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Gentili PL, Stano P. Living cells and biological mechanisms as prototypes for developing chemical artificial intelligence. Biochem Biophys Res Commun 2024; 720:150060. [PMID: 38754164 DOI: 10.1016/j.bbrc.2024.150060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Artificial Intelligence (AI) is having a revolutionary impact on our societies. It is helping humans in facing the global challenges of this century. Traditionally, AI is developed in software or through neuromorphic engineering in hardware. More recently, a brand-new strategy has been proposed. It is the so-called Chemical AI (CAI), which exploits molecular, supramolecular, and systems chemistry in wetware to mimic human intelligence. In this work, two promising approaches for boosting CAI are described. One regards designing and implementing neural surrogates that can communicate through optical or chemical signals and give rise to networks for computational purposes and to develop micro/nanorobotics. The other approach concerns "bottom-up synthetic cells" that can be exploited for applications in various scenarios, including future nano-medicine. Both topics are presented at a basic level, mainly to inform the broader audience of non-specialists, and so favour the rise of interest in these frontier subjects.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Perugia, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.
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Rossi F, Ristori S, Abou-Hassan A. Multiscale Approach for Tuning Communication among Chemical Oscillators Confined in Biomimetic Microcompartments. Acc Chem Res 2024. [PMID: 38991143 DOI: 10.1021/acs.accounts.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
ConspectusInspired by the biological world, new cross-border disciplines and technologies have emerged. Relevant examples include systems chemistry, which offers a bottom-up approach toward chemical complexity, and bio/chemical information and communication technology (bio/chemical ICT), which explores the conditions for propagating signals among individual microreactors separated by selectively permeable membranes. To fabricate specific arrays of microreactors, microfluidics has been demonstrated as an excellent method. In particular, droplet-based microfluidics is a powerful tool for encapsulating biological entities and chemical reagents in artificial microenvironments, mostly water-in-oil microdroplets. In these systems, the interfaces are liquid-liquid, and their physicochemical properties are key factors for tuning the coupling between molecular diffusion. Simple and double emulsions, where aqueous domains are in equilibrium with oil domains through boundary layers of amphiphilic molecules, are organized assemblies with high interfacial-area-to-volume ratios. These membranes can be engineered to obtain different surface charges, single- or multilayer stacking, and a variable degree of defects in molecular packing. Emulsions find application in many fields, including the food industry, pharmaceutics, and cosmetics. Furthermore, micro- and nanoemulsions can be used to model the propagation of chemical species through long distances, which is not only vital for cell signaling but also significant in molecular computing. Here we present in-depth research on the faceted world of solutions confined in restricted environments. In particular, we focused on the multiscale aspects of structure and dynamics from molecular to micro and macro levels. The Belousov-Zhabotinsky chemical reaction, known for its robustness and well-documented oscillatory behavior, was selected to represent a generic signal emitter/receiver confined within microenvironments separated by liquid-liquid interfaces. In this pulse generator, the temporal and spatial progressions are governed by periodic fluctuations in the concentration of chemical species, which act as activatory or inhibitory messengers over long distances. When organized into "colonies" or arrays, these micro-oscillators exhibit emergent dynamical behaviors at the population level. These behaviors can be finely tuned by manipulating the geometrical distribution of the oscillators and the properties of the interfaces at the nanoscale. By carefully selecting the membrane composition, it is possible to drive the system toward either in-phase, antiphase, or mixed synchronization regimes among individual oscillators, depending on messenger molecules. This relatively simple lab-scale model replicates some of the communication strategies commonly found in biological systems, particularly those based on the passive diffusion of chemical and electrical signals. It can help shed light on fundamental life processes and inspire new implementations in molecular computing and smart materials.
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Affiliation(s)
- Federico Rossi
- Department of Physical Science, Earth and Environment, University of Siena, Pian dei Mantellini, 44, 53100 Siena, Siena, Italy
| | - Sandra Ristori
- Department of Chemistry & CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Ali Abou-Hassan
- Sorbonne Université, CNRS, PHysico-chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), F-75005 Paris, France
- Institut Universitaire de France (IUF), 75231 Paris, France
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Gentili PL. The Conformational Contribution to Molecular Complexity and Its Implications for Information Processing in Living Beings and Chemical Artificial Intelligence. Biomimetics (Basel) 2024; 9:121. [PMID: 38392167 PMCID: PMC10886813 DOI: 10.3390/biomimetics9020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
This work highlights the relevant contribution of conformational stereoisomers to the complexity and functions of any molecular compound. Conformers have the same molecular and structural formulas but different orientations of the atoms in the three-dimensional space. Moving from one conformer to another is possible without breaking covalent bonds. The interconversion is usually feasible through the thermal energy available in ordinary conditions. The behavior of most biopolymers, such as enzymes, antibodies, RNA, and DNA, is understandable if we consider that each exists as an ensemble of conformers. Each conformational collection confers multi-functionality and adaptability to the single biopolymers. The conformational distribution of any biopolymer has the features of a fuzzy set. Hence, every compound that exists as an ensemble of conformers allows the molecular implementation of a fuzzy set. Since proteins, DNA, and RNA work as fuzzy sets, it is fair to say that life's logic is fuzzy. The power of processing fuzzy logic makes living beings capable of swift decisions in environments dominated by uncertainty and vagueness. These performances can be implemented in chemical robots, which are confined molecular assemblies mimicking unicellular organisms: they are supposed to help humans "colonise" the molecular world to defeat diseases in living beings and fight pollution in the environment.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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Gentili PL, Szaciłowski K, Adamatzky A. Editorial: Approaching human intelligence through chemical systems: development of unconventional chemical artificial intelligence. Front Chem 2023; 11:1332647. [PMID: 38025075 PMCID: PMC10666623 DOI: 10.3389/fchem.2023.1332647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Perugia, Italy
| | - Konrad Szaciłowski
- Academic Centre for Materials and Nanotechnology, AGH University of Kraków, Kraków, Poland
| | - Andrew Adamatzky
- Unconventional Computing Laboratory, University of the West of England, Bristol, United Kingdom
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Gentili PL, Stano P. Tracing a new path in the field of AI and robotics: mimicking human intelligence through chemistry. Part II: systems chemistry. Front Robot AI 2023; 10:1266011. [PMID: 37915426 PMCID: PMC10616823 DOI: 10.3389/frobt.2023.1266011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Abstract
Inspired by some traits of human intelligence, it is proposed that wetware approaches based on molecular, supramolecular, and systems chemistry can provide valuable models and tools for novel forms of robotics and AI, being constituted by soft matter and fluid states as the human nervous system and, more generally, life, is. Bottom-up mimicries of intelligence range from the molecular world to the multicellular level, i.e., from the Ångström (10 - 10 meters) to the micrometer scales (10 - 6 meters), and allows the development of unconventional chemical robotics. Whereas conventional robotics lets humans explore and colonise otherwise inaccessible environments, such as the deep oceanic abysses and other solar system planets, chemical robots will permit us to inspect and control the microscopic molecular and cellular worlds. This article suggests that systems made of properly chosen molecular compounds can implement all those modules that are the fundamental ingredients of every living being: sensory, processing, actuating, and metabolic networks. Autonomous chemical robotics will be within reach when such modules are compartmentalised and assembled. The design of a strongly intertwined web of chemical robots, with or without the involvement of living matter, will give rise to collective forms of intelligence that will probably reproduce, on a minimal scale, some sophisticated performances of the human intellect and will implement forms of "general AI." These remarkable achievements will require a productive interdisciplinary collaboration among chemists, biotechnologists, computer scientists, engineers, physicists, neuroscientists, cognitive scientists, and philosophers to be achieved. The principal purpose of this paper is to spark this revolutionary collaborative scientific endeavour.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Perugia, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DISTeBA), University of Salento, Lecce, Italy
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Stano P. Chemical Systems for Wetware Artificial Life: Selected Perspectives in Synthetic Cell Research. Int J Mol Sci 2023; 24:14138. [PMID: 37762444 PMCID: PMC10532297 DOI: 10.3390/ijms241814138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The recent and important advances in bottom-up synthetic biology (SB), in particular in the field of the so-called "synthetic cells" (SCs) (or "artificial cells", or "protocells"), lead us to consider the role of wetware technologies in the "Sciences of Artificial", where they constitute the third pillar, alongside the more well-known pillars hardware (robotics) and software (Artificial Intelligence, AI). In this article, it will be highlighted how wetware approaches can help to model life and cognition from a unique perspective, complementary to robotics and AI. It is suggested that, through SB, it is possible to explore novel forms of bio-inspired technologies and systems, in particular chemical AI. Furthermore, attention is paid to the concept of semantic information and its quantification, following the strategy recently introduced by Kolchinsky and Wolpert. Semantic information, in turn, is linked to the processes of generation of "meaning", interpreted here through the lens of autonomy and cognition in artificial systems, emphasizing its role in chemical ones.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
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Gentili PL, Stano P. Tracing a new path in the field of AI and robotics: mimicking human intelligence through chemistry. Part I: molecular and supramolecular chemistry. Front Robot AI 2023; 10:1238492. [PMID: 37744185 PMCID: PMC10514506 DOI: 10.3389/frobt.2023.1238492] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Chemical Artificial Intelligence (CAI) is a brand-new research line that exploits molecular, supramolecular, and systems chemistry in wetware (i.e., in fluid solutions) to imitate some performances of human intelligence and promote unconventional robotics based on molecular assemblies, which act in the microscopic world, otherwise tough to be accessed by humans. It is undoubtedly worth spreading the news that AI researchers can rely on the help of chemists and biotechnologists to reach the ambitious goals of building intelligent systems from scratch. This article reports the first attempt at building a Chemical Artificial Intelligence knowledge map and describes the basic intelligent functions that can be implemented through molecular and supramolecular chemistry. Chemical Artificial Intelligence provides new tools and concepts to mimic human intelligence because it shares, with biological intelligence, the same principles and materials. It enables peculiar dynamics, possibly not accessible in software and hardware domains. Moreover, the development of Chemical Artificial Intelligence will contribute to a deeper understanding of the strict link between intelligence and life, which are two of the most remarkable emergent properties shown by the Complex Systems we call biological organisms.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Perugia, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
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Bianchini F. Autopoiesis of the artificial: From systems to cognition. Biosystems 2023:104936. [PMID: 37279825 DOI: 10.1016/j.biosystems.2023.104936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/08/2023]
Abstract
In the seminal work on autopoiesis by Varela, Maturana, and Uribe, they start by addressing the confusion between processes that are history dependent and processes that are history independent in the biological world. The former is particularly linked to evolution and ontogenesis, while the latter pertains to the organizational features of biological individuals. Varela, Maturana, and Uribe reject this framework and propose their original theory of autopoietic organization, which emphasizes the strong complementarity of temporal and non-temporal phenomena. They argue that the dichotomy between structure and organization lies at the core of the unity of living systems. By opposing history-dependent and history-independent processes, methodological challenges arise in explaining phenomena related to living systems and cognition. Consequently, Maturana and Varela reject this approach in defining autopoietic organization. I argue, however, that this relationship presents an issue that can be found in recent developments of the science of artificial intelligence (AI) in different ways, giving rise to related concerns. While highly capable AI systems exist that can perform cognitive tasks, their internal workings and the specific contributions of their components to the overall system behavior, understood as a unified whole, remain largely uninterpretable. This article explores the connection between biological systems, cognition, and recent developments in AI systems that could potentially be linked to autopoiesis and related concepts such as autonomy and organization. The aim is to assess the advantages and disadvantages of employing autopoiesis in the synthetic (artificial) explanation for biological cognitive systems and to determine if and how the notion of autopoiesis can still be fruitful in this perspective.
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Gentili PL, Capaccioni A, Germani R, Fantacci S. The Versatile Photo-Thermal Behaviour of a 2-Hydroxyazobenzene. Molecules 2023; 28:molecules28031183. [PMID: 36770849 PMCID: PMC9920310 DOI: 10.3390/molecules28031183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Photochromic compounds are employed in implementing neuron surrogates. They will boost the development of neuromorphic engineering in wetware. In this work, the photochromic behaviours of (E)-3,4,6-trichloro-2-(p-diazenil)-phenol (t-DZH) and its conjugated phenoxide base (t-DZ) have been investigated experimentally in three different media: (1) pure acetonitrile, (2) in water and acetonitrile mixed in a 1/1 volume ratio, and (3) in an aqueous micellar solution of 3-(N,N-Dimethylmyristylammonio)propanesulfonate (SB3-14). The analysis of the spectral and kinetic features of t-DZH and t-DZ has been supported by quantum-mechanical DFT calculations, the maximum entropy method, and the determination of their colourability (C). The versatility of t-DZH and t-DZ makes them promising molecular probes of micro-environments and potential ingredients of photochemical oscillators required for implementing pacemaker neurons capable of communicating through optical signals in wetware.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: ; Tel.: +39-0755855573
| | - Antonio Capaccioni
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Raimondo Germani
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Simona Fantacci
- Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta” (CNR-SCITEC), 06123 Perugia, Italy
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McCauley SC, Glaser R. Origin of the Second-Order Proton Catalysis of Ferriin Reduction in Belousov-Zhabotinsky Reactions: Density Functional Studies of Ferroin and Ferriin Aggregates with Outer Sphere Ligands Sulfate, Bisulfate, and Sulfuric Acid. J Phys Chem A 2022; 126:7261-7272. [PMID: 36194679 DOI: 10.1021/acs.jpca.2c05879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The detailed mechanisms of Belousov-Zhabotinsky oscillating reactions continue to present grand challenges, even after half a century of study. The origin of the pH dependence of the oscillation pattern had never been rigorously identified. In our recent kinetic study of one of the key Belousov-Zhabotinsky reactions, the iron-catalyzed bromate oxidation of malonic acid, compelling agreement between experiments and kinetic simulations was achieved only with the inclusion of second-order proton catalysis of the reduction of the [Fe(phen)3]3+ species. After exhausting all other avenues in search of an explanation of this proton catalysis, we considered the possibility that the parent iron-phenanthroline complexes could aggregate with neutral and anionic outer sphere ligands (OSLs) in the highly concentrated sulfuric acid solution, and we hypothesized that OSL protonation would increase the capacity of the aggregated complex to oxidize the organic fuel. We performed potential energy surface analyses at the SMD(APFD/6-311G*) level of complexes of the types [Fe(phen)3(SO42-)m(HSO4-)n(H2SO4)o](c-2m-n)+ for ferriin (c = 3) and ferroin (c = 2) aggregated with m sulfate, n bisulfate, and o sulfuric acid OSLs. We present structures of the OSL aggregates, develop a nomenclature for their description, and characterize their electronic structure. The structural chemistry provides the foundation to discuss the ferroin/ferriin redox couple with emphasis on the relationship between the vertical electron affinities of ferriin aggregates and their OSL protonation states. For proton catalysis to manifest itself, double-protonation paths that are slightly endergonic should be present, and proton affinities of aggregated OSLs allow the identification of such double-protonation chains. As a first test of our mechanistic proposal for the second-order proton catalysis of the Belousov-Zhabotinsky reaction, the results presented here provide compelling evidence in support of the importance of outer sphere ligation of the iron catalyst.
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Affiliation(s)
- Sara C McCauley
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri65401, United States
| | - Rainer Glaser
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri65401, United States
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Design of a new photochromic oscillator: towards dynamical models of pacemaker neurons. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-021-02122-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Liu L, Bi M, Wang Y, Liu J, Jiang X, Xu Z, Zhang X. Artificial intelligence-powered microfluidics for nanomedicine and materials synthesis. NANOSCALE 2021; 13:19352-19366. [PMID: 34812823 DOI: 10.1039/d1nr06195j] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Artificial intelligence (AI) is an emerging technology with great potential, and its robust calculation and analysis capabilities are unmatched by traditional calculation tools. With the promotion of deep learning and open-source platforms, the threshold of AI has also become lower. Combining artificial intelligence with traditional fields to create new fields of high research and application value has become a trend. AI has been involved in many disciplines, such as medicine, materials, energy, and economics. The development of AI requires the support of many kinds of data, and microfluidic systems can often mine object data on a large scale to support AI. Due to the excellent synergy between the two technologies, excellent research results have emerged in many fields. In this review, we briefly review AI and microfluidics and introduce some applications of their combination, mainly in nanomedicine and material synthesis. Finally, we discuss the development trend of the combination of the two technologies.
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Affiliation(s)
- Linbo Liu
- John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA
| | - Mingcheng Bi
- Institute of Process Equipment, College of Energy Engineering, Zhejiang University, Hangzhou 310027, P.R. China
| | - Yunhua Wang
- John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA
| | - Junfeng Liu
- Institute of Process Equipment, College of Energy Engineering, Zhejiang University, Hangzhou 310027, P.R. China
| | - Xiwen Jiang
- College of Biological Science and Engineering, Fuzhou university, Fuzhou 350108, P.R. China
| | - Zhongbin Xu
- Institute of Process Equipment, College of Energy Engineering, Zhejiang University, Hangzhou 310027, P.R. China
| | - Xingcai Zhang
- John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA
- School of Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Gentili PL. Establishing a New Link between Fuzzy Logic, Neuroscience, and Quantum Mechanics through Bayesian Probability: Perspectives in Artificial Intelligence and Unconventional Computing. Molecules 2021; 26:5987. [PMID: 34641530 PMCID: PMC8512172 DOI: 10.3390/molecules26195987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/25/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Human interaction with the world is dominated by uncertainty. Probability theory is a valuable tool to face such uncertainty. According to the Bayesian definition, probabilities are personal beliefs. Experimental evidence supports the notion that human behavior is highly consistent with Bayesian probabilistic inference in both the sensory and motor and cognitive domain. All the higher-level psychophysical functions of our brain are believed to take the activities of interconnected and distributed networks of neurons in the neocortex as their physiological substrate. Neurons in the neocortex are organized in cortical columns that behave as fuzzy sets. Fuzzy sets theory has embraced uncertainty modeling when membership functions have been reinterpreted as possibility distributions. The terms of Bayes' formula are conceivable as fuzzy sets and Bayes' inference becomes a fuzzy inference. According to the QBism, quantum probabilities are also Bayesian. They are logical constructs rather than physical realities. It derives that the Born rule is nothing but a kind of Quantum Law of Total Probability. Wavefunctions and measurement operators are viewed epistemically. Both of them are similar to fuzzy sets. The new link that is established between fuzzy logic, neuroscience, and quantum mechanics through Bayesian probability could spark new ideas for the development of artificial intelligence and unconventional computing.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Via Elce di sotto 8, 06123 Perugia, Italy
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The Fuzziness in Molecular, Supramolecular, and Systems Chemistry. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25163634. [PMID: 32785069 PMCID: PMC7463983 DOI: 10.3390/molecules25163634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022]
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15
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Light and chemical oscillations: Review and perspectives. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2019.100321] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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A contribution to neuromorphic engineering: neuromodulation implemented through photochromic compounds maintained out of equilibrium by UV–visible radiation. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2020. [DOI: 10.1007/s12210-020-00869-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Vanag VK. Hierarchical network of pulse coupled chemical oscillators with adaptive behavior: Chemical neurocomputer. CHAOS (WOODBURY, N.Y.) 2019; 29:083104. [PMID: 31472522 DOI: 10.1063/1.5099979] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
We consider theoretically a network of pulse coupled oscillators with time delays. Each oscillator is described by the Oregonator-like model for the Belousov-Zhabotinsky (BZ) reaction. Different groups of oscillators constitute five functional units: (1) a central pattern generator (CPG), (2) a "reader" unit that can identify dynamical modes of the CPG, (3) an antenna (A) unit that receives external signals and responds on them by generating different dynamical modes, (4) another reader unit for identification of the dynamical modes in the A unit, and (5) a decision making unit that switches the current dynamical mode of the CPG to the mode that is similar to the current mode in the A unit. We call this network a chemical neurocomputer, since chemical BZ reaction occurs in each micro-oscillator, while pulse connectivity of these cells is inspired by the brain.
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Affiliation(s)
- Vladimir K Vanag
- Center for Nonlinear Chemistry, Immanuel Kant Baltic Federal University, 14 A. Nevskogo Str., Kaliningrad 236041, Russia
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18
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Gentili PL. The Fuzziness of the Molecular World and Its Perspectives. Molecules 2018; 23:molecules23082074. [PMID: 30126225 PMCID: PMC6222855 DOI: 10.3390/molecules23082074] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 11/27/2022] Open
Abstract
Scientists want to comprehend and control complex systems. Their success depends on the ability to face also the challenges of the corresponding computational complexity. A promising research line is artificial intelligence (AI). In AI, fuzzy logic plays a significant role because it is a suitable model of the human capability to compute with words, which is relevant when we make decisions in complex situations. The concept of fuzzy set pervades the natural information systems (NISs), such as living cells, the immune and the nervous systems. This paper describes the fuzziness of the NISs, in particular of the human nervous system. Moreover, it traces three pathways to process fuzzy logic by molecules and their assemblies. The fuzziness of the molecular world is useful for the development of the chemical artificial intelligence (CAI). CAI will help to face the challenges that regard both the natural and the computational complexity.
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Affiliation(s)
- Pier Luigi Gentili
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di sotto 8, 06123 Perugia, Italy.
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Pilarczyk K, Wlaźlak E, Przyczyna D, Blachecki A, Podborska A, Anathasiou V, Konkoli Z, Szaciłowski K. Molecules, semiconductors, light and information: Towards future sensing and computing paradigms. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.03.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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Ianni F, Scorzoni S, Gentili PL, Di Michele A, Frigoli M, Camaioni E, Ortica F, Sardella R. Chiral separation of helical chromenes with chloromethyl phenylcarbamate polysaccharide-based stationary phases. J Sep Sci 2018; 41:1266-1273. [DOI: 10.1002/jssc.201701293] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Federica Ianni
- Department of Pharmaceutical Sciences; University of Perugia; Perugia Italy
| | - Stefania Scorzoni
- Department of Pharmaceutical Sciences; University of Perugia; Perugia Italy
| | - Pier Luigi Gentili
- Department of Chemistry; Biology and Biotechnology; University of Perugia; Perugia Italy
| | | | - Michel Frigoli
- Institut Lavoisier de Versaille; Université de Versailles Saint-Quentin-en-Yvelines; Versailles France
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences; University of Perugia; Perugia Italy
| | - Fausto Ortica
- Department of Chemistry; Biology and Biotechnology; University of Perugia; Perugia Italy
- Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Perugia; Perugia Italy
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences; University of Perugia; Perugia Italy
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21
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Fianchini M. Synthesis meets theory: Past, present and future of rational chemistry. PHYSICAL SCIENCES REVIEWS 2017. [DOI: 10.1515/psr-2017-0134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
Chemical synthesis has its roots in the empirical approach of alchemy. Nonetheless, the birth of the scientific method, the technical and technological advances (exploiting revolutionary discoveries in physics) and the improved management and sharing of growing databases greatly contributed to the evolution of chemistry from an esoteric ground into a mature scientific discipline during these last 400 years. Furthermore, thanks to the evolution of computational resources, platforms and media in the last 40 years, theoretical chemistry has added to the puzzle the final missing tile in the process of “rationalizing” chemistry. The use of mathematical models of chemical properties, behaviors and reactivities is nowadays ubiquitous in literature. Theoretical chemistry has been successful in the difficult task of complementing and explaining synthetic results and providing rigorous insights when these are otherwise unattainable by experiment. The first part of this review walks the reader through a concise historical overview on the evolution of the “model” in chemistry. Salient milestones have been highlighted and briefly discussed. The second part focuses more on the general description of recent state-of-the-art computational techniques currently used worldwide by chemists to produce synergistic models between theory and experiment. Each section is complemented by key-examples taken from the literature that illustrate the application of the technique discussed therein.
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22
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Park S, Park JH, Hwang S, Kwak J. Programmable Electrochemical Rectifier Based on a Thin-Layer Cell. ACS APPLIED MATERIALS & INTERFACES 2017; 9:20955-20962. [PMID: 28541653 DOI: 10.1021/acsami.7b02215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A programmable electrochemical rectifier based on thin-layer electrochemistry is described here. Both the rectification ratio and the response time of the device are programmable by controlling the gap distance of the thin-layer electrochemical cell, which is easily controlled using commercially available beads. One of the electrodes was modified using a ferrocene-terminated self-assembled monolayer to offer unidirectional charge transfers via soluble redox species. The thin-layer configuration provided enhanced mass transport, which was determined by the gap thickness. The device with the smallest gap thickness (∼4 μm) showed an unprecedented, high rectification ratio (up to 160) with a fast response time in a two-terminal configuration using conventional electronics.
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Affiliation(s)
- Seungjin Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology , Daejeon 34141, Korea
| | - Jun Hui Park
- Department of Chemistry Education and Institute of Fusion Science, Chonbuk National University , Jeonju 54896, Korea
| | - Seongpil Hwang
- Department of Advanced Materials Chemistry, Korea University , Sejong 30019, Korea
| | - Juhyoun Kwak
- Department of Chemistry, Korea Advanced Institute of Science and Technology , Daejeon 34141, Korea
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23
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Gentili PL, Giubila MS, Germani R, Romani A, Nicoziani A, Spalletti A, Heron BM. Optical Communication among Oscillatory Reactions and Photo-Excitable Systems: UV and Visible Radiation Can Synchronize Artificial Neuron Models. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Maria Sole Giubila
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Raimondo Germani
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Aldo Romani
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Andrea Nicoziani
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - Anna Spalletti
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Via Elce di sotto 8 06123 Perugia Italy
| | - B. Mark Heron
- Department of Chemical Sciences; School of Applied Science; University of Huddersfield, Queensgate; Huddersfield HD1 3DH UK
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24
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Blachecki A, Mech-Piskorz J, Gajewska M, Mech K, Pilarczyk K, Szaciłowski K. Organotitania-Based Nanostructures as a Suitable Platform for the Implementation of Binary, Ternary, and Fuzzy Logic Systems. Chemphyschem 2017; 18:1798-1810. [PMID: 28449282 DOI: 10.1002/cphc.201700292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/25/2017] [Indexed: 12/31/2022]
Abstract
Titanium dioxide nanocomposites were synthesized in hierarchical architectures through the use of a 1,4-dihydroxyanthraquinone photosensitizer. In the first step, the dye was either incorporated into the TiO2 core or adsorbed on its surface. In the subsequent phase, both structures were covered with an outer layer of titanium dioxide. The structure, morphology, aggregation, spectroscopic, and electrochemical properties of the synthesized TiO2 -based materials are presented with emphasis on the photosensitization and the photocurrent switching phenomena, which are also discussed within the context of the optical logic gates implementation and fuzzy logic systems operation. We present three different interpretations of the photocurrent action spectra yielding binary, ternary, or fuzzy logic circuits.
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Affiliation(s)
- Andrzej Blachecki
- Faculty of Non-Ferrous Metals, AGH University of Science and Technology, al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Justyna Mech-Piskorz
- Institute of Physical Chemistry, Polish Academy of Sciences ul., Kasprzaka 44/52, 01-224, Warszawa, Poland
| | - Marta Gajewska
- Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Krzysztof Mech
- Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Kacper Pilarczyk
- Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, al. Mickiewicza 30, 30-059, Kraków, Poland.,Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Konrad Szaciłowski
- Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, al. Mickiewicza 30, 30-059, Kraków, Poland
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25
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Gentili PL, Giubila MS, Germani R, Romani A, Nicoziani A, Spalletti A, Heron BM. Optical Communication among Oscillatory Reactions and Photo-Excitable Systems: UV and Visible Radiation Can Synchronize Artificial Neuron Models. Angew Chem Int Ed Engl 2017; 56:7535-7540. [PMID: 28560808 DOI: 10.1002/anie.201702289] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/27/2017] [Indexed: 11/08/2022]
Abstract
Neuromorphic engineering promises to have a revolutionary impact in our societies. A strategy to develop artificial neurons (ANs) is to use oscillatory and excitable chemical systems. Herein, we use UV and visible radiation as both excitatory and inhibitory signals for the communication among oscillatory reactions, such as the Belousov-Zhabotinsky and the chemiluminescent Orban transformations, and photo-excitable photochromic and fluorescent species. We present the experimental results and the simulations regarding pairs of ANs communicating by either one or two optical signals, and triads of ANs arranged in both feed-forward and recurrent networks. We find that the ANs, powered chemically and/or by the energy of electromagnetic radiation, can give rise to the emergent properties of in-phase, out-of-phase, anti-phase synchronizations and phase-locking, dynamically mimicking the communication among real neurons.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Maria Sole Giubila
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Raimondo Germani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Aldo Romani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Andrea Nicoziani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - Anna Spalletti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123, Perugia, Italy
| | - B Mark Heron
- Department of Chemical Sciences, School of Applied Science, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
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26
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Gentili PL, Giubila MS, Heron BM. Processing Binary and Fuzzy Logic by Chaotic Time Series Generated by a Hydrodynamic Photochemical Oscillator. Chemphyschem 2017; 18:1831-1841. [DOI: 10.1002/cphc.201601443] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/02/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology; University of Perugia; 06123 Perugia Italy
| | - Maria Sole Giubila
- Department of Chemistry, Biology and Biotechnology; University of Perugia; 06123 Perugia Italy
| | - B. Mark Heron
- Department of Chemical and Biological Sciences, School of Applied Science; University of Huddersfield; Queensgate Huddersfield HD1 3DH UK
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27
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Torbensen K, Rossi F, Ristori S, Abou-Hassan A. Chemical communication and dynamics of droplet emulsions in networks of Belousov-Zhabotinsky micro-oscillators produced by microfluidics. LAB ON A CHIP 2017; 17:1179-1189. [PMID: 28239705 DOI: 10.1039/c6lc01583b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical communication leading to synchronization and collective behaviour of dynamic elements, such as cell colonies, is a widespread phenomenon with biological, physical and chemical importance. Such synchronization between elements proceeds via chemical communication by emmision, interdiffusion and reception of specific messenger molecules. On a lab scale, these phenomena can be modeled by encapsulating an oscillating chemical reaction, which serves as a signal (information) sender/receiver element, inside microcompartments such as droplet emulsions, liposomes and polymersomes. Droplets can thus be regarded as single units, able to generate chemical messengers that diffuse in the environment and hence can interact with other compartments. The Belousov-Zhabotinsky (BZ) reaction is a well-known chemical oscillator largely used as a model for complex nonlinear phenomena, including chemical, physical and biological examples. When the BZ-reaction is encapsulated inside microcompartments, its chemical intermediates can serve as messengers by diffusing among different microcompartments, to trigger specific reactions leading to a collective behavior between the elements. The geometry and constitution of the diffusion pathways play an important role in governing the collective behaviour of the system. In this context, microfluidics is not only a versatile tool for mastering the encapsulation process of the BZ-reaction in monodisperse microcompartments, but also for creating geometries and networks with well defined boundaries. The individual compartments can be engineered with selected properties using different surfactants in the case of simple emulsions, or with specific membrane properties in the case of liposomes. Furthermore, it enables the arrangement of these microcompartments in various geometric configurations, where the diffusive coupling pathways between individual compartments are both spatially and chemically well-defined. In this tutorial paper, we review a number of articles reporting various approaches to generate networks of compartmentalized Belousov-Zhabotinsky (BZ) chemical oscillators using microfluidics. In contrast to biological cellular networks, the dynamical characteristics of the BZ-reaction is well-known and, when confined in microcompartments arranged in different configurations with a pure interdiffusive coupling, these communicative microreactors can serve to mimic various types of bio-physical networks, aiding to comprehend the concept of chemical communication.
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Affiliation(s)
- Kristian Torbensen
- UMR 8234, Laboratoire Physico-chimie des Electrolytes, Nanosystèmes InterfaciauX (PHENIX), UPMC Univ Paris 06, Sorbonne Universités, 4 place Jussieu - case 51, 75252 Paris cedex 05, France.
| | - Federico Rossi
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, Fisciano (SA), Italy
| | - Sandra Ristori
- Department of Earth Sciences & CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Ali Abou-Hassan
- UMR 8234, Laboratoire Physico-chimie des Electrolytes, Nanosystèmes InterfaciauX (PHENIX), UPMC Univ Paris 06, Sorbonne Universités, 4 place Jussieu - case 51, 75252 Paris cedex 05, France.
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28
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Gentili PL, Rightler AL, Heron BM, Gabbutt CD. Extending human perception of electromagnetic radiation to the UV region through biologically inspired photochromic fuzzy logic (BIPFUL) systems. Chem Commun (Camb) 2016; 52:1474-7. [PMID: 26658700 DOI: 10.1039/c5cc09290f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Photochromic fuzzy logic systems have been designed that extend human visual perception into the UV region. The systems are founded on a detailed knowledge of the activation wavelengths and quantum yields of a series of thermally reversible photochromic compounds. By appropriate matching of the photochromic behaviour unique colour signatures are generated in response differing UV activation frequencies.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123 Perugia, Italy.
| | - Amanda L Rightler
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123 Perugia, Italy. and Department of Chemistry and Biochemistry, University of Tulsa, Tulsa, Oklahoma, USA
| | - B Mark Heron
- Department of Chemical and Biological Sciences, School of Applied Science, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Christopher D Gabbutt
- Department of Chemical and Biological Sciences, School of Applied Science, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
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29
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Pilarczyk K, Daly B, Podborska A, Kwolek P, Silverson VA, de Silva AP, Szaciłowski K. Coordination chemistry for information acquisition and processing. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.04.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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30
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Hayashi K, Gotoda H, Gentili PL. Probing and exploiting the chaotic dynamics of a hydrodynamic photochemical oscillator to implement all the basic binary logic functions. CHAOS (WOODBURY, N.Y.) 2016; 26:053102. [PMID: 27249942 DOI: 10.1063/1.4948590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The convective motions within a solution of a photochromic spiro-oxazine being irradiated by UV only on the bottom part of its volume, give rise to aperiodic spectrophotometric dynamics. In this paper, we study three nonlinear properties of the aperiodic time series: permutation entropy, short-term predictability and long-term unpredictability, and degree distribution of the visibility graph networks. After ascertaining the extracted chaotic features, we show how the aperiodic time series can be exploited to implement all the fundamental two-inputs binary logic functions (AND, OR, NAND, NOR, XOR, and XNOR) and some basic arithmetic operations (half-adder, full-adder, half-subtractor). This is possible due to the wide range of states a nonlinear system accesses in the course of its evolution. Therefore, the solution of the convective photochemical oscillator results in hardware for chaos-computing alternative to conventional complementary metal-oxide semiconductor-based integrated circuits.
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Affiliation(s)
- Kenta Hayashi
- Department of Mechanical Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu-shi, Shiga 525-8577, Japan
| | - Hiroshi Gotoda
- Department of Mechanical Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
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31
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Cesaretti A, Carlotti B, Gentili PL, Clementi C, Germani R, Elisei F. Doxycycline and oxytetracycline loading of a zwitterionic amphoteric surfactant-gel and their controlled release. Phys Chem Chem Phys 2015; 16:23096-107. [PMID: 25251135 DOI: 10.1039/c4cp03488k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Oxytetracycline (OX) and doxycycline (DX) are antibiotics belonging to the family of tetracyclines. We present a UV-Visible steady state and time-resolved experimental study of OX and DX and their biologically active Mg(2+) complexes loaded within a hydrogel matrix. Hydrogels are a three dimensional network of worm-like micelles, mutually intertwined, forming a pattern of hydrophobic domains and water pools. We resorted to a hydrogel, made of a zwitterionic N-oxide surfactant (p-dodecyloxybenzyldimethylamine N-oxide, pDoAO), which showed promising features as a drug vehicle. The spectral and photophysical properties of the drugs are significantly altered by the inclusion in the hydrophobic domains of the gel and these variations are indicators of the permeation ratio of the drug in between the micelles forming the gel network. We thus get a clear picture of the distribution of the drug molecules and metal chelates into the two different kinds of environment, where the hydrophobic domains are also able to cause a gel-induced deprotonation of these two drugs. Furthermore, the amphoteric nature of the surfactant is responsible for its peculiar acid-base behaviour: under acidic pH conditions, the surfactant gets protonated and the stability of the gel network is damaged. This feature can be thus exploited for the pH controlled release of the tetracycline drugs.
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Affiliation(s)
- A Cesaretti
- Department of Chemistry, Biology and Biotechnology and Centre of Excellence on Nanostructured Innovative Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
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32
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Varghese S, Elemans JAAW, Rowan AE, Nolte RJM. Molecular computing: paths to chemical Turing machines. Chem Sci 2015; 6:6050-6058. [PMID: 28717447 PMCID: PMC5504628 DOI: 10.1039/c5sc02317c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/06/2015] [Indexed: 11/21/2022] Open
Abstract
In this perspective, we highlight some of the recent advances in the development of molecular and biomolecular systems for performing logic operations and computing. We also present a blueprint of a chemical Turing machine using a processive catalytic approach.
To comply with the rapidly increasing demand of information storage and processing, new strategies for computing are needed. The idea of molecular computing, where basic computations occur through molecular, supramolecular, or biomolecular approaches, rather than electronically, has long captivated researchers. The prospects of using molecules and (bio)macromolecules for computing is not without precedent. Nature is replete with examples where the handling and storing of data occurs with high efficiencies, low energy costs, and high-density information encoding. The design and assembly of computers that function according to the universal approaches of computing, such as those in a Turing machine, might be realized in a chemical way in the future; this is both fascinating and extremely challenging. In this perspective, we highlight molecular and (bio)macromolecular systems that have been designed and synthesized so far with the objective of using them for computing purposes. We also present a blueprint of a molecular Turing machine, which is based on a catalytic device that glides along a polymer tape and, while moving, prints binary information on this tape in the form of oxygen atoms.
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Affiliation(s)
- Shaji Varghese
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Johannes A A W Elemans
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Alan E Rowan
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Roeland J M Nolte
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
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33
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Torbensen K, Rossi F, Pantani OL, Ristori S, Abou-Hassan A. Interaction of the Belousov–Zhabotinsky Reaction with Phospholipid Engineered Membranes. J Phys Chem B 2015; 119:10224-30. [DOI: 10.1021/acs.jpcb.5b04572] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Kristian Torbensen
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
| | - Federico Rossi
- Department
of Chemistry and Biology, University of Salerno, Via Giovanni
Paolo II 132, Fisciano (SA), Italy
| | - Ottorino L. Pantani
- Department
of Agrifood Production and Environmental Sciences, University of Florence, P.le delle Cascine 28, 50144 Firenze, Italy
| | - Sandra Ristori
- Department of Earth Sciences & CSGI, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Ali Abou-Hassan
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
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34
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Frigoli M, Marrot J, Gentili PL, Jacquemin D, Vagnini M, Pannacci D, Ortica F. P-Type Photochromism of New Helical Naphthopyrans: Synthesis and Photochemical, Photophysical and Theoretical Study. Chemphyschem 2015; 16:2447-58. [PMID: 26103956 DOI: 10.1002/cphc.201500251] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 11/12/2022]
Abstract
Two novel helical naphthopyrans have been synthesised. The helical scaffold has the interesting effect of increasing the thermal stability of the transoid-trans (TT) open isomer formed upon UV irradiation of the closed form (CF), which transforms these naphthopyrans from thermal to photochemical photochromes. The photochromic performance is excellent in both polar and apolar solvents and the conversion percentage from the CF to the TT form can be as high as 92.8 %. We propose a new method to determine the quantum yields of the photochemical processes that lead to transoid-cis (TC) and TT isomers, and their molar absorption coefficients. The thermal stability of the TT and TC isomers has been studied in different solvents. The quantum yields of fluorescence before and after irradiation, along with the decay lifetimes, have also been measured. TD-DFT calculations have been performed to determine the relative thermodynamic stability of the species involved in the photochromic mechanism and to rationalise their spectral properties.
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Affiliation(s)
- Michel Frigoli
- Institut Lavoisier de Versailles, UMR CNRS 8080, Université de Versailles Saint-Quentin-en-Yvelines, 45 av des Etats-Unis, 78035 Versailles (France).
| | - Jérôme Marrot
- Institut Lavoisier de Versailles, UMR CNRS 8080, Université de Versailles Saint-Quentin-en-Yvelines, 45 av des Etats-Unis, 78035 Versailles (France)
| | - Pier Luigi Gentili
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia (Italy)
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230, Université de Nantes et Institut Universitaire de France, 2, rue de la Houssinière, 44322 Nantes (France). .,Institut Universitaire de France, 103, blvd Saint-Michel, 75005 Paris Cedex 05 (France).
| | - Manuela Vagnini
- Associazione Laboratorio di Diagnostica per i Beni Culturali di Spoleto, Piazza Campello, 2 06049, Spoleto (PG) (Italy)
| | - Danilo Pannacci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia (Italy)
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia (Italy). .,Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Perugia - Via Pascoli, 06123 Perugia (Italy).
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35
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Gentili PL, Gotoda H, Dolnik M, Epstein IR. Analysis and prediction of aperiodic hydrodynamic oscillatory time series by feed-forward neural networks, fuzzy logic, and a local nonlinear predictor. CHAOS (WOODBURY, N.Y.) 2015; 25:013104. [PMID: 25637915 DOI: 10.1063/1.4905458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Forecasting of aperiodic time series is a compelling challenge for science. In this work, we analyze aperiodic spectrophotometric data, proportional to the concentrations of two forms of a thermoreversible photochromic spiro-oxazine, that are generated when a cuvette containing a solution of the spiro-oxazine undergoes photoreaction and convection due to localized ultraviolet illumination. We construct the phase space for the system using Takens' theorem and we calculate the Lyapunov exponents and the correlation dimensions to ascertain the chaotic character of the time series. Finally, we predict the time series using three distinct methods: a feed-forward neural network, fuzzy logic, and a local nonlinear predictor. We compare the performances of these three methods.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Hiroshi Gotoda
- Department of Mechanical Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu-shi, Shiga 525-8577, Japan
| | - Milos Dolnik
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | - Irving R Epstein
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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36
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Warzecha M, Oszajca M, Pilarczyk K, Szaciłowski K. A three-valued photoelectrochemical logic device realising accept anything and consensus operations. Chem Commun (Camb) 2015; 51:3559-61. [DOI: 10.1039/c4cc09980j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A new application of a hybrid material exhibiting the photoelectrochemical photocurrent switching (peps) effect in a three-valued logic device is reported.
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Affiliation(s)
- M. Warzecha
- Strathclyde Institute of Pharmacy and Biomedical Sciences
- University of Strathclyde
- Glasgow
- UK
| | - M. Oszajca
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - K. Pilarczyk
- AGH University of Science and Technology
- Faculty of Physics and Applied Computer Science
- 30-059 Kraków
- Poland
- AGH University of Science and Technology
| | - K. Szaciłowski
- AGH University of Science and Technology
- Academic Centre for Materials and Nanotechnology
- 30-059 Kraków
- Poland
- AGH University of Science and Technology
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37
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Eppel S, Portnoy M. Reversible Multistep Synthesis with Equilibrium Properties Based on a Selection-Oriented Process with a Repetitive Sequence of Steps. J Phys Chem B 2014; 118:9733-44. [DOI: 10.1021/jp5051645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sagi Eppel
- School of Chemistry, Raymond
and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moshe Portnoy
- School of Chemistry, Raymond
and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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38
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Cesaretti A, Carlotti B, Gentili PL, Clementi C, Germani R, Elisei F. Spectroscopic Investigation of the pH Controlled Inclusion of Doxycycline and Oxytetracycline Antibiotics in Cationic Micelles and Their Magnesium Driven Release. J Phys Chem B 2014; 118:8601-13. [DOI: 10.1021/jp502278z] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alessio Cesaretti
- Department
of Chemistry,
Biology and Biotechnology and Centre of Excellence on Nanostructured
Innovative Materials (CEMIN), University of Perugia, via Elce
di Sotto 8, 06123 Perugia, Italy
| | - Benedetta Carlotti
- Department
of Chemistry,
Biology and Biotechnology and Centre of Excellence on Nanostructured
Innovative Materials (CEMIN), University of Perugia, via Elce
di Sotto 8, 06123 Perugia, Italy
| | - Pier Luigi Gentili
- Department
of Chemistry,
Biology and Biotechnology and Centre of Excellence on Nanostructured
Innovative Materials (CEMIN), University of Perugia, via Elce
di Sotto 8, 06123 Perugia, Italy
| | - Catia Clementi
- Department
of Chemistry,
Biology and Biotechnology and Centre of Excellence on Nanostructured
Innovative Materials (CEMIN), University of Perugia, via Elce
di Sotto 8, 06123 Perugia, Italy
| | - Raimondo Germani
- Department
of Chemistry,
Biology and Biotechnology and Centre of Excellence on Nanostructured
Innovative Materials (CEMIN), University of Perugia, via Elce
di Sotto 8, 06123 Perugia, Italy
| | - Fausto Elisei
- Department
of Chemistry,
Biology and Biotechnology and Centre of Excellence on Nanostructured
Innovative Materials (CEMIN), University of Perugia, via Elce
di Sotto 8, 06123 Perugia, Italy
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39
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Sedighi M, Ghasemi M, Mohammadi M, Hassan SHA. A novel application of a neuro–fuzzy computational technique in modeling of thermal cracking of heavy feedstock to light olefin. RSC Adv 2014. [DOI: 10.1039/c4ra02392g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Tomasi R, Noël JM, Zenati A, Ristori S, Rossi F, Cabuil V, Kanoufi F, Abou-Hassan A. Chemical communication between liposomes encapsulating a chemical oscillatory reaction. Chem Sci 2014. [DOI: 10.1039/c3sc53227e] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Electrochemical measurements and numerical simulations are employed to understand the chemical communication between liposomes prepared in microfluidics and encapsulating a chemical oscillator.
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Affiliation(s)
- Raphaël Tomasi
- UPMC Univ Paris 6
- PECSA
- UMR 7195
- équipe Colloïdes Inorganiques
- Université Paris 6 (UPMC) Bat F(74)
| | - Jean-Marc Noël
- ESPCI ParisTech
- PECSA
- UMR 7195
- F-75231 Paris Cedex 05, France
| | - Aymen Zenati
- UPMC Univ Paris 6
- PECSA
- UMR 7195
- équipe Colloïdes Inorganiques
- Université Paris 6 (UPMC) Bat F(74)
| | | | - Federico Rossi
- Department of Chemistry and Biology
- University of Salerno
- Fisciano (SA), Italy
| | - Valérie Cabuil
- UPMC Univ Paris 6
- PECSA
- UMR 7195
- équipe Colloïdes Inorganiques
- Université Paris 6 (UPMC) Bat F(74)
| | | | - Ali Abou-Hassan
- UPMC Univ Paris 6
- PECSA
- UMR 7195
- équipe Colloïdes Inorganiques
- Université Paris 6 (UPMC) Bat F(74)
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41
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Stano P, Wodlei F, Carrara P, Ristori S, Marchettini N, Rossi F. Approaches to Molecular Communication Between Synthetic Compartments Based on Encapsulated Chemical Oscillators. COMMUNICATIONS IN COMPUTER AND INFORMATION SCIENCE 2014. [DOI: 10.1007/978-3-319-12745-3_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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