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NUPACK: Analysis and design of nucleic acid systems
The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems and algorithms are formulated in terms ofucleic acid secondary structure.
A partition function algorithm for nucleic acid secondary structure including pseudoknots
An O(N5) dynamic programming algorithm is described, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures, to determine the probability of sampling the lowest energy structure, or any other structure of particular interest.
Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust
Third-generation in situ HCR v3.0 exploits automatic background suppression to enable multiplexed quantitative mRNA imaging and flow cytometry with dramatically enhanced performance and ease of use.
An Introduction to the Adjoint Approach to Design
An introduction to the subject, emphasising the simplicity of the ideas when viewed in the context of linear algebra, and examples of the use of adjoint methods for optimising the design of business jets are presented.
Triggered amplification by hybridization chain reaction.
This work introduces the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, which allows DNA to act as an amplifying transducer for biosensing applications.
Adjoint equations in CFD: duality, boundary conditions and solution behaviour
The first half of this paper derives the adjoint equations for inviscid and viscous compressible flow, with the emphasis being on the correct formulation of the adjoint boundary conditions and…
Programming biomolecular self-assembly pathways
Diverse molecular self-assembly and disassembly pathways are program using a ‘reaction graph’ abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif.
Protein design is NP-hard.
It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard.
Nucleic acid sequence design via efficient ensemble defect optimization
An algorithm for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium is described and exhibits asymptotic optimality and the exponent in the time complexity bound is sharp.
Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability
Next-generation DNA HCR amplifiers are designed that maximize the free energy benefit per polymerization step while preserving the kinetic trapping property that underlies conditional polymerization, dramatically increasing signal gain, reducing reagent cost, and improving reagent durability.