The Experts below are selected from a list of 44805 Experts worldwide ranked by ideXlab platform
Prasanna A De Silva - One of the best experts on this subject based on the ideXlab platform.
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molecular memory with downstream Logic Processing exemplified by switchable and self indicating guest capture and release
Nature Communications, 2019Co-Authors: Brian Daly, Thomas S Moody, Allen J M Huxley, Benjamin Schazmann, Andre Alvesareias, John F Malone, H Nimal Q Gunaratne, Peter Nockemann, Prasanna A De SilvaAbstract:Molecular-Logic based computation (MLBC) has grown by accumulating many examples of combinational Logic gates and a few sequential variants. In spite of many inspirations being available in biology, there are virtually no examples of MLBC in chemistry where sequential and combinational operations are integrated. Here we report a simple alcohol-ketone redox interconversion which switches a macrocycle between a large or small cavity, with erect aromatic walls which create a deep hydrophobic space or with collapsed walls respectively. Small aromatic guests can be captured or released in an all or none manner upon chemical command. During capture, the fluorescence of the alcohol macrocycle is quenched via fluorescent photoinduced electron transfer switching, meaning that its occupancy state is self-indicated. This represents a chemically-driven RS Flip-Flop, one of whose outputs is fed into an INHIBIT gate. Processing of outputs from memory stores is seen in the injection of packaged neurotransmitters into synaptic clefts for onward neural signalling. Overall, capture-release phenomena from discrete supermolecules now have a Boolean basis. While many processes in bioLogical cells can be understood in terms of molecular Logic gates that process information sequentially and combinationally, the design and construction of such devices in the laboratory are unknown. Here the authors achieve this by the reversibly-controlled capture and release of guest molecules from host containers.
Brian Daly - One of the best experts on this subject based on the ideXlab platform.
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molecular memory with downstream Logic Processing exemplified by switchable and self indicating guest capture and release
Nature Communications, 2019Co-Authors: Brian Daly, Thomas S Moody, Allen J M Huxley, Benjamin Schazmann, Andre Alvesareias, John F Malone, H Nimal Q Gunaratne, Peter Nockemann, Prasanna A De SilvaAbstract:Molecular-Logic based computation (MLBC) has grown by accumulating many examples of combinational Logic gates and a few sequential variants. In spite of many inspirations being available in biology, there are virtually no examples of MLBC in chemistry where sequential and combinational operations are integrated. Here we report a simple alcohol-ketone redox interconversion which switches a macrocycle between a large or small cavity, with erect aromatic walls which create a deep hydrophobic space or with collapsed walls respectively. Small aromatic guests can be captured or released in an all or none manner upon chemical command. During capture, the fluorescence of the alcohol macrocycle is quenched via fluorescent photoinduced electron transfer switching, meaning that its occupancy state is self-indicated. This represents a chemically-driven RS Flip-Flop, one of whose outputs is fed into an INHIBIT gate. Processing of outputs from memory stores is seen in the injection of packaged neurotransmitters into synaptic clefts for onward neural signalling. Overall, capture-release phenomena from discrete supermolecules now have a Boolean basis. While many processes in bioLogical cells can be understood in terms of molecular Logic gates that process information sequentially and combinationally, the design and construction of such devices in the laboratory are unknown. Here the authors achieve this by the reversibly-controlled capture and release of guest molecules from host containers.
Eric H Davidson - One of the best experts on this subject based on the ideXlab platform.
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genomic control process development and evolution
2015Co-Authors: Isabelle S Peter, Eric H DavidsonAbstract:In our time, the sheer volume of published experimental measurements, their scope and technical sophistication, compounded with a proliferation of diverse approaches, objectives, and model systems, has made it particularly difficult to see the conceptual forest for the trees. Yet all of the elegant and sophisticated though disparate and unconnected data sets with which we are confronted represent bioLogical output of the same fundamental operating principles. Each experimental system provides a different window which offers a pathway to these principles. In this book we provide a conceptual framework that we hope will make accessible the principles by which the genomic control system operates developmental and evolutionary process. This framework grows from the realization that the most fundamental causal principles in biology, which distinguish biology from all other sciences, emerge from the existence and function of genomic information. From the genomic sequence are to be recovered the determinants of body plan development in animals. Of course, the processes of biology are subject to the same laws of physics and chemistry as are those of the inanimate world, but it is the genome that mandates bioLogical organization. This is not a metaphor, it is a description of mechanisms that we can now begin to perceive as an unbroken chain of causal connections, leading from the A’s, C’s, G’s and T’s of the genomic DNA to the developmental formulation of the elements of the organism. The new field that is coalescing around the concepts of genomic information Processing partakes of principles and evidence from systems biology, developmental molecular biology, various aspects of body plan evolution and phylogenetics, as well as bioLogical engineering and computational modeling. We found it useful to select and incorporate insights from all of these fields, where these illuminate the genomic control of development, without operating wholly within the paradigms of any one of them. In this book we focus on the main characteristics of the genomic control system, which include its hierarchy, its Logic Processing functions and its structural organization in the form of gene regulatory networks. Such networks encompass at a system level the recognition interactions between transcription factors and DNA sequence that lie at the heart of the whole regulatory process. The general operational properties of genomic regulatory systems are shared across the Bilateria, while diversity in animal forms directly reflects diversity in genomic developmental programs. Focus on the genomic programs controlling development provides a single conceptual lens through which the most disparate phenomena of development and evolution can be viewed, causally understood and interpreted.
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predictive computation of genomic Logic Processing functions in embryonic development
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Isabelle S Peter, Emmanuel Faure, Eric H DavidsonAbstract:Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory Logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out in silico perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test in silico regulatory circuitry and developmental perturbations.
H Nimal Q Gunaratne - One of the best experts on this subject based on the ideXlab platform.
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molecular memory with downstream Logic Processing exemplified by switchable and self indicating guest capture and release
Nature Communications, 2019Co-Authors: Brian Daly, Thomas S Moody, Allen J M Huxley, Benjamin Schazmann, Andre Alvesareias, John F Malone, H Nimal Q Gunaratne, Peter Nockemann, Prasanna A De SilvaAbstract:Molecular-Logic based computation (MLBC) has grown by accumulating many examples of combinational Logic gates and a few sequential variants. In spite of many inspirations being available in biology, there are virtually no examples of MLBC in chemistry where sequential and combinational operations are integrated. Here we report a simple alcohol-ketone redox interconversion which switches a macrocycle between a large or small cavity, with erect aromatic walls which create a deep hydrophobic space or with collapsed walls respectively. Small aromatic guests can be captured or released in an all or none manner upon chemical command. During capture, the fluorescence of the alcohol macrocycle is quenched via fluorescent photoinduced electron transfer switching, meaning that its occupancy state is self-indicated. This represents a chemically-driven RS Flip-Flop, one of whose outputs is fed into an INHIBIT gate. Processing of outputs from memory stores is seen in the injection of packaged neurotransmitters into synaptic clefts for onward neural signalling. Overall, capture-release phenomena from discrete supermolecules now have a Boolean basis. While many processes in bioLogical cells can be understood in terms of molecular Logic gates that process information sequentially and combinationally, the design and construction of such devices in the laboratory are unknown. Here the authors achieve this by the reversibly-controlled capture and release of guest molecules from host containers.
Andre Alvesareias - One of the best experts on this subject based on the ideXlab platform.
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molecular memory with downstream Logic Processing exemplified by switchable and self indicating guest capture and release
Nature Communications, 2019Co-Authors: Brian Daly, Thomas S Moody, Allen J M Huxley, Benjamin Schazmann, Andre Alvesareias, John F Malone, H Nimal Q Gunaratne, Peter Nockemann, Prasanna A De SilvaAbstract:Molecular-Logic based computation (MLBC) has grown by accumulating many examples of combinational Logic gates and a few sequential variants. In spite of many inspirations being available in biology, there are virtually no examples of MLBC in chemistry where sequential and combinational operations are integrated. Here we report a simple alcohol-ketone redox interconversion which switches a macrocycle between a large or small cavity, with erect aromatic walls which create a deep hydrophobic space or with collapsed walls respectively. Small aromatic guests can be captured or released in an all or none manner upon chemical command. During capture, the fluorescence of the alcohol macrocycle is quenched via fluorescent photoinduced electron transfer switching, meaning that its occupancy state is self-indicated. This represents a chemically-driven RS Flip-Flop, one of whose outputs is fed into an INHIBIT gate. Processing of outputs from memory stores is seen in the injection of packaged neurotransmitters into synaptic clefts for onward neural signalling. Overall, capture-release phenomena from discrete supermolecules now have a Boolean basis. While many processes in bioLogical cells can be understood in terms of molecular Logic gates that process information sequentially and combinationally, the design and construction of such devices in the laboratory are unknown. Here the authors achieve this by the reversibly-controlled capture and release of guest molecules from host containers.
