85 citations · 200 across the 9 of their papers we have counts for
9 papers
Automated rendering of multi-stranded DNA complexes with pseudoknots
Malgorzata Nowicka, Vinay K. Gautam, Pekka Orponen
We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted…
Cotranscriptional kinetic folding of RNA secondary structures including pseudoknots
Vo Hong Thanh, Dani Korpela, Pekka Orponen
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from…
Search Methods for Tile Sets in Patterned DNA Self-Assembly
Mika Göös, Tuomo Lempiäinen, Eugen Czeizler +1
The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a set of coloured tiles that, starting from…
Witness of unsatisfiability for a random 3-satisfiability formula
Lu-Lu Wu, Hai-Jun Zhou, Mikko Alava +2
The random 3-satisfiability (3-SAT) problem is in the unsatisfiable (UNSAT) phase when the clause density exceeds a critical value . However, rigorously prov…
Synthesizing Minimal Tile Sets for Patterned DNA Self-Assembly
Mika Göös, Pekka Orponen
The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an e…
Locally computable approximations for spectral clustering and absorption times of random walks
Pekka Orponen, Satu Elisa Schaeffer, Vanesa Avalos Gaytán
We address the problem of determining a natural local neighbourhood or "cluster" associated to a given seed vertex in an undirected graph. We formulate the task in terms of absorpt…