Jonas Braband Jensen

Fictional separation logic

Separation logic formalizes the idea of local reasoning for heap-manipulating programs via the frame rule and the separating conjunction P * Q, which describes states that can be split into separate parts, with one satisfying P and the other satisfying Q. In standard separation logic, separation means physical separation. In this paper, we introduce fictional separation logic, which includes more general forms of fictional separating conjunctions P * Q, where * does not require physical separation, but may also be used in situations where the memory resources described by P and Q overlap. We demonstrate, via a range of examples, how fictional separation logic can be used to reason locally and modularly about mutable abstract data types, possibly implemented using sophisticated sharing. Fictional separation logic is defined on top of standard separation logic, and both the meta-theory and the application of the logic is much simpler than earlier related approaches.

Verifying object-oriented programs with higher-order separation logic in Coq

We present a shallow Coq embedding of a higher-order separation logic with nested triples for an object-oriented programming language. Moreover, we develop novel specification and proof patterns for reasoning in higher-order separation logic with nested triples about programs that use interfaces and interface inheritance. In particular, we show how to use the higher-order features of the Coq formalisation to specify and reason modularly about programs that (1) depend on some unknown code satisfying a specification or that (2) return objects conforming to a certain specification. All of our results have been formally verified in the interactive theorem prover Coq.

A Behavioral Synthesis Frontend to the Haste/TiDE Design Flow

This paper presents a complete design tool which performs automatic behavioral synthesis of asynchronous circuits (resource sharing, scheduling and binding).The tool targets a traditional control-datapath-style template architecture. Within the limitations set by this template architecture it is possible to optimize for area (which is our main focus) or for speed. This is done by simply using different cost functions.Input to the tool is a behavioral description in the Haste language, and output from the tool is a Haste program describing the synthesized implementation consisting of adatapath and a controller. The tool may be seen as an add-on to the Haste/TiDE tool flow, and it can be used to automatically optimize parts of a design and to quickly explore alternative optimizations. The paper outlines the design flow, explains key elements of the design tool, and presents a number of benchmark results.

Modular verification of linked lists with views via separation logic

We present a separation logic specification and verification of linked lists with views, a data structure from the C5 collection library for C#. A view is a generalization of the well-known concept of an iterator. Linked lists with views form an interesting case study for verification since they allow mutation of multiple possibly-overlapping views of the same underlying list. For modularity, we present our specification in a fragment of higher-order separation logic and use abstract predicates to give a specification with respect to which clients can be proved correct. We introduce a novel mathematical model of lists with views, and formulate succinct modular abstract specifications of the operations on the data structure. To show that the concrete implementation realizes the specification, we use fractional permissions in a novel way to capture the sharing of data between views and their underlying list. We conclude by suggesting directions for future research that arose from conducting this case study.

Structure and binding properties of a cameloid nanobody raised against KDM5B

The histone demethylase KDM5B is considered to be a promising target for anticancer therapy. Single-chain antibodies from llama (nanobodies) have been raised to aid in crystallization and structure determination of this enzyme. The antigen-binding properties of 15 of these nanobodies have been characterized. The crystal structure of one of these (NB17) has been determined to a resolution of 1.85 Å. NB17 crystallizes in space group P4322 with six molecules in the asymmetric unit. The six molecules in the asymmetric unit pack as an entity with approximate D3 symmetry with interactions mediated by the CDR loops, which could act as a crystallization nucleus. NB17 does not bind to monomeric KDM5B residues 1-820, but is found to bind to aggregates formed after incubation at 310 K.