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Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming… (More)

Biologists working in the area of computational protein design have never doubted the seriousness of the algorithmic challenges that face them in attempting in silico sequence selection. It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard. The purpose of this paper is to explain the context of… (More)

Motivated by applications in computational fluid dynamics, a method is presented for obtaining estimates of integral functionals, such as lift or drag, that have twice the order of accuracy of the computed flow solution on which they are based. This is achieved through error analysis that uses an adjoint PDE to relate the local errors in approximating the… (More)

In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into… (More)

Hybridization chain reaction (HCR) provides multiplexed, isothermal, enzyme-free, molecular signal amplification in diverse settings. Within intact vertebrate embryos, where signal-to-background is at a premium, HCR in situ amplification enables simultaneous mapping of multiple target mRNAs, addressing a longstanding challenge in the biological sciences.… (More)

We present two error estimation approaches for bounding or correcting the error in functional estimates such as lift or drag. Adjoint methods quantify the error in a particular output functional that results from residual errors in approximating the solution to the partial differential equation. Defect methods can be used to bound or reduce the error in the… (More)

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to… (More)

We describe an algorithm for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. Sequence design is formulated as an optimization problem with the goal of reducing the ensemble defect below a user-specified stop condition. For a candidate sequence and a given target secondary… (More)

The behavior of analytic and numerical adjoint solutions is examined for the quasi-1D Euler equations. For shocked ow, the derivation of the adjoint problem reveals that the adjoint variables are continuous with zero gradient at the shock and that an internal adjoint boundary condition is required at the shock. A Green's function approach is used to derive… (More)

UNLABELLED
The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables:
ANALYSIS
thermodynamic analysis of dilute solutions of interacting nucleic acid strands.
DESIGN
sequence design for complexes of nucleic acid strands intended to… (More)