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All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

Generalized Symbolic Execution for Model Checking and Testing

Modern software systems, which often are concurrent and manipulate complex data structures must be extremely reliable. We present a novel framework based on symbolic execution, for automated checking of such systems. We provide a two-fold generalization of traditional symbolic execution based approaches: one, we define a program instrumentation, which enables standard model checkers to perform symbolic execution; two, we give a novel symbolic execution algorithm that handles dynamically allocated structures (e.g., lists and trees), method preconditions (e.g., acyclicity of lists), data (e.g., integers and strings) and concurrency. The program instrumentation enables a model checker to automatically explore program heap configurations (using a systematic treatment of aliasing) and manipulate logical formulae on program data values (using a decision procedure). We illustrate two applications of our framework: checking correctness of multi-threaded programs that take inputs from unbounded domains with complex structure and generation of non-isomorphic test inputs that satisfy a testing criterion. Our implementation for Java uses the Java PathFinder model checker.

Khurshid, Sarfraz↗
NASA NTRS1993

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

NASA Discipline Number 52-20↗