Search for: All records

Molecular programmers and nanostructure engineers use domain-level design to abstract away messy DNA/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded DNA/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, with 2-domain strands, we find that the MFE decision problem is NP-complete, even without pseudoknots, and requires exponential time algorithms assuming SAT does. On the other hand, in the simplest case of 1-domain strands there are efficient MFE algorithms for various binding modes. However, even in this single-domain case, MFE is P-hard for promiscuous binding, where one domain may bind to multiple as experimentally used by Nikitin [Nat Chem., 2023], which in turn implies that strands consisting of a single domain efficiently implement arbitrary Boolean circuits. 

Imagine t ≤ mn unit-square tiles in an m×n rectangular box that you can tilt to cause all tiles to slide maximally in one of the four orthogonal directions. Given two tiles of interest, is there a tilt sequence that brings them to adjacent squares? We give a linear-time algorithm for this problem, motivated by 2048 endgames. We also bound the number of reachable configurations, and design instances where all t tiles permute according to a cyclic permutation every four tilts. 

A determinacy race occurs if two or more logically parallel instructions access the same memory location and at least one of them tries to modify its content. Races are often undesirable as they can lead to nondeterministic and incorrect program behavior. A data race is a special case of a determinacy race which can be eliminated by associating a mutual-exclusion lock with the memory location in question or allowing atomic accesses to it. However, such solutions can reduce parallelism by serializing all accesses to that location. For associative and commutative updates to a memory cell, one can instead use a reducer, which allows parallel race-free updates at the expense of using some extra space. More extra space usually leads to more parallel updates, which in turn contributes to potentially lowering the overall execution time of the program. We start by asking the following question. Given a fixed budget of extra space for mitigating the cost of races in a parallel program, which memory locations should be assigned reducers and how should the space be distributed among those reducers in order to minimize the overall running time?We argue that under reasonable conditions the races of a program can be captured by a directed acyclic graph (DAG), with nodes representing memory cells and arcs representing read-write dependencies between cells. We then formulate our original question as an optimization problem on this DAG. We concentrate on a variation of this problem where space reuse among reducers is allowed by routing every unit of extra space along a (possibly different) source to sink path of the DAG and using it in the construction of multiple (possibly zero) reducers along the path. We consider two different ways of constructing a reducer and the corresponding duration functions (i.e., reduction time as a function of space budget).