Zobrazeno 1 - 10
of 140
pro vyhledávání: '"Orponen, Pekka"'
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, and if a planar rendering is possible, the method will determine one
Externí odkaz:
http://arxiv.org/abs/2308.06392
Publikováno v:
Journal of Computational Biology, 2021
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 a fully synthesized sequence. Experimental evidence, however, has sho
Externí odkaz:
http://arxiv.org/abs/2007.05228
Akademický článek
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Publikováno v:
J. Comput. Syst. Sci. 80 (2014) 297-319
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 a bordering seed structure, self-assembles to a given rectangular col
Externí odkaz:
http://arxiv.org/abs/1412.7219
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America, 2019 Sep . 116(39), 19282-19287.
Externí odkaz:
https://www.jstor.org/stable/26855161
Publikováno v:
Physical Review E 87, 052807 (2013)
The random 3-satisfiability (3-SAT) problem is in the unsatisfiable (UNSAT) phase when the clause density $\alpha$ exceeds a critical value $\alpha_s \approx 4.267$. However, rigorously proving the unsatisfiability of a given large 3-SAT instance is
Externí odkaz:
http://arxiv.org/abs/1303.2413
Autor:
Göös, Mika, Orponen, Pekka
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 exhaustive branch-and-bound algorithm to find tile sets of minimum card
Externí odkaz:
http://arxiv.org/abs/0911.2924
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 absorption times of random walks from other vertices to the vertex of interes
Externí odkaz:
http://arxiv.org/abs/0810.4061
Autor:
Alava, Mikko, Ardelius, John, Aurell, Erik, Kaski, Petteri, Krishnamurthy, Supriya, Orponen, Pekka, Seitz, Sakari
We study the performance of stochastic local search algorithms for random instances of the $K$-satisfiability ($K$-SAT) problem. We introduce a new stochastic local search algorithm, ChainSAT, which moves in the energy landscape of a problem instance
Externí odkaz:
http://arxiv.org/abs/0711.4902
A local search algorithm solving an NP-complete optimisation problem can be viewed as a stochastic process moving in an 'energy landscape' towards eventually finding an optimal solution. For the random 3-satisfiability problem, the heuristic of focus
Externí odkaz:
http://arxiv.org/abs/cond-mat/0501707