Modeling technologies and methods for DNA origami

The creation of correctly assembling DNA origami often requires several iterations wherein a researcher tries and troubleshoots an incremental design. In each iteration there exists one or more costly failures that often take immense time or materials to find. These failures occur in part due to a lack of in-depth understanding of how DNA origami self-assembles and functions. To aid researchers in developing correct DNA origami designs, this thesis describes the creation of a DNA origami failure catalog as well as models for elucidating as-of-yet only partially understood properties of DNA origami. The failure catalog helps laboratory scientists gather requirements to preempt failures in their origami designs, and helps laboratory scientists troubleshoot their experiments after the implementation of a design by querying the catalog. Use of the catalog then helps verify the properties of new macro and micro models for DNA origami introduced here. These micro and macro models open up future ways to evaluate DNA origami through a mathematically more rigorous framework. By using both captured knowledge of previous design failures and novel theoretical modeling techniques, this work seeks to reduce the gap in understanding between design and implementation of DNA origami

Spin observables and the determination of the parity of Θ+\Theta^+ in photoproduction reactions

Spin observables in the photoproduction of the $\Theta^+$ are explored for the purpose of determining the parity of the $\Theta^+$. Based on reflection symmetry in the scattering plane, we show that certain spin observables in the photoproduction of the $\Theta^+$ can be related directly to its parity. We also show that measurements of both the target nucleon asymmetry and the $\Theta^+$ polarization may be useful in determining the parity of $\Theta^+$ in a model-independent way. Furthermore, we show that no combination of spin observables involving only the polarization of the photon and/or nucleon in the initial state can determine the parity of $\Theta^+$ unambiguously.Comment: LaTeX, 11 pages, minor revisio

On the Universal Tachyon and Geometrical Tachyon

We study properties of non-BPS D(p+1)-brane in the background of k NS5-branes, with one transverse direction compactified on a circle, from the point of view of Dirac-Born-Infeld action. We present the analysis of two different embedding of non-BPS D(p+1)-brane in given background and study the classical solutions of given world-volume theory. We argue for the configuration of a non-BPS D(p+1)-brane which allows us to find solutions of the equations of motion that give unified descriptions of G and U-type branes.Comment: 24 pages, minor change

Fuzzy Sphere Dynamics and Non-Abelian DBI in Curved Backgrounds

We consider the non-Abelian action for the dynamics of $N Dp'$-branes in the background of $M Dp$-branes, which parameterises a fuzzy sphere using the SU(2) algebra. We find that the curved background leads to collapsing solutions for the fuzzy sphere except when we have $D0$ branes in the $D6$ background, which is a realisation of the gravitational Myers effect. Furthermore we find the equations of motion in the Abelian and non-Abelian theories are identical in the large $N$ limit. By picking a specific ansatz we find that we can incorporate angular momentum into the action, although this imposes restriction upon the dimensionality of the background solutions. We also consider the case of non-Abelian non-BPS branes, and examine the resultant dynamics using world-volume symmetry transformations. We find that the fuzzy sphere always collapses but the solutions are sensitive to the combination of the two conserved charges and we can find expanding solutions with turning points. We go on to consider the coincident $NS$5-brane background, and again construct the non-Abelian theory for both BPS and non-BPS branes. In the latter case we must use symmetry arguments to find additional conserved charges on the world-volumes to solve the equations of motion. We find that in the Non-BPS case there is a turning solution for specific regions of the tachyon and radion fields. Finally we investigate the more general dynamics of fuzzy $\mathbb{S}^{2k}$ in the $Dp$-brane background, and find collapsing solutions in all cases.Comment: 49 pages, 3 figures, Latex; Version to appear in JHE

Albedo heterogeneity on the surface of (1943) Anteros

We have investigated the effect of rotation on the polarization of scattered light for the near-Earth asteroid (1943) Anteros using the Dual Beam Imaging Polarimeter on the University of Hawaii's 2.2 m telescope. Anteros is an L-type asteroid that has not been previously observed polarimetrically. We find weak but significant variations in the polarization of Anteros as a function of rotation, indicating albedo changes across the surface. Specifically, we find that Anteros has a background albedo of p_v = 0.18 +/- 0.02 with a dark spot of p_v < 0.09 covering < 2% of the surface.Comment: Accepted to Icarus, 15 pages, 3 fig

Dynamics of D1-brane in I-brane Background

This paper is devoted to the study of the effective field theory description of the probe D1-brane in the background of the system of two stacks of fivebranes in type IIB theory that intersect on $R^{1,1}$. We study the properties of the Dirac-Born-Infeld action for D1-brane moving in this background. We will argue that this action is invariant under an additional symmetry in the near horizon limit and that this new symmetry is closely related to the enhanced symmetry of the I-brane background considered recently in [hep-th/0508025]. We also solve explicitly the equation of motion of D1-brane in the near horizon limit.Comment: 21 pages, references adde

Geometrical Tachyon Kinks and NS5 Branes

We further investigate the $NS$5 ring background using the tachyon map. Mapping the radion fields to the rolling tachyon helps to explain the motion of a probe $Dp$-brane in this background. It turns out that the radion field becomes tachyonic when the brane is confined to one dimensional motion inside the ring. We find explicit solutions for the geometrical tachyon field that describe stable kink solutions which are similar to those of the open string tachyon. Interestingly in the case of the geometric tachyon, the dynamics is controlled by a cosine potential. In addition, we couple a constant electric field to the probe-brane, but find that the only stable kink solutions occur when there is zero electric field or a critical field value. We also investigate the behaviour of Non-BPS branes in this background, and find that the end state of any probe brane is that of tachyonic matter 'trapped' around the interior of the ring. We conclude by considering compactification of the ring solution in one of the transverse directions.Comment: Latex, 24 pages, 1 eps fig; clarifying comments added to Section 2; typos correcte

D-Brane Propagation in Two-Dimensional Black Hole Geometries

We study propagation of D0-brane in two-dimensional Lorentzian black hole backgrounds by the method of boundary conformal field theory of SL(2,R)/U(1) supercoset at level k. Typically, such backgrounds arise as near-horizon geometries of k coincident non-extremal NS5-branes, where 1/k measures curvature of the backgrounds in string unit and hence size of string worldsheet effects. At classical level, string worldsheet effects are suppressed and D0-brane propagation in the Lorentzian black hole geometry is simply given by the Wick rotation of D1-brane contour in the Euclidean black hole geometry. Taking account of string worldsheet effects, boundary state of the Lorentzian D0-brane is formally constructible via Wick rotation from that of the Euclidean D1-brane. However, the construction is subject to ambiguities in boundary conditions. We propose exact boundary states describing the D0-brane, and clarify physical interpretations of various boundary states constructed from different boundary conditions. As it falls into the black hole, the D0-brane radiates off to the horizon and to the infinity. From the boundary states constructed, we compute physical observables of such radiative process. We find that part of the radiation to infinity is in effective thermal distribution at the Hawking temperature. We also find that part of the radiation to horizon is in the Hagedorn distribution, dominated by massive, highly non-relativistic closed string states, much like the tachyon matter. Remarkably, such distribution emerges only after string worldsheet effects are taken exactly into account. From these results, we observe that nature of the radiation distribution changes dramatically across the conifold geometry k=1 (k=3 for the bosonic case), exposing the `string - black hole transition' therein.Comment: 51 pages, 5 figures, v2: referece added, note added replying the comment made in hep-th/060206