Abstract:
In this paper bounded model checking of asynchronous concurrent systems is introduced as a promising application area for answer set programming. As the model of asynchronous systems a generalisation of communicating automata, 1-safe Petri nets, are used. It is shown how a 1-safe Petri net and a requirement on the behaviour of the net can be translated into a logic program such that the bounded model checking problem for the net can be solved by computing stable models of the corresponding program. The use of the stable model semantics leads to compact encodings of bounded reachability and deadlock detection tasks as well as the more general problem of bounded model checking of linear temporal logic. Correctness proofs of the devised translations are given, and some experimental results using the translation and the Smodels system are presented.

Abstract:
Answer set programming (ASP) is a paradigm for declarative problem solving where problems are first formalized as rule sets, i.e., answer-set programs, in a uniform way and then solved by computing answer sets for programs. The satisfiability modulo theories (SMT) framework follows a similar modelling philosophy but the syntax is based on extensions of propositional logic rather than rules. Quite recently, a translation from answer-set programs into difference logic was provided---enabling the use of particular SMT solvers for the computation of answer sets. In this paper, the translation is revised for another SMT fragment, namely that based on fixed-width bit-vector theories. Thus, even further SMT solvers can be harnessed for the task of computing answer sets. The results of a preliminary experimental comparison are also reported. They suggest a level of performance which is similar to that achieved via difference logic.

Abstract:
Propositional satisfiability (SAT) solvers, which typically operate using conjunctive normal form (CNF), have been successfully applied in many domains. However, in some application areas such as circuit verification, bounded model checking, and logical cryptanalysis, instances can have many parity (xor) constraints which may not be handled efficiently if translated to CNF. Thus, extensions to the CNF-driven search with various parity reasoning engines ranging from equivalence reasoning to incremental Gaussian elimination have been proposed. This paper studies how stronger parity reasoning techniques in the DPLL(XOR) framework can be simulated by simpler systems: resolution, unit propagation, and parity explanations. Such simulations are interesting, for example, for developing the next generation SAT solvers capable of handling parity constraints efficiently.

Abstract:
Instances of logical cryptanalysis, circuit verification, and bounded model checking can often be succinctly represented as a combined satisfiability (SAT) problem where an instance is a combination of traditional clauses and parity constraints. This paper studies how such combined problems can be efficiently solved by augmenting a modern SAT solver with an xor-reasoning module in the DPLL(XOR) framework. A new xor-reasoning module that deduces all possible implied literals using incremental Gauss-Jordan elimination is presented. A decomposition technique that can greatly reduce the size of parity constraint matrices while allowing still to deduce all implied literals is presented. It is shown how to eliminate variables occuring only in parity constraints while preserving the decomposition. The proposed techniques are evaluated experimentally.

Abstract:
Modeling time related aspects is important in many applications of verification methods. For precise results, it is necessary to interpret time as a dense domain, e.g. using timed automata as a formalism, even though the system's resulting infinite state space is challenging for verification methods. Furthermore, fully symbolic treatment of both timing related and non-timing related elements of the state space seems to offer an attractive approach to model checking timed systems with a large amount of non-determinism. This paper presents an SMT-based timed system extension to the IC3 algorithm, a SAT-based novel, highly efficient, complete verification method for untimed systems. Handling of the infinite state spaces of timed system in the extended IC3 algorithm is based on suitably adapting the well-known region abstraction for timed systems. Additionally, $k$-induction, another symbolic verification method for discrete time systems, is extended in a similar fashion to support timed systems. Both new methods are evaluated and experimentally compared to a booleanization-based verification approach that uses the original discrete time IC3 algorithm.

Abstract:
Modern conflict-driven clause learning (CDCL) SAT solvers are very good in solving conjunctive normal form (CNF) formulas. However, some application problems involve lots of parity (xor) constraints which are not necessarily efficiently handled if translated into CNF. This paper studies solving CNF formulas augmented with xor-clauses in the DPLL(XOR) framework where a CDCL SAT solver is coupled with a separate xor-reasoning module. New techniques for analyzing xor-reasoning derivations are developed, allowing one to obtain smaller CNF clausal explanations for xor-implied literals and also to derive and learn new xor-clauses. It is proven that these new techniques allow very short unsatisfiability proofs for some formulas whose CNF translations do not have polynomial size resolution proofs, even when a very simple xor-reasoning module capable only of unit propagation is applied. The efficiency of the proposed techniques is evaluated on a set of challenging logical cryptanalysis instances.

Abstract:
Timed automata (TAs) are a common formalism for modeling timed systems. Bounded model checking (BMC) is a verification method that searches for runs violating a property using a SAT or SMT solver. MITL is a real-time extension of the linear time logic LTL. Originally, MITL was defined for traces of non-overlapping time intervals rather than the "super-dense" time traces allowing for intervals overlapping in single points that are employed by the nowadays common semantics of timed automata. In this paper we extend the semantics of a fragment of MITL to super-dense time traces and devise a bounded model checking encoding for the fragment. We prove correctness and completeness in the sense that using a sufficiently large bound a counter-example to any given non-holding property can be found. We have implemented the proposed bounded model checking approach and experimentally studied the efficiency and scalability of the implementation.

Abstract:
Parity constraints, common in application domains such as circuit verification, bounded model checking, and logical cryptanalysis, are not necessarily most efficiently solved if translated into conjunctive normal form. Thus, specialized parity reasoning techniques have been developed in the past for propagating parity constraints. This paper studies the questions of deciding whether unit propagation or equivalence reasoning is enough to achieve full propagation in a given parity constraint set. Efficient approximating tests for answering these questions are developed. It is also shown that equivalence reasoning can be simulated by unit propagation by adding a polynomial amount of redundant parity constraints to the problem. It is proven that without using additional variables, an exponential number of new parity constraints would be needed in the worst case. The presented classification and propagation methods are evaluated experimentally.

Abstract:
In the future liquid biofuels will need to be renewable, sustainable, as well as technically and economically viable. This paper provides an overview of the challenges that the biochemical production of cellulosic ethanol process still faces. The main emphasis of the paper is on challenges that emerge from the scale of liquid biofuel production. These challenges include raw material availability, other consumables, and side stream handling. The pretreatment, C5 fermentation, and concentration of sugars in processing need improvements, too. Sustainability issues and greenhouse gas reduction also pose a challenge for implementation and require development of internationally recognized sustainability principles and standards, and certification of sustainable operation. Economics of cellulosic ethanol processes are still also an area under development and debate. Yet, the Energy Independence and Security Act mandate together with the European Union Renewable Energy Directive and other local targets are driving the development and implementation forward towards more significant contribution of biofuels in the transportation sector.

Abstract:
Our aim was to compare the effects of calcium carbonate and sevelamer-HCl treatments on calcium-phosphate metabolism and renal function in 5/6 nephrectomized (NX) rats so that long-term disease progression preceded the treatment. After 15-week progression, calcium carbonate (3.0%), sevelamer-HCl (3.0%), or control diets (0.3% calcium) were given for 9 weeks. Subtotal nephrectomy reduced creatinine clearance (？40%), plasma calcidiol (？25%), and calcitriol (？70%) and increased phosphate (+37%), parathyroid hormone (PTH) (11-fold), and fibroblast growth factor-23 (FGF-23) (4-fold). In NX rats, calcium carbonate diet increased plasma (+20%) and urinary calcium (6-fold), reduced plasma phosphate (？50%) and calcidiol (？30%), decreased creatinine clearance (？35%) and FGF 23 (？85%), and suppressed PTH without influencing blood pH. In NX rats, sevelamer-HCl increased urinary calcium (4-fold) and decreased creatinine clearance (？45%), PTH (？75%), blood pH (by 0.20 units), plasma calcidiol (？40%), and calcitriol (？65%). Plasma phosphate and FGF-23 were unchanged. In conclusion, when initiated after long-term progression of experimental renal insufficiency, calcium carbonate diet reduced plasma phosphate and FGF-23 while sevelamer-HCl did not. The former induced hypercalcemia, the latter induced acidosis, while both treatments reduced vitamin D metabolites and deteriorated renal function. Thus, delayed initiation influences the effects of these phosphate binders in remnant kidney rats. 1. Introduction Cardiovascular disease is a major cause of mortality in chronic renal insufficiency (CRI) with a 20-fold increase in the risk of cardiovascular death compared with normal population [1]. Hyperphosphatemia and secondary hyperparathyroidism (SHPT) [2] significantly contribute to the cardiovascular pathology and mineral-bone disorders in CRI. In order to halt these changes, oral phosphate binders such as calcium carbonate and sevelamer are widely used. High intake of calcium carbonate may predispose to vascular calcifications in CRI, especially if the phosphate levels remain inappropriately high [2]. Consequently, treatment with sevelamer, a calcium- and aluminium-free and nonabsorbable polyallylamine anion exchange resin, may result in less vascular calcifications and reduced mortality in dialysis patients. However, according to recent Cochrane review, the superiority of sevelamer over calcium carbonate remains unclear [3]. In experimental animal models, increased calcium intake has resulted in beneficial effects on blood pressure (BP), endothelial function,