10271 Abstracts Collection -- Verification over discrete-continuous boundaries

From 4 July 2010 to 9 July 2010, the Dagstuhl Seminar 10271 ``Verification over discrete-continuous boundaries\u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Biomolecular System Design: Architecture, Synthesis, and Simulation

The advancements in systems and synthetic biology have been broadening the range of realizable systems with increasing complexity both in vitro and in vivo. Systems for digital logic operations, signal processing, analog computation, program flow control, as well as those composed of different functions – for example an on-site diagnostic system based on multiple biomarker measurements and signal processing – have been realized successfully. However, the efforts to date tend to tackle each design problem separately, relying on ad hoc strategies rather than providing more general solutions based on a unified and extensible architecture, resulting in long development cycle and rigid systems that require redesign even for small specification changes.Inspired by well-tested techniques adopted in electronics design automation (EDA), this work aims to remedy current design methodology by establishing a standardized, complete flow for realizing biomolecular systems. Given a behavior specification, the flow streamlines all the steps from modeling, synthesis, simulation, to final technology mapping onto implementing chassis. The resulted biomolecular systems of our design flow are all built on top of an FPGA-like reconfigurable architecture with recurring modules. Each module is designed the function of eachmodule depends on the concentrations of assigned auxiliary species acting as the “tuning knobs.” Reconfigurability not only simplifies redesign for altered specification or post-simulation correction, but also makes post-manufacture fine-tuning – even after system deployment – possible. This flexibility is especially important in synthetic biology due to the unavoidable variations in both the deployed biological environment and the biomolecular reactions forming the designed system.In fact, by combining the system’s reconfigurability and neural network’s self-adaptiveness through learning, we further demonstrate the high compatibility of neuromorphic computation to our proposed architecture. Simulation results verified that with each module implementing a neuron of selected model (ex. spike-based, threshold-gate-like, etc.), accompanied by an appropriate choice of reconfigurable properties (ex. threshold value, synaptic weight, etc.), the system built from our proposed flow can indeed perform desired neuromorphic functions

\u3ci\u3eDemocracy\u27s Discontent\u3c/i\u3e in a Complex World: Can Avalanches, Sandpiles, and Finches Optimize Michael Sandel\u27s Civic Republican Community?

In Democracy\u27s Discontent: America in Search of a Public Philosophy, Michael Sandel looks about him and finds a vast and complex world governed by impersonal institutions and structures, in which discontented, anxious, and frustrated individuals are losing control over the forces that govern their lives, and in which the moral fabric of community is unraveling. His solution is to revitalize the civic strand of freedom found in republican politics and thus equip individuals to govern themselves. Sandel wonders how civic republicanism can exist in today\u27s world. Historically, republicanism has found a home in small, bounded places, which were largely self-sufficient and inhabited by people whose living conditions, education, and commonality enabled them to deliberate about public concerns. His structural answer is to disperse sovereignty both upwards and downwards of the modem nation state into a multiplicity of political communities and social institutions. His normative answer is to infuse substantive moral discourse back into public political debate

Understanding of photosynthesis concepts related to students’ age

In Croatian schools, the complex photosynthesis concept is presented several times during primary and secondary school, each time with more detail. The problems in understanding photosynthesis processes are known from many previous studies and our own research ; thus we aimed to investigate how the students’ understanding of the basic photosynthesis concepts increases during the schooling period, and is it enhanced by gradual introduction of new contents. The present study was conducted on 269 students from 6 schools and 35 students preparing to be biology teachers. To test the students’ conceptual understanding, we implemented a question about the trends of O2 and CO2 gas concentrations during the night, which was expected to lead students to a correct explanation of photosynthesis, including the issues of the plants’ respiration and the absence of photosynthesis. Students of all age groups gave mainly incomplete explanations. The best result was achieved by the youngest participants in the age of 11, who have relied on the freshly acquired and well trained, but reproductive knowledge. Older students’ answers (aged 15, 17 and 22), which include more detail about the light-dependent and light-independent reactions, suggested that they developed misconceptions such as the belief that “oxygen is produced in Calvin cycle during the night” and that “CO2 converts to O2”. Student's explanations indicate the consistency of their understanding of the process, which does not change with gradual introduction of new contents as they are older. The observed misunderstanding could be linked to the cumulative introduction of the complex theoretical contents, but excluding research- based learning, as well as to inadequate time dedicated to establishing connections between students’ pre-conceptions and novel information. Our research results might be a strong argument supporting the upcoming change in the national curriculum

A review of modelling and verification approaches for computational biology

This paper reviews most frequently used computational modelling approaches and formal verification techniques in computational biology. The paper also compares a number of model checking tools and software suits used in analysing biological systems and biochemical networks and verifiying a wide range of biological properties

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Hierarchical dynamics of individual RNA helix base pair formation and disruption

This thesis explores the RNA folding problem using single-molecule field effect transistors (smFETs) to measure the lifetimes of individual RNA base-pairing rearrangements. In the course of this research, considerable computational, chemical, and engineering contributions were developed so that the single-molecule measurements could be conducted and quantified. These advancements have allowed, on the basis of the smFET data collected herein, the quantification of a kinetic model for RNA stem-loop structures which has been generalized to quantitatively explore the phenomenological observation that an RNA found in the bacillus subtilis strain acts as a metabolite-sensing switch, allowing RNA polymerase to transcribe the messenger RNA when the metabolite is present and preventing transcription when the metabolite is absent. Together, the data presented quantify a simple model for the base pairing rearrangements that underlie RNA folding