Design of Geometric Molecular Bonds

An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the affinity of the DNA base A for T, but not for C, G, or another A. Recent experimental breakthroughs in DNA nanotechnology demonstrate that a particular nonspecific like-like bond ("blunt-end DNA stacking" that occurs between the ends of any pair of DNA double-helices) can be used to create specific "macrobonds" by careful geometric arrangement of many nonspecific blunt ends, motivating the need for sets of macrobonds that are orthogonal: two macrobonds not intended to bind should have relatively low binding strength, even when misaligned. To address this need, we introduce geometric orthogonal codes that abstractly model the engineered DNA macrobonds as two-dimensional binary codewords. While motivated by completely different applications, geometric orthogonal codes share similar features to the optical orthogonal codes studied by Chung, Salehi, and Wei. The main technical difference is the importance of 2D geometry in defining codeword orthogonality.Comment: Accepted to appear in IEEE Transactions on Molecular, Biological, and Multi-Scale Communication

Urban Wind Generation: Comparing Horizontal and Vertical Axis Wind Turbines at Clark University in Worcester, Massachusetts

Electricity production must shift towards carbon neutral sources such as wind power to mitigate the impacts of climate change. The wind resource in urban environments is challenging to predict but technologies, including computational fluid dynamics software, are making it possible. This software pinpoints suitable placement for wind turbines through models that show wind acceleration patterns over a building. Horizontal axis wind turbines (HAWTs) have dominated the wind industry but vertical axis wind turbines (VAWTs) offer potential to outperform HAWTs in urban environments. VAWTs can handle turbulent and unconventional wind and generate energy at slower speeds, which is beneficial for these areas. A case study at Clark University in Worcester, Massachusetts analyzes the functionality of a HAWT and a VAWT. The machines are compared by their efficiencies due to an imbalance of rated power outputs. The machines’ average maximum power coefficients are similar. However, when the R2 values of the turbine’s power curves are compared the VAWT demonstrates greater capacity to track changes in the wind. This research is the first step in redefining the power systems employed at Clark University and the data will be utilized to find better locations for the wind turbines

Size-Dependent Tile Self-Assembly: Constant-Height Rectangles and Stability

We introduce a new model of algorithmic tile self-assembly called size-dependent assembly. In previous models, supertiles are stable when the total strength of the bonds between any two halves exceeds some constant temperature. In this model, this constant temperature requirement is replaced by an nondecreasing temperature function $\tau : \mathbb{N} \rightarrow \mathbb{N}$ that depends on the size of the smaller of the two halves. This generalization allows supertiles to become unstable and break apart, and captures the increased forces that large structures may place on the bonds holding them together. We demonstrate the power of this model in two ways. First, we give fixed tile sets that assemble constant-height rectangles and squares of arbitrary input size given an appropriate temperature function. Second, we prove that deciding whether a supertile is stable is coNP-complete. Both results contrast with known results for fixed temperature.Comment: In proceedings of ISAAC 201

A Quasilinear-Time Algorithm for Tiling the Plane Isohedrally with a Polyomino

A plane tiling consisting of congruent copies of a shape is isohedral provided that for any pair of copies, there exists a symmetry of the tiling mapping one copy to the other. We give a O(n log2 n)-time algorithm for deciding if a polyomino with n edges can tile the plane isohedrally. This improves on the O(n18)-time algorithm of Keating and Vince and generalizes recent work by Brlek, Provençal, Fédou, and the second author.SCOPUS: cp.pinfo:eu-repo/semantics/publishe

Optimal Staged Self-Assembly of General Shapes

We analyze the number of tile types $t$, bins $b$, and stages necessary to assemble $n \times n$ squares and scaled shapes in the staged tile assembly model. For $n \times n$ squares, we prove $\mathcal{O}(\frac{\log{n} - tb - t\log t}{b^2} + \frac{\log \log b}{\log t})$ stages suffice and $\Omega(\frac{\log{n} - tb - t\log t}{b^2})$ are necessary for almost all $n$. For shapes $S$ with Kolmogorov complexity $K(S)$, we prove $\mathcal{O}(\frac{K(S) - tb - t\log t}{b^2} + \frac{\log \log b}{\log t})$ stages suffice and $\Omega(\frac{K(S) - tb - t\log t}{b^2})$ are necessary to assemble a scaled version of $S$, for almost all $S$. We obtain similarly tight bounds when the more powerful flexible glues are permitted.Comment: Abstract version appeared in ESA 201

Spanning Properties of Theta-Theta-6

We show that, unlike the Yao-Yao graph $YY_6$, the Theta-Theta graph $\Theta\Theta_6$ defined by six cones is a spanner for sets of points in convex position. We also show that, for sets of points in non-convex position, the spanning ratio of $\Theta\Theta_6$ is unbounded.Comment: 13 pages, 9 figure

Spanning Properties of Theta-Theta-6

We show that, unlike the Yao–Yao graph YY6, the Theta–Theta graph ΘΘ6 defined by six cones is a spanner for sets of points in convex position. We also show that, for sets of points in non-convex position, the spanning ratio of ΘΘ6 is unbounded