312,474 research outputs found

    The role of Computer Aided Process Engineering in physiology and clinical medicine

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    This paper discusses the potential role for Computer Aided Process Engineering (CAPE) in developing engineering analysis and design approaches to biological systems across multiple levels—cell signalling networks, gene, protein and metabolic networks, cellular systems, through to physiological systems. The 21st Century challenge in the Life Sciences is to bring together widely dispersed models and knowledge in order to enable a system-wide understanding of these complex systems. This systems level understanding should have broad clinical benefits. Computer Aided Process Engineering can bring systems approaches to (i) improving understanding of these complex chemical and physical (particularly molecular transport in complex flow regimes) interactions at multiple scales in living systems, (ii) analysis of these models to help to identify critical missing information and to explore the consequences on major output variables resulting from disturbances to the system, and (iii) ‘design’ potential interventions in in vivo systems which can have significant beneficial, or potentially harmful, effects which need to be understood. This paper develops these three themes drawing on recent projects at UCL. The first project has modeled the effects of blood flow on endothelial cells lining arteries, taking into account cell shape change resulting in changes in the cell skeleton which cause consequent chemical changes. A second is a project which is building an in silico model of the human liver, tieing together models from the molecular level to the liver. The composite model models glucose regulation in the liver and associated organs. Both projects involve molecular transport, chemical reactions, and complex multiscale systems, tackled by approaches from CAPE. Chemical Engineers solve multiple scale problems in manufacturing processes – from molecular scale through unit operations scale to plant-wide and enterprise wide systems – so have an appropriate skill set for tackling problems in physiology and clinical medicine, in collaboration with life and clinical scientists

    Nano-scale reservoir computing

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    This work describes preliminary steps towards nano-scale reservoir computing using quantum dots. Our research has focused on the development of an accumulator-based sensing system that reacts to changes in the environment, as well as the development of a software simulation. The investigated systems generate nonlinear responses to inputs that make them suitable for a physical implementation of a neural network. This development will enable miniaturisation of the neurons to the molecular level, leading to a range of applications including monitoring of changes in materials or structures. The system is based around the optical properties of quantum dots. The paper will report on experimental work on systems using Cadmium Selenide (CdSe) quantum dots and on the various methods to render the systems sensitive to pH, redox potential or specific ion concentration. Once the quantum dot-based systems are rendered sensitive to these triggers they can provide a distributed array that can monitor and transmit information on changes within the material.Comment: 8 pages, 9 figures, accepted for publication in Nano Communication Networks, http://www.journals.elsevier.com/nano-communication-networks/. An earlier version was presented at the 3rd IEEE International Workshop on Molecular and Nanoscale Communications (IEEE MoNaCom 2013

    Path mutual information for a class of biochemical reaction networks

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    Living cells encode and transmit information in the temporal dynamics of biochemical components. Gaining a detailed understanding of the input-output relationship in biological systems therefore requires quantitative measures that capture the interdependence between complete time trajectories of biochemical components. Mutual information provides such a measure but its calculation in the context of stochastic reaction networks is associated with mathematical challenges. Here we show how to estimate the mutual information between complete paths of two molecular species that interact with each other through biochemical reactions. We demonstrate our approach using three simple case studies.Comment: 6 pages, 2 figure

    Satisfiability, sequence niches, and molecular codes in cellular signaling

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    Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling involves somewhat fuzzy and promiscuous recognition of molecular sequences and structures, which can leave systems vulnerable to crosstalk. This paper examines a simple computational model of protein-protein interactions which reveals both a sharp onset of crosstalk and a fragmentation of the neutral network of viable solutions as more proteins compete for regions of sequence space, revealing intrinsic limits to reliable signaling in the face of promiscuity. These results suggest connections to both phase transitions in constraint satisfaction problems and coding theory bounds on the size of communication codes

    Molecular quantum spin network controlled by a single qubit

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    Scalable quantum technologies will require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. Here we present the working principle of such a basic unit, engineered using molecular chemistry, whose control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular sidegroups separated by a few nanometers. We demonstrate the readout and coherent manipulation of very few (≤6\leq 6 ) of these S=1/2S=1/2 electronic spin systems and access their direct dipolar coupling tensor. Our results show, that it is feasible to use spin-labeled peptides as a resource for a molecular-qubit based network, while at the same time providing simple optical readout of single quantum states through NV-magnetometry. This work lays the foundation for building arbitrary quantum networks using well-established chemistry methods, which has many applications ranging from mapping distances in single molecules to quantum information processing.Comment: Author name typ
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