1,944 research outputs found

    Using Emulation to Engineer and Understand Simulations of Biological Systems

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    Modeling and simulation techniques have demonstrated success in studying biological systems. As the drive to better capture biological complexity leads to more sophisticated simulators, it becomes challenging to perform statistical analyses that help translate predictions into increased understanding. These analyses may require repeated executions and extensive sampling of high-dimensional parameter spaces: analyses that may become intractable due to time and resource limitations. Significant reduction in these requirements can be obtained using surrogate models, or emulators, that can rapidly and accurately predict the output of an existing simulator. We apply emulation to evaluate and enrich understanding of a previously published agent-based simulator of lymphoid tissue organogenesis, showing an ensemble of machine learning techniques can reproduce results obtained using a suite of statistical analyses within seconds. This performance improvement permits incorporation of previously intractable analyses, including multi-objective optimization to obtain parameter sets that yield a desired response, and Approximate Bayesian Computation to assess parametric uncertainty. To facilitate exploitation of emulation in simulation-focused studies, we extend our open source statistical package, spartan, to provide a suite of tools for emulator development, validation, and application. Overcoming resource limitations permits enriched evaluation and refinement, easing translation of simulator insights into increased biological understanding

    Two-photon quantum walks in an elliptical direct-write waveguide array

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    Integrated optics provides an ideal test bed for the emulation of quantum systems via continuous-time quantum walks. Here we study the evolution of two-photon states in an elliptic array of waveguides. We characterise the photonic chip via coherent-light tomography and use the results to predict distinct differences between temporally indistinguishable and distinguishable two-photon inputs which we then compare with experimental observations. Our work highlights the feasibility for emulation of coherent quantum phenomena in three-dimensional waveguide structures.Comment: 8 pages, 7 figure

    Analogue Quantum Simulation: A Philosophical Prospectus

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    This paper provides the first systematic philosophical analysis of an increasingly important part of modern scientific practice: analogue quantum simulation. We introduce the distinction between `simulation' and `emulation' as applied in the context of two case studies. Based upon this distinction, and building upon ideas from the recent philosophical literature on scientific understanding, we provide a normative framework to isolate and support the goals of scientists undertaking analogue quantum simulation and emulation. We expect our framework to be useful to both working scientists and philosophers of science interested in cutting-edge scientific practice

    Heterogeneity in pure microbial systems: experimental measurements and modeling

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    Cellular heterogeneity influences bioprocess performance in ways that until date are not completely elucidated. In order to account for this phenomenon in the design and operation of bioprocesses, reliable analytical and mathematical descriptions are required. We present an overview of the single cell analysis, and the mathematical modeling frameworks that have potential to be used in bioprocess control and optimization, in particular for microbial processes. In order to be suitable for bioprocess monitoring, experimental methods need to be high throughput and to require relatively short processing time. One such method used successfully under dynamic conditions is flow cytometry. Population balance and individual based models are suitable modeling options, the latter one having in particular a good potential to integrate the various data collected through experimentation. This will be highly beneficial for appropriate process design and scale up as a more rigorous approach may prevent a priori unwanted performance losses. It will also help progressing synthetic biology applications to industrial scale

    Analogue Quantum Simulation: A Philosophical Prospectus

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    This paper provides the first systematic philosophical analysis of an increasingly important part of modern scientific practice: analogue quantum simulation. We introduce the distinction between `simulation' and `emulation' as applied in the context of two case studies. Based upon this distinction, and building upon ideas from the recent philosophical literature on scientific understanding, we provide a normative framework to isolate and support the goals of scientists undertaking analogue quantum simulation and emulation. We expect our framework to be useful to both working scientists and philosophers of science interested in cutting-edge scientific practice

    Impact of alife simulation of Darwinian and Lamarckian evolutionary theories

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    Dissertation presented as the partial requirement for obtaining a Master's degree in Information Management, specialization in Information Systems and Technologies ManagementUntil nowadays, the scientific community firmly rejected the Theory of Inheritance of Acquired Characteristics, a theory mostly associated with the name of Jean-Baptiste Lamarck (1774-1829). Though largely dismissed when applied to biological organisms, this theory found its place in a young discipline called Artificial Life. Based on the two abstract models of Darwinian and Lamarckian evolutionary theories built using neural networks and genetic algorithms, this research aims to present a notion of the potential impact of implementation of Lamarckian knowledge inheritance across disciplines. In order to obtain our results, we conducted a focus group discussion between experts in biology, computer science and philosophy, and used their opinions as qualitative data in our research. As a result of completing the above procedure, we have found some implications of such implementation in each mentioned discipline. In synthetic biology, this means that we would engineer organisms precisely up to our specific needs. At the moment, we can think of better drugs, greener fuels and dramatic changes in chemical industry. In computer science, Lamarckian evolutionary algorithms have been used for quite some years, and quite successfully. However, their application in strong ALife can only be approximated based on the existing roadmaps of futurists. In philosophy, creating artificial life seems consistent with nature and even God, if there is one. At the same time, this implementation may contradict the concept of free will, which is defined as the capacity for an agent to make choices in which the outcome has not been determined by past events. This study has certain limitations, which means that larger focus group and more prepared participants would provide more precise results

    Noise Reduction in Complex Biological Switches

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    Cells operate in noisy molecular environments via complex regulatory networks. It is possible to understand how molecular counts are related to noise in specific networks, but it is not generally clear how noise relates to network complexity, because different levels of complexity also imply different overall number of molecules. For a fixed function, does increased network complexity reduce noise, beyond the mere increase of overall molecular counts? If so, complexity could provide an advantage counteracting the costs involved in maintaining larger networks. For that purpose, we investigate how noise affects multistable systems, where a small amount of noise could lead to very different outcomes; thus we turn to biochemical switches. Our method for comparing networks of different structure and complexity is to place them in conditions where they produce exactly the same deterministic function. We are then in a good position to compare their noise characteristics relatively to their identical deterministic traces. We show that more complex networks are better at coping with both intrinsic and extrinsic noise. Intrinsic noise tends to decrease with complexity, and extrinsic noise tends to have less impact. Our findings suggest a new role for increased complexity in biological networks, at parity of function

    Digital system for spiking neural network emulation

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    The present project is about the design, simulation and an experimentational test of a digital system in a single chip able to emulate the behavior of spiking neural networks, which is possible thanks to the use of mathematical models that emulate the behavior of these networks in the brain. A modular system has been proposed in order to provide the necessary flexibility and scalability for the simulation of different neural networks. At the same time the most flexible, simple and efficient option has been chosen in order to have a good performance without losing or reducing the necessary accuracy and exactitude for the emulation of the neural networks. The solution has been implemented by making use of different combinational blocks and totally synchronous flip-flops from a 100 MHz clock signal, besides, the description of the system was performed by using the high-level hardware description language VHDL. Finally, a neural network for pattern recognition has been implemented on a programmable logical device FPGA in order to demonstrate the correct operation of the digital system
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