Advanced flow-based type systems for object-oriented languages

Ph.DDOCTOR OF PHILOSOPH

Automated Specification Inference in a Combined Domain via User-Defined Predicates

Discovering program specifications automatically for heap-manipulating programs is a challenging task due\ud to the complexity of aliasing and mutability of data structures. This task is further complicated by an\ud expressive domain that combines shape, numerical and bag information. In this paper, we propose a compositional analysis framework that would derive the summary for each method in the expressive abstract\ud domain, independently from its callers. We propose a novel abstraction method with a bi-abduction technique in the combined domain to discover pre-/post-conditions that could not be automatically inferred\ud before. The analysis does not only infer memory safety properties, but also finds relationships between pure\ud and shape domains towards full functional correctness of programs. A prototype of the framework has been\ud implemented and initial experiments have shown that our approach can discover interesting properties for\ud non-trivial programs

A specialization calculus for pruning disjunctive predicates to support verification

10.1007/978-3-642-22110-1_23Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)6806 LNCS293-30

In silico study of PEI-PEG-squalene-dsDNA polyplex formation: the delicate role of the PEG length in the binding of PEI to DNA

Using a two step simulation protocol the atomistic interactions between PEG and b-PEI and the effect of these interactions on DNA binding were determined

Tunable Composition of Dynamic Non-Viral Vectors over the DNA Polyplex Formation and Nucleic Acid Transfection

Polyethylene glycol (PEG) functionalization of non-viral vectors represents a powerful tool through the formation of an overall surface charge shielding ability, which is fundamental for efficient nucleic acid delivery systems. The degree of non-viral vector PEGylation and the molecular weight of utilized PEG is crucial since the excessive use of PEG units may lead to a considerable reduction of the DNA-binding capacity and, subsequently, in a reduction of in vitro transfection efficiency. Herein, we report a detailed study on a series of dynamic combinatorial frameworks (DCFs) containing PEGylated squalene, poly-(ethyleneglycol)-bis(3-aminopropyl) of different lengths, and branched low molecular weight polyethylenimine components, reversibly connected in hyperbranched structures, as efficient dynamic non-viral vectors. The obtained frameworks were capable of forming distinct supramolecular amphiphilic architectures, shown by transmission electron microscopy (TEM) and dynamic light scattering (DLS), with sizes and stability depending on the length of PEG units. The interaction of PEGylated DCFs with nucleic acids was investigated by agarose gel retardation assay and atomic force microscopy (AFM), while their transfection efficiency (using pCS2+MT-Luc DNA as a reporter gene) and cytotoxicity were evaluated in HeLa cells. In addition, the data on the influence of the poly-(ethyleneglycol)-bis(3-aminopropyl) length in composition of designed frameworks over transfection efficiency and tolerance in human cells were analyzed and compared

Discovering Specifications for Unknown Procedures- Work in Progress

We study automated verification of pointer safety for heap-manipulating imperative programs with unknown procedure calls or code pointers. Given the specification of a procedure whose body contains calls to an unknown procedure, we try to infer the possible specifications for the unknown procedure from its calling contexts. We employ a forward shape analysis with separation logic and an abductive inference mechanism to synthesize both pre- and postconditions for the unknown procedure. The inferred specification is a partial specification ofthe unknownprocedure. Therefore it is subject toalater verification when the code or the complete specification for the unknown procedure are available. Our inferred specifications can also be used for program understanding.