12 research outputs found
On Optimization Modulo Theories, MaxSMT and Sorting Networks
Optimization Modulo Theories (OMT) is an extension of SMT which allows for
finding models that optimize given objectives. (Partial weighted) MaxSMT --or
equivalently OMT with Pseudo-Boolean objective functions, OMT+PB-- is a
very-relevant strict subcase of OMT. We classify existing approaches for MaxSMT
or OMT+PB in two groups: MaxSAT-based approaches exploit the efficiency of
state-of-the-art MAXSAT solvers, but they are specific-purpose and not always
applicable; OMT-based approaches are general-purpose, but they suffer from
intrinsic inefficiencies on MaxSMT/OMT+PB problems.
We identify a major source of such inefficiencies, and we address it by
enhancing OMT by means of bidirectional sorting networks. We implemented this
idea on top of the OptiMathSAT OMT solver. We run an extensive empirical
evaluation on a variety of problems, comparing MaxSAT-based and OMT-based
techniques, with and without sorting networks, implemented on top of
OptiMathSAT and {\nu}Z. The results support the effectiveness of this idea, and
provide interesting insights about the different approaches.Comment: 17 pages, submitted at Tacas 1
Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization
The process of protein misfolding and self-assembly into various, polymorphic aggregates is associated with a number of important neurodegenerative diseases. Only recently, crystal structures of several short peptides have provided detailed structural insights into -sheet rich aggregates, known as amyloid fibrils. Knowledge about early events of the formation and interconversion of small oligomeric states, an inevitable step in the cascade of peptide self-assembly, however, remains still limited