture factor magnitudes along reciprocal space rods (starting with random phases) and a density of the correct sign, the complex scattered amplitudes may be found (J. Struct Biol 144, 209 (2003)). However this one-dimensional support function fails to link the rod phases correctly unless a low-resolution real-space map is also available. Minimum prior information required for successful three-dimensional (3D) structure retrieval from a 2D crystal XFEL diffraction dataset were investigated, when using the HIO algorithm. This method provides an alternative way to phase 2D crystal dataset, with less dependence on the high quality model used in the molecular replacement method.

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Created

Date Created
  • 2016