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

Computer Aided Verification

This open access two-volume set LNCS 11561 and 11562 constitutes the refereed proceedings of the 31st International Conference on Computer Aided Verification, CAV 2019, held in New York City, USA, in July 2019. The 52 full papers presented together with 13 tool papers and 2 case studies, were carefully reviewed and selected from 258 submissions. The papers were organized in the following topical sections: Part I: automata and timed systems; security and hyperproperties; synthesis; model checking; cyber-physical systems and machine learning; probabilistic systems, runtime techniques; dynamical, hybrid, and reactive systems; Part II: logics, decision procedures; and solvers; numerical programs; verification; distributed systems and networks; verification and invariants; and concurrency

Computer Aided Verification

This open access two-volume set LNCS 11561 and 11562 constitutes the refereed proceedings of the 31st International Conference on Computer Aided Verification, CAV 2019, held in New York City, USA, in July 2019. The 52 full papers presented together with 13 tool papers and 2 case studies, were carefully reviewed and selected from 258 submissions. The papers were organized in the following topical sections: Part I: automata and timed systems; security and hyperproperties; synthesis; model checking; cyber-physical systems and machine learning; probabilistic systems, runtime techniques; dynamical, hybrid, and reactive systems; Part II: logics, decision procedures; and solvers; numerical programs; verification; distributed systems and networks; verification and invariants; and concurrency

Essays on Numerical Evaluation of Derivatives

In general, this thesis contemplates the potential of series expansion methods in evaluating financial derivatives. Recently, instead of relying on closed-form solutions, the usage of numerical methods became increasingly popular. The contribution of the thesis at hand is three-folded: First, we present and analyze a new method to price European options that are written on a single underlying asset by introducing Gabor series methods into option pricing. The resulting procedure shows to be a very robust pricing tool with a special strength in calculating short-term contracts. Second, we dedicate our attention to multi-asset derivatives. Multi-asset contracts are notoriously hard to deal with in case the user demands both, advanced stochastic processes and fast evaluation. Compared to single underlying derivatives, these multi-asset exotic options are studied to a much lower degree. We focus on European multi-asset options as well as on discrete barrier multi-asset options. To the best of our knowledge, the valuation of multi-asset barrier options in terms of multi-dimensional Fourier series methods has not been addressed in literature before. Third, as recent events in the market for credit risk have shown, there is a need for further research in methods to evaluate credit derivatives. Therefore, we focused on extending the standard Gaussian factor model to price synthetic collateralized debt obligations. The new models are able to cope with a wide range of market conditions. However, given a crisis as severe as the financial crisis of 2008, questions, such as market liquidity, that are outside the scope of pure modeling overlay the approximation quality. Nevertheless, the models presented are flexible instruments to price synthetic collateralized debt obligations while still staying in the intuitive framework of a factor model

Conference on Charge-Coupled Device Technology and Applications

Papers were presented from the conference on charge coupled device technology and applications. The following topics were investigated: data processing; infrared; devices and testing; electron-in, x-ray, radiation; and applications. The emphasis was on the advances of mutual relevance and potential significance both to industry and NASA's current and future requirements in all fields of imaging, signal processing and memory

Knowledge of knots: shapes in action

Logic is to natural language what knot theory is to natural knots. Logic is concerned with some cognitive performances; in particular, some natural language inferences are captured by various types of calculi (propositional, predicate, modal, deontic, quantum, probabilistic, etc.), which in turn may generate inferences that are arguably beyond natural logic abilities, or non-well synchronized therewith (eg. ex falso quodlibet, material implication). Mathematical knot theory accounts for some abilities - such as recognizing sameness or differences of some knots, and in turn generates a formalism for distinctions that common sense is blind to. Logic has proven useful in linguistics and in accounting for some aspects of reasoning, but which knotting performaces are there, over and beyond some intuitive discriminating abilities, that may require extensions or restrictions of the normative calculus of knots? Are they amenable to mathematical treatment? And what role is played in the game by mental representations? I shall draw from a corpus of techniques and practices to show to what extent compositionality, lexical and normative elements are present in natural knots, with the prospect of formally exploring an area of human competence that interfaces thought, perception and action in a complex fabric

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

The discrimination and representation of relative and absolute number in pigeons and humans.

The ability to discriminate relative and absolute number has been researched widely in both human and nonhuman species. However, the full extent of numerical ability in nonhuman animals, and the nature of the underlying numerical representation, on which discriminations are based, is still unclear. The aim of the current research was to examine the performance of pigeons and humans in tasks that require the discrimination of relative number (a bisection procedure), and absolute number (in a reproduction procedure). One of the main research questions was whether numerical control over responding could be obtained, above and beyond control by temporal cues in nonhuman animals, and if so, whether it was possible to quantify the relative influences of number and time on responding. Experiment 1 examines nonhuman performance in a numerical bisection task; subjects were presented with either 2 and 6, 4 and 12, or 8 and 24 keylight flashes across three different conditions, and were required to classify these flash sequences as either a “large” or “small” number, by pecking the blue or white key, respectively. Subjects were then tested with novel values within and 2 values higher and lower than the training values. Experiments 2-4 investigate responding in a novel numerical reproduction procedure, in which pigeons were trained to match the number of responses made during a production phase to the number of keylight flashes (2, 4, or 6) in a recently completed sample phase. Experiments 2 and 2A examined discrimination performance when the temporal variables, flash rate and sample phase duration, were perfectly correlated (Experiment 2) or only weakly correlated (Experiment 2a) with flash number. Acquisition of performance in the numerical reproduction procedure was investigated in Experiment 3. For Experiments 1-3, hierarchical regression analyses showed significant control by number over responding, after controlling for temporal cues. Additionally, positive transfer to novel values both within and outside the training range was obtained when the temporal organization of test sequences was similar to baseline training. Experiment 4 investigated the effects of increasing or decreasing the retention interval (RI) on performance in the reproduction procedure, and found this produced a response bias towards larger numbers, contrary to predictions based on previous RI research, and suggested responding was not affected by memorial decay processes. The structure of the representation of number developed by subjects in the bisection and reproduction procedures was investigated using analyses of responding and response variability in Chapters 2 and 6, respectively. Bisection points obtained in Experiment 1 were located at the arithmetic, not geometric mean of all three scales, and coefficients of variation (CVs) obtained in both the bisection and reproduction experiments tended to decrease as flash number increased. Additionally, analyses of the acquisition data found differences in average response number was better fit by a linear than logarithmic scale. These results show that responding did not conform to scalar variability and is largely inconsistent with previous nonhuman research. Together these results suggest responding appeared to be based on a linear scale of number with constant generalisation between values, similar to that associated with human verbal counting, rather than a logarithmic scale with constant generalisation or a linear scale with scalar generalisation between values. Experiment 5 compared pigeons’ and humans’ verbal and nonverbal discrimination performance with numbers 1-20 in analogous bisection, reproduction and report tasks. Human verbal and nonverbal performance in the three tasks was similar and resembled nonhuman performance, although verbal discriminations were more accurate and less variable. The main findings from Experiments 1 and 2A were replicated with humans; bisection points were located at the arithmetic mean, average response number increased linearly as sample number increased, though there was a tendency to underestimate sample number, and decreasing CVs were also obtained for values less than 8. An additional, interesting finding was that CVs showed scalar variability for values greater than 8, suggesting a less exact representation and discrimination process was being used for these values. Collectively, these five experiments provide new evidence for a nonverbal ability to discriminate relative and absolute number with increasing relative accuracy resembling human verbal counting in both human and nonhumans

System modelling and control

Not Availabl

Gatecliff Shelter

552 p. : ill., maps ; 26 cm.Includes bibliographical references (p. 530-552)