49 Matching Results

Results open in a new window/tab.

AdS/QCD, Light-Front Holography, and Sublimated Gluons (open access)

AdS/QCD, Light-Front Holography, and Sublimated Gluons

The gauge/gravity duality leads to a simple analytical and phenomenologically compelling nonperturbative approximation to the full light-front QCD Hamiltonian - 'Light-Front Holography', which provides a Lorentz-invariant first-approximation to QCD, and successfully describes the spectroscopy of light-quark meson and baryons, their elastic and transition form factors, and other hadronic properties. The bound-state Schroedinger and Dirac equations of the soft-wall AdS/QCD model predict linear Regge trajectories which have the same slope in orbital angular momentum L and radial quantum number n for both mesons and baryons. Light-front holography connects the fifth-dimensional coordinate of AdS space z to an invariant impact separation variable {zeta} in 3+1 space at fixed light-front time. A key feature is the determination of the frame-independent light-front wavefunctions of hadrons - the relativistic analogs of the Schroedinger wavefunctions of atomic physics which allow one to compute form factors, transversity distributions, spin properties of the valence quarks, jet hadronization, and other hadronic observables. One thus obtains a one-parameter color-confining model for hadron physics at the amplitude level. AdS/QCD also predicts the form of the non-perturbative effective coupling {alpha}{sub s}{sup AdS} (Q) and its {beta}-function with an infrared fixed point which agrees with the effective coupling a{sub g1} (Q{sup 2}) extracted …
Date: February 16, 2012
Creator: Brodsky, Stanley J. & de Teramond, Guy F.
System: The UNT Digital Library
CALIBRATION OF X-RAY IMAGING DEVICES FOR ACCURATE INTENSITY MEASUREMENT (open access)

CALIBRATION OF X-RAY IMAGING DEVICES FOR ACCURATE INTENSITY MEASUREMENT

National Security Technologies (NSTec) has developed calibration procedures for X-ray imaging systems. The X-ray sources that are used for calibration are both diode type and diode/fluorescer combinations. Calibrating the X-ray detectors is key to accurate calibration of the X-ray sources. Both energy dispersive detectors and photodiodes measuring total flux were used. We have developed calibration techniques for the detectors using radioactive sources that are traceable to the National Institute of Standards and Technology (NIST). The German synchrotron at Physikalische Technische Bundestalt (PTB) is used to calibrate silicon photodiodes over the energy range from 50 eV to 60 keV. The measurements on X-ray cameras made using the NSTec X-ray sources have included quantum efficiency averaged over all pixels, camera counts per photon per pixel, and response variation across the sensor. The instrumentation required to accomplish the calibrations is described. X-ray energies ranged from 720 eV to 22.7 keV. The X-ray sources produce narrow energy bands, allowing us to determine the properties as a function of X-ray energy. The calibrations were done for several types of imaging devices. There were back illuminated and front illuminated CCD (charge coupled device) sensors, and a CID (charge injection device) type camera. The CCD and CID …
Date: February 16, 2012
Creator: Haugh, M. J.; Charest, M. R.; Ross, P. W.; Lee, J. J.; Schneider, M. B.; Palmer, N. E. et al.
System: The UNT Digital Library
Visualization of Target Inspection data at the National Ignition Facility (open access)

Visualization of Target Inspection data at the National Ignition Facility

As the National Ignition Facility continues its campaign to achieve ignition, new methods and tools will be required to measure the quality of the target capsules used to achieve this goal. Techniques have been developed to measure capsule surface features using a phase-shifting diffraction interferometer and Leica Microsystems confocal microscope. These instruments produce multi-gigabyte datasets which consist of tens to hundreds of files. Existing software can handle viewing a small subset of an entire dataset, but none can view a dataset in its entirety. Additionally, without an established mode of transport that keeps the target capsules properly aligned throughout the assembly process, a means of aligning the two dataset coordinate systems is needed. The goal of this project is to develop web based software utilizing WebGL which will provide high level overview visualization of an entire dataset, with the capability to retrieve finer details on demand, in addition to facilitating alignment of multiple datasets with one another based on common features that have been visually identified by users of the system.
Date: February 16, 2012
Creator: Potter, D & Antipa, N
System: The UNT Digital Library
Transversity from First Principles in QCD (open access)

Transversity from First Principles in QCD

Transversity observables, such as the T-odd Sivers single-spin asymmetry measured in deep inelastic lepton scattering on polarized protons and the distributions which are measured in deeply virtual Compton scattering, provide important constraints on the fundamental quark and gluon structure of the proton. In this talk I discuss the challenge of computing these observables from first principles; i.e.; quantum chromodynamics, itself. A key step is the determination of the frame-independent light-front wavefunctions (LFWFs) of hadrons - the QCD eigensolutions which are analogs of the Schroedinger wavefunctions of atomic physics. The lensing effects of initial-state and final-state interactions, acting on LFWFs with different orbital angular momentum, lead to T-odd transversity observables such as the Sivers, Collins, and Boer-Mulders distributions. The lensing effect also leads to leading-twist phenomena which break leading-twist factorization such as the breakdown of the Lam-Tung relation in Drell-Yan reactions. A similar rescattering mechanism also leads to diffractive deep inelastic scattering, as well as nuclear shadowing and non-universal antishadowing. It is thus important to distinguish 'static' structure functions, the probability distributions computed the target hadron's light-front wavefunctions, versus 'dynamical' structure functions which include the effects of initial- and final-state rescattering. I also discuss related effects such as the J = …
Date: February 16, 2012
Creator: Brodsky, Stanley J. & /SLAC /Southern Denmark U., CP3-Origins
System: The UNT Digital Library
Using the X-FEL to understand X-ray Thomson scattering for partially ionized plasmas (open access)

Using the X-FEL to understand X-ray Thomson scattering for partially ionized plasmas

None
Date: July 16, 2012
Creator: Nilsen, J; Johnson, W R & Cheng, K T
System: The UNT Digital Library
Scale Setting Using the Extended Re normalization Group and the Principle of Maximal Conformality: the QCD Coupling at Four Loops (open access)

Scale Setting Using the Extended Re normalization Group and the Principle of Maximal Conformality: the QCD Coupling at Four Loops

A key problem in making precise perturbative QCD predictions is to set the proper renormalization scale of the running coupling. The extended renormalization group equations, which express the invariance of physical observables under both the renormalization scale- and scheme-parameter transformations, provide a convenient way for estimating the scale- and scheme-dependence of the physical process. In this paper, we present a solution for the scale-equation of the extended renormalization group equations at the four-loop level. Using the principle of maximum conformality (PMC)/Brodsky-Lepage-Mackenzie (BLM) scale-setting method, all non-conformal {beta}{sub i} terms in the perturbative expansion series can be summed into the running coupling, and the resulting scale-fixed predictions are independent of the renormalization scheme. Different schemes lead to different effective PMC/BLM scales, but the final results are scheme independent. Conversely, from the requirement of scheme independence, one not only can obtain scheme-independent commensurate scale relations among different observables, but also determine the scale displacements among the PMC/BLM scales which are derived under different schemes. In principle, the PMC/BLM scales can be fixed order-by-order, and as a useful reference, we present a systematic and scheme-independent procedure for setting PMC/BLM scales up to NNLO. An explicit application for determining the scale setting of R{sub …
Date: February 16, 2012
Creator: Brodsky, Stanley J. & Wu, Xing-Gang
System: The UNT Digital Library
Vibration Model Validation for Linear Collider Detector Platforms (open access)

Vibration Model Validation for Linear Collider Detector Platforms

The ILC and CLIC reference designs incorporate reinforced-concrete platforms underneath the detectors so that the two detectors can each be moved onto and off of the beamline in a Push-Pull configuration. These platforms could potentially amplify ground vibrations, which would reduce luminosity. In this paper we compare vibration models to experimental data on reinforced concrete structures, estimate the impact on luminosity, and summarize implications for the design of a reinforced concrete platform for the ILC or CLIC detectors.
Date: May 16, 2012
Creator: Bertsche, Kirk; Amann, J. W.; Markiewicz, T. W.; Oriunno, M.; Weidemann, A. & White, G.
System: The UNT Digital Library
Physics Opportunities of a Fixed-Target Experiment using the LHC Beams (open access)

Physics Opportunities of a Fixed-Target Experiment using the LHC Beams

We outline the many physics opportunities offered by a multi-purpose fixed-target experiment using the proton and lead-ion beams of the LHC extracted by a bent crystal. In a proton run with the LHC 7-TeV beam, one can analyze pp, pd and pA collisions at center-of-mass energy {radical}s{sub NN} {approx_equal} 115 GeV and even higher using the Fermi motion of the nucleons in a nuclear target. In a lead run with a 2.76 TeV-per-nucleon beam, {radical}s{sub NN} is as high as 72 GeV. Bent crystals can be used to extract about 5 x 10{sup 8} protons/sec; the integrated luminosity over a year reaches 0.5 fb{sup -1} on a typical 1 cm-long target without nuclear species limitation. We emphasize that such an extraction mode does not alter the performance of the collider experiments at the LHC. By instrumenting the target-rapidity region, gluon and heavy-quark distributions of the proton and the neutron can be accessed at large x and even at x larger than unity in the nuclear case. Single diffractive physics and, for the first time, the large negative-xF domain can be accessed. The nuclear target-species versatility provides a unique opportunity to study nuclear matter versus the features of the hot and …
Date: March 16, 2012
Creator: Brodsky, S.J.; /SLAC; Fleuret, F.; Polytechnique, /Ecole; Hadjidakis, C.; Lansberg, J.P. et al.
System: The UNT Digital Library
A Non-Invasive Energy/Angle Diagnostic for Charged Particle Beams (open access)

A Non-Invasive Energy/Angle Diagnostic for Charged Particle Beams

A diagnostic for charged particle beams based on Compton scattering is presented. The particular case of an electron beam is treated in detail relativistically.
Date: March 16, 2012
Creator: Christensen, C. R.
System: The UNT Digital Library
Analytic Coleman-de Luccia Geometries (open access)

Analytic Coleman-de Luccia Geometries

We present the necessary and sufficient conditions for a Euclidean scale factor to be a solution of the Coleman-de Luccia equations for some analytic potential V ({psi}), with a Lorentzian continuation describing the growth of a bubble of lower-energy vacuum surrounded by higher-energy vacuum. We then give a set of explicit examples that satisfy the conditions and thus are closed-form analytic examples of Coleman-de Luccia geometries.
Date: February 16, 2012
Creator: Dong, Xi; /Stanford U., ITP /Stanford U., Phys. Dept. /SLAC; Harlow, Daniel & /Stanford U., ITP /Stanford U., Phys. Dept.
System: The UNT Digital Library
The Luminosity Function of Fermi-detected Flat-Spectrum Radio Quasars (open access)

The Luminosity Function of Fermi-detected Flat-Spectrum Radio Quasars

Fermi has provided the largest sample of {gamma}-ray selected blazars to date. In this work we use a complete sample of FSRQs detected during the first year of operation to determine the luminosity function (LF) and its evolution with cosmic time. The number density of FSRQs grows dramatically up to redshift {approx}0.5-2.0 and declines thereafter. The redshift of the peak in the density is luminosity dependent, with more luminous sources peaking at earlier times; thus the LF of {gamma}-ray FSRQs follows a luminosity-dependent density evolution similarly to that of radio-quiet AGN. Also using data from the Swift Burst Alert Telescope we derive the average spectral energy distribution of FSRQs in the 10 keV-100GeV band and show that there is no correlation of the peak {gamma}-ray luminosity with {gamma}-ray peak frequency. The coupling of the SED and LF allows us to predict that the contribution of FSRQs to the Fermi isotropic {gamma}-ray background is 9.3{sub -1.0}{sup +1.6}% ({+-}3% systematic uncertainty) in the 0.1-100GeV band. Finally we determine the LF of unbeamed FSRQs, finding that FSRQs have an average Lorentz factor of {gamma} = 11.7{sub -2.2}{sup +3.3}, that most are seen within 5{sup o} of the jet axis, and that they represent …
Date: April 16, 2012
Creator: Ajello, M.; Shaw, M. S.; Romani, R. W.; Dermer, C. D.; Costamante, L.; King, O. G. et al.
System: The UNT Digital Library
Elementary Steps of Syngas Reactions on Mo2C(001): Adsorption Thermochemistry and Bond Dissociation (open access)

Elementary Steps of Syngas Reactions on Mo2C(001): Adsorption Thermochemistry and Bond Dissociation

Density functional theory (DFT) and ab initio thermodynamics are applied in order to investigate the most stable surface and subsurface terminations of Mo{sub 2}C(001) as a function of chemical potential and in the presence of syngas. The Mo-terminated (001) surface is then used as a model surface to evaluate the thermochemistry and energetic barriers for key elementary steps in syngas reactions. Adsorption energy scaling relations and Broensted-Evans-Polanyi relationships are established and used to place Mo{sub 2}C into the context of transition metal surfaces. The results indicate that the surface termination is a complex function of reaction conditions and kinetics. It is predicted that the surface will be covered by either C{sub 2}H{sub 2} or O depending on conditions. Comparisons to transition metals indicate that the Mo-terminated Mo{sub 2}C(001) surface exhibits carbon reactivity similar to transition metals such as Ru and Ir, but is significantly more reactive towards oxygen.
Date: February 16, 2012
Creator: Medford, Andrew
System: The UNT Digital Library
FACET: SLAC’s New User Facility (open access)

FACET: SLAC’s New User Facility

FACET (Facility for Advanced Accelerator Experimental Tests) is a new User Facility at SLAC National Accelerator Laboratory. The first User Run started in spring 2012 with 20 GeV, 3 nC electron beams. The facility is designed to provide short (20 {micro}m) bunches and small (20 {micro}m wide) spot sizes, producing uniquely high power beams. FACET supports studies from many fields but in particular those of Plasma Wakefield Acceleration and Dielectric Wakefield Acceleration. The creation of drive and witness bunches and shaped bunch profiles is possible with 'Notch' Collimation. FACET is also a source of THz radiation for material studies. Positrons will be available at FACET in future user runs. We present the User Facility and the available tools and opportunities for future experiments.
Date: May 16, 2012
Creator: Clarke, C. I.; Decker, F. -J.; England, R. J.; Erickson, R. A.; Hast, C.; Hogan, M. J. et al.
System: The UNT Digital Library
2d Affine XY-Spin Model/4d Gauge Theory Duality and Deconfinement (open access)

2d Affine XY-Spin Model/4d Gauge Theory Duality and Deconfinement

We introduce a duality between two-dimensional XY-spin models with symmetry-breaking perturbations and certain four-dimensional SU(2) and SU(2) = Z{sub 2} gauge theories, compactified on a small spatial circle R{sup 1,2} x S{sup 1}, and considered at temperatures near the deconfinement transition. In a Euclidean set up, the theory is defined on R{sup 2} x T{sup 2}. Similarly, thermal gauge theories of higher rank are dual to new families of 'affine' XY-spin models with perturbations. For rank two, these are related to models used to describe the melting of a 2d crystal with a triangular lattice. The connection is made through a multi-component electric-magnetic Coulomb gas representation for both systems. Perturbations in the spin system map to topological defects in the gauge theory, such as monopole-instantons or magnetic bions, and the vortices in the spin system map to the electrically charged W-bosons in field theory (or vice versa, depending on the duality frame). The duality permits one to use the two-dimensional technology of spin systems to study the thermal deconfinement and discrete chiral transitions in four-dimensional SU(N{sub c}) gauge theories with n{sub f} {ge} 1 adjoint Weyl fermions.
Date: August 16, 2012
Creator: Anber, Mohamed M.; Poppitz, Erich; U., /Toronto; Unsal, Mithat & /SLAC /Stanford U., Phys. Dept. /San Francisco State U.
System: The UNT Digital Library
A Fisheye Lens as a Photonic Doppler Velocimetry Probe (open access)

A Fisheye Lens as a Photonic Doppler Velocimetry Probe

These presentation visuals report an instrument that, by use of a fish-eye lens, generates a beat signal using fiber mixing of unshifted light with Doppler-shifted light and measures the beat frequency. Ray trace diagrams are shown to illustrate advantages and disadvantages. The authors find their instrument has a long tracking distance, and large angle coverage. Index matching eases assembly, reduces return loss and flattens the field.
Date: August 16, 2012
Creator: Frogget, B. C.
System: The UNT Digital Library
Aerial Radiation Measurements from the Fukushima Dai-ichi Nuclear Power Plant Accident (open access)

Aerial Radiation Measurements from the Fukushima Dai-ichi Nuclear Power Plant Accident

This document is a slide show type presentation concerning DOE and Aerial Measuring System (AMS) activities and results with respect to assessing the consequences of the releases from the Fukushima Dai-ichi Nuclear Power Plant. These include ground monitoring and aerial monitoring.
Date: July 16, 2012
Creator: Guss, P. P.
System: The UNT Digital Library
Search for Dark Matter Satellites Using the FERMI-LAT (open access)

Search for Dark Matter Satellites Using the FERMI-LAT

Numerical simulations based on the {Lambda}CDM model of cosmology predict a large number of as yet unobserved Galactic dark matter satellites. We report the results of a Large Area Telescope (LAT) search for these satellites via the {gamma}-ray emission expected from the annihilation of weakly interacting massive particle (WIMP) dark matter. Some dark matter satellites are expected to have hard {gamma}-ray spectra, finite angular extents, and a lack of counterparts at other wavelengths. We sought to identify LAT sources with these characteristics, focusing on {gamma}-ray spectra consistent with WIMP annihilation through the b{bar b} channel. We found no viable dark matter satellite candidates using one year of data, and we present a framework for interpreting this result in the context of numerical simulations to constrain the velocity-averaged annihilation cross section for a conventional 100 GeV WIMP annihilating through the b{bar b} channel.
Date: August 16, 2012
Creator: Ackermann, M.; Albert, A.; Baldini, L.; Ballet, J.; Barbiellini, G.; Bastieri, D. et al.
System: The UNT Digital Library
Simple Limits on Achieving A Quasi-Linear Magnetic Compression for an FEL Driver (open access)

Simple Limits on Achieving A Quasi-Linear Magnetic Compression for an FEL Driver

Free electron lasers (FEL) need a very bright electron beam in three dimensions and a high peak charge density. In order to compress an initially longer electron bunch generated from the photoinjector, magnetic bunch compression systems are widely employed. In this paper, first harmonic RF linearization and its associated requirements are reviewed. Meanwhile it is also briefly discussed what is the relation between a proper initial bunch length and main RF frequency, when a harmonic RF linearization is included. Then given a reasonable bunch compression ratio, a proper initial bunch length as a function of the main RF frequency and RF phase is estimated analytically by several approaches, assuming that no harmonic RF section is needed to linearize the energy modulation introduced during main RF acceleration, and at the same time still linearly compress the bunch length. Next the upper limit of the bunch compression ratio in a single stage is evaluated analytically. The analytical relations derived on choosing a proper initial bunch length as a function of main RF frequency are confirmed by numerical simulation. These simple limit provide rough estimations and may be beneficial for choosing bunch compression ratios in different stages of an FEL driver, especially in …
Date: February 16, 2012
Creator: Sun, Yipeng
System: The UNT Digital Library
Light-Front Holographic QCD (open access)

Light-Front Holographic QCD

The relation between the hadronic short-distance constituent quark and gluon particle limit and the long-range confining domain is yet one of the most challenging aspects of particle physics due to the strong coupling nature of Quantum Chromodynamics, the fundamental theory of the strong interactions. The central question is how one can compute hadronic properties from first principles; i.e., directly from the QCD Lagrangian. The most successful theoretical approach thus far has been to quantize QCD on discrete lattices in Euclidean space-time. Lattice numerical results follow from computation of frame-dependent moments of distributions in Euclidean space and dynamical observables in Minkowski spacetime, such as the time-like hadronic form factors, are not amenable to Euclidean lattice computations. The Dyson-Schwinger methods have led to many important insights, such as the infrared fixed point behavior of the strong coupling constant, but in practice, the analyses are limited to ladder approximation in Landau gauge. Baryon spectroscopy and the excitation dynamics of nucleon resonances encoded in the nucleon transition form factors can provide fundamental insight into the strong-coupling dynamics of QCD. New theoretical tools are thus of primary interest for the interpretation of the results expected at the new mass scale and kinematic regions accessible to …
Date: February 16, 2012
Creator: Brodsky, Stanley J.; /SLAC /Southern Denmark U., CP3-Origins; de Teramond, Guy F. & U., /Costa Rica
System: The UNT Digital Library
AdS/QCD and Applications of Light-Front Holography (open access)

AdS/QCD and Applications of Light-Front Holography

Light-Front Holography leads to a rigorous connection between hadronic amplitudes in a higher dimensional anti-de Sitter (AdS) space and frame-independent light-front wavefunctions of hadrons in 3 + 1 physical space-time, thus providing a compelling physical interpretation of the AdS/CFT correspondence principle and AdS/QCD, a useful framework which describes the correspondence between theories in a modified AdS5 background and confining field theories in physical space-time. To a first semiclassical approximation, where quantum loops and quark masses are not included, this approach leads to a single-variable light-front Schroedinger equation which determines the eigenspectrum and the light-front wavefunctions of hadrons for general spin and orbital angular momentum. The coordinate z in AdS space is uniquely identified with a Lorentz-invariant coordinate {zeta} which measures the separation of the constituents within a hadron at equal light-front time. The internal structure of hadrons is explicitly introduced and the angular momentum of the constituents plays a key role. We give an overview of the light-front holographic approach to strongly coupled QCD. In particular, we study the photon-to-meson transition form factors (TFFs) F{sub M{gamma}}(Q{sup 2}) for {gamma}{gamma}* {yields} M using light-front holographic methods. The results for the TFFs for the {eta} and {eta}' mesons are also presented. Some …
Date: February 16, 2012
Creator: Brodsky, Stanley J.; /SLAC /Southern Denmark U., CP3-Origins; Cao, Fu-Guang; U., /Massey; de Teramond, Guy F. & U., /Costa Rica
System: The UNT Digital Library
Particle Energy Spectrum, Revisited from a Counting Statistics Perspective (open access)

Particle Energy Spectrum, Revisited from a Counting Statistics Perspective

This document is a slide show type presentation of a new covariance estimation for gamma spectra and neutron cross section.
Date: July 16, 2012
Creator: Yuan, D., Marks, D. G., Guss, P. P.
System: The UNT Digital Library
Atoms in Flight: The Remarkable Connections between Atomic and Hadronic Physics (open access)

Atoms in Flight: The Remarkable Connections between Atomic and Hadronic Physics

Atomic physics and hadron physics are both based on Yang Mills gauge theory; in fact, quantum electrodynamics can be regarded as the zero-color limit of quantum chromodynamics. I review a number of areas where the techniques of atomic physics provide important insight into the theory of hadrons in QCD. For example, the Dirac-Coulomb equation, which predicts the spectroscopy and structure of hydrogenic atoms, has an analog in hadron physics in the form of light-front relativistic equations of motion which give a remarkable first approximation to the spectroscopy, dynamics, and structure of light hadrons. The renormalization scale for the running coupling, which is unambiguously set in QED, leads to a method for setting the renormalization scale in QCD. The production of atoms in flight provides a method for computing the formation of hadrons at the amplitude level. Conversely, many techniques which have been developed for hadron physics, such as scaling laws, evolution equations, and light-front quantization have equal utility for atomic physics, especially in the relativistic domain. I also present a new perspective for understanding the contributions to the cosmological constant from QED and QCD.
Date: February 16, 2012
Creator: Brodsky, Stanley J.
System: The UNT Digital Library
Pair Production Constraints on Superluminal Neutrinos Revisited (open access)

Pair Production Constraints on Superluminal Neutrinos Revisited

We revisit the pair creation constraint on superluminal neutrinos considered by Cohen and Glashow in order to clarify which types of superluminal models are constrained. We show that a model in which the superluminal neutrino is effectively light-like can evade the Cohen-Glashow constraint. In summary, any model for which the CG pair production process operates is excluded because such timelike neutrinos would not be detected by OPERA or other experiments. However, a superluminal neutrino which is effectively lightlike with fixed p{sup 2} can evade the Cohen-Glashow constraint because of energy-momentum conservation. The coincidence involved in explaining the SN1987A constraint certainly makes such a picture improbable - but it is still intrinsically possible. The lightlike model is appealing in that it does not violate Lorentz symmetry in particle interactions, although one would expect Hughes-Drever tests to turn up a violation eventually. Other evasions of the CG constraints are also possible; perhaps, e.g., the neutrino takes a 'short cut' through extra dimensions or suffers anomalous acceleration in matter. Irrespective of the OPERA result, Lorentz-violating interactions remain possible, and ongoing experimental investigation of such possibilities should continue.
Date: February 16, 2012
Creator: Brodsky, Stanley J. & Gardner, Susan
System: The UNT Digital Library
Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations (open access)

Holliday Triangle Hunter (HolT Hunter): Efficient Software for Identifying Low Strain DNA Triangular Configurations

Synthetic DNA nanostructures are typically held together primarily by Holliday junctions. One of the most basic types of structures possible to assemble with only DNA and Holliday junctions is the triangle. To date, however, only equilateral triangles have been assembled in this manner - primarily because it is difficult to figure out what configurations of Holliday triangles have low strain. Early attempts at identifying such configurations relied upon calculations that followed the strained helical paths of DNA. Those methods, however, were computationally expensive, and failed to find many of the possible solutions. I have developed a new approach to identifying Holliday triangles that is computationally faster, and finds well over 95% of the possible solutions. The new approach is based on splitting the problem into two parts. The first part involves figuring out all the different ways that three featureless rods of the appropriate length and diameter can weave over and under one another to form a triangle. The second part of the computation entails seeing whether double helical DNA backbones can fit into the shape dictated by the rods in such a manner that the strands can cross over from one domain to the other at the appropriate spots. …
Date: April 16, 2012
Creator: Sherman, W.B.
System: The UNT Digital Library