Hybrid automata, reachability, and Systems Biology

Hybrid automata are a powerful formalism for the representation of systems evolving according to both discrete and continuous laws. Unfortunately, undecidability soon emerges when one tries to automatically verify hybrid automata properties. An important verification problem is the reachability one that demands to decide whether a set of points is reachable from a starting region.If we focus on semi-algebraic hybrid automata the reachability problem is semi-decidable. However, high computational costs have to be afforded to solve it. We analyse this problem by exploiting some existing tools and we show that even simple examples cannot be efficiently solved. It is necessary to introduce approximations to reduce the number of variables, since this is the main source of runtime requirements. We propose some standard approximation methods based on Taylor polynomials and ad hoc strategies. We implement our methods within the software SAHA-Tool and we show their effectiveness on two biological examples: the Repressilator and the Delta-Notch protein signaling.     

PHON: A program to calculate phonons using the small displacement method

The program phon calculates force constant matrices and phonon frequencies in crystals. From the frequencies it also calculates various thermodynamic quantities, like the Helmholtz free energy, the entropy, the specific heat and the internal energy of the harmonic crystal. The procedure is based on the small displacement method, and can be used in combination with any program capable to calculate forces on the atoms of the crystal. In order to examine the usability of the method, I present here two examples: metallic Al and insulating MgO. The phonons of these two materials are calculated using density functional theory. The small displacement method results are compared with those obtained using the linear response method. In the case of Al the method provides accurate phonon frequencies everywhere in the Brillouin Zone (BZ). In the case of MgO the longitudinal branch of the optical phonons near the centre of the BZ is incorrectly described as degenerate with the two transverse branches, because the non-analytical part of the dynamical matrix is ignored here; however, thermodynamic properties like the Helmholtz free are essentially unaffected.

Program summary

Program title: PHONCatalogue identifier: AEDP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDP_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 19 580No. of bytes in distributed program, including test data, etc.: 612 193Distribution format: tar.gzProgramming language: Fortran 90Computer: Any Unix, LinuxOperating system: UnixRAM: Depends on super-cell size, but usually negligibleClassification: 7.8External routines: Subprograms ZHEEV and DSYEV (Lapack); needs BLAS. A tutorial is provided with the distribution which requires the installation of the quantum-espresso package (http://www.quantum-espresso.org)Nature of problem: Stable crystals at low temperature can be well described by expanding the potential energy around the atomic equilibrium positions. The movements of the atoms around their equilibrium positions can then be described using harmonic theory, and is characterised by global vibrations called phonons, which can be identified by vectors in the Brillouin zone of the crystal, and there are 3 phonon branches for each atom in the primitive cell. The problem is to calculate the frequencies of these phonons for any arbitrary choice of q-vector in the Brillouin zone.Solution method: The small displacement method: each atom in the primitive cell is displaced by a small amount, and the forces induced on all the other atoms in the crystal are calculated and used to construct the force constant matrix. Supercells of ∼100 atoms are usually large enough to describe the force constant matrix up to the range where its elements have fallen to negligibly small values. The force constant matrix is then used to compute the dynamical matrix at any chosen q-vector in the Brillouin zone, and the diagonalisation of the dynamical matrix provides the squares of the phonon frequencies. The PHON code needs external programs to calculate these forces, and it can be used with any program capable of calculating forces in crystals. The most useful applications are obtained with codes based on density functional theory, but there is no restriction on what can be used.Running time: Negligible, typically a few seconds (or at most a few minutes) on a PC. It can take longer if very dense meshes of q-points are needed, for example, to compute very accurate phonon density of states.     

Lane-change detection using a computational driver model

OBJECTIVE: This paper introduces a robust, real-time system for detecting driver lane changes. Background: As intelligent transportation systems evolve to assist drivers in their intended behaviors, the systems have demonstrated a need for methods of inferring driver intentions and detecting intended maneuvers. METHOD: Using a "model tracing" methodology, our system simulates a set of possible driver intentions and their resulting behaviors using a simplification of a previously validated computational model of driver behavior. The system compares the model's simulated behavior with a driver's actual observed behavior and thus continually infers the driver's unobservable intentions from her or his observable actions. RESULTS: For data collected in a driving simulator, the system detects 82% of lane changes within 0.5 s of maneuver onset (assuming a 5% false alarm rate), 93% within 1 s, and 95% before the vehicle moves one fourth of the lane width laterally. For data collected from an instrumented vehicle, the system detects 61% within 0.5 s, 77% within 1 s, and 84% before the vehicle moves one-fourth of the lane width laterally. CONCLUSION: The model-tracing system is the first system to demonstrate high sample-by-sample accuracy at low false alarm rates as well as high accuracy over the course of a lane change with respect to time and lateral movement. APPLICATION: By providing robust real-time detection of driver lane changes, the system shows good promise for incorporation into the next generation of intelligent transportation systems.     

Evolutionary morphogenesis for multi-cellular systems

With a gene required for each phenotypic trait, direct genetic encodings may show poor scalability to increasing phenotype length. Developmental systems may alleviate this problem by providing more efficient indirect genotype to phenotype mappings. A novel classification of multi-cellular developmental systems in evolvable hardware is introduced. It shows a category of developmental systems that up to now has rarely been explored. We argue that this category is where most of the benefits of developmental systems lie (e.g. speed, scalability, robustness, inter-cellular and environmental interactions that allow fault-tolerance or adaptivity). This article describes a very simple genetic encoding and developmental system designed for multi-cellular circuits that belongs to this category. We refer to it as the morphogenetic system. The morphogenetic system is inspired by gene expression and cellular differentiation. It focuses on low computational requirements which allows fast execution and a compact hardware implementation. The morphogenetic system shows better scalability compared to a direct genetic encoding in the evolution of structures of differentiated cells, and its dynamics provides fault-tolerance up to high fault rates. It outperforms a direct genetic encoding when evolving spiking neural networks for pattern recognition and robot navigation. The results obtained with the morphogenetic system indicate that this “minimalist” approach to developmental systems merits further study.

Analysis and implementation of the multiprocessor bandwidth inheritance protocol

The Multiprocessor Bandwidth Inheritance (M-BWI) protocol is an extension of the Bandwidth Inheritance (BWI) protocol for symmetric multiprocessor systems. Similar to Priority Inheritance, M-BWI lets a task that has locked a resource execute in the resource reservations of the blocked tasks, thus reducing their blocking time. The protocol is particularly suitable for open systems where different kinds of tasks dynamically arrive and leave, because it guarantees temporal isolation among independent subsets of tasks without requiring any information on their temporal parameters. Additionally, if the temporal parameters of the interacting tasks are known, it is possible to compute an upper bound to the interference suffered by a task due to other interacting tasks. Thus, it is possible to provide timing guarantees for a subset of interacting hard real-time tasks. Finally, the M-BWI protocol is neutral to the underlying scheduling policy: it can be implemented in global, clustered and semi-partitioned scheduling. After introducing the M-BWI protocol, in this paper we formally prove its isolation properties, and propose an algorithm to compute an upper bound to the interference suffered by a task. Then, we describe our implementation of the protocol for the?LITMUS ^RT real-time testbed, and measure its overhead. Finally, we compare M-BWI against FMLP and OMLP, two other protocols for resource sharing in multiprocessor systems.     

A platform for the development of patient applications in the domain of personalized health

Personalized health (p-health) systems can contribute significantly to the sustainability of healthcare systems, though their feasibility is yet to be proven. One of the problems related to their development is the lack of well-established development tools for this domain. As the p-health paradigm is focused on patient self-management, big challenges arise around the design and implementation of patient systems. This paper presents a reference platform created for the development of these applications, and shows the advantages of its adoption in a complex project dealing with cardio-vascular diseases.     

Proactive thermal management in green datacenters

The increasing demand for faster computing and high storage capacity has resulted in an increase in energy consumption and heat generation in datacenters. Because of the increase in heat generation, cooling requirements have become a critical concern, both in terms of growing operating costs as well as their environmental and societal impacts. Presently, thermal management techniques make an effort to thermally profile and control datacenters’ cooling equipment to increase their efficiency. In conventional thermal management techniques, cooling systems are triggered by the temperature crossing predefined thresholds. Such reactive approaches result in delayed response as the temperature may already be too high, which can result in performance degradation of hardware.     

Near-infrared photodetection with a diruthenium complex having redox-switchable wavelength response

We report on the electrochromic behavior of a dinuclear ruthenium complex, which provides high environmental stability together with an intense absorption maximum at 1237 nm in solution in its +3 oxidation state. To verify its optoelectronic properties, we used this complex as the photoactive material in a planar photodetector prototype for near-infrared light pulses, succeeding in the detection of a train of light pulses at a wavelength of 1280 nm.     

Is Java really secure?

During a recent conference on Information Security, a group of experts raised the issue of the potential problems with the security of Java, initiating an interesting discussion between the developers and technicians at Sun Microsystems. This article considers Java security from an Italian perspective.     

Metabolic Pathways for Observed Impacts of Crop Load on Floral Induction in Apple

The triggers of biennial bearing are thought to coincide with embryonic development in apple and occurs within the first 70 days after full bloom (DAFB). Strong evidence suggests hormonal signals are perceived by vegetative apple spur buds to induce flowering. The hormonal response is typically referred to as the floral induction (FI) phase in bud meristem development. To determine the metabolic pathways activated in FI, young trees of the biennial bearing cultivar ‘Nicoter’ and the less susceptible cultivar ‘Rosy Glow’ were forced into an alternate cropping cycle over five years and an inverse relationship of crop load and return bloom was established. Buds were collected over a four-week duration within 70 DAFB from trees that had maintained a four-year biennial bearing cycle. Metabolomics profiling was undertaken to determine the differentially expressed pathways and key signalling molecules associated with biennial bearing. Marked metabolic differences were observed in trees with high and low crop load treatments. Significant effects were detected in members of the phenylpropanoid pathway comprising hydroxycinnamates, salicylates, salicylic acid biosynthetic pathway intermediates and flavanols. This study identifies plant hormones associated with FI in apples using functional metabolomics analysis.