131,874 research outputs found
Graphically balanced equilibria and stationary measures of reaction networks
No full textThe graph-related symmetries of a reaction network give rise to certain special equilibria (such as complex balanced equilibria) in deterministic models of dynamics of the reaction network. Correspondingly, in the stochastic setting, when modeled as a continuous time Markov chain, these symmetries give rise to certain special stationary measures. Previous work by Anderson, Craciun, and Kurtz [Bull Math. Biol., 72 (2010), pp. 1947-1970] identified stationary distributions of a complex balanced network; later, Cappelletti and Wiuf [SIAM J. Appl. Math., 76 (2016), pp. 411-432] developed the notion of complex balancing for stochastic systems. We define and establish the relations between reaction balanced measure, complex balanced measure, reaction vector balanced measure, and cycle balanced measure and prove that with mild additional hypotheses, the former two are stationary distributions. Furthermore, in the spirit of an earlier work by Joshi [Discrete Contin. Dyn. Syst. Ser. B, 20 (2015), pp. 1077-1105] we give sufficient conditions under which detailed balance of the stationary distribution of Markov chain models implies the existence of positive detailed balance equilibria for the related deterministic reaction network model. Finally, we provide a complete map of the implications between balancing properties of deterministic and corresponding stochastic reaction systems, such as complex balance, reaction balance, reaction vector balance, and cycle balance
Photo-renewable engineered sensor based on silica, silver nanoparticles and titania
No full textElectrode surface passivation and fouling are important challenges in electroanalysis when using modified electrodes in complex matrices, especially in the biomedical and environmental fields [1-2].
In order to overcome such problems, the production of highly engineered ad hoc designed devices could provide really effective sensors [2]. In particular, a reliable and reusable sensor, that could be cleaned by a simple irradiation with UV or solar light, could be perfect for this purpose.
In this context, a three-layered transparent electrode, in which silver nanoparticles are embedded between a bottom silica and a top titania layer is developed [3-4]. Such structure confers to the device multifunctional properties which can be conveniently used in the detection and quantification of some neurotransmitters: dopamine, norepinephrine and serotonin.
The sensor is thoroughly investigated by structural, morphological and electrochemical characterizations in order to understand the role of each component with the aim to improve the robustness and efficiency of the electroanalytical system. In particular, the size distribution of silver nanoparticles, the device architecture and surface homogeneity are inspected by electron microscopy. As confirmed by X-ray diffraction the overlayer is made of anatase (the active polymorph of titanium dioxide), capable of photodegrading model contaminants. Furthermore, electrochemical techniques (cyclic voltammetry and electrochemical impedance spectroscopy) revealed that a highly ordered distribution of silver nanoparticles constitutes the active analytical core of the device, allowing easier electron transfer and better quantification of the analytes.
The system presents good sensing performances, reaching low detection limits even in the presence of typical interferents such as ascorbic and uric acids. Moreover, the titania photoactive top layer allows the complete recovery of the device performance in terms of sensitivity after a fast and simple UV-A cleaning step, affordable with different UV sources. In particular, three lamps (different in terms of power and wavelength) were tested, reaching the total removal of the contaminants in 10-15 minutes [5]. This “self-cleaning” property, combined with a remarkable resistance against aging and ease of use, allows to employ the sensor also for detection in real matrixes, such as liquor and serum.
ACKNOWLEDGEMENTS
The Authors would like to thank MIUR (Ministero dell’Istruzione, dell’Università e della Ricerca) for the fundings in the framework of the PRIN 2012 Project (20128ZZS2H)
REFERENCES
[1] C.M.A. Brett, Pure Appl. Chem. 73, 2001, pp 1969–1977.
[2] C.M. Welch, R.G. Compton, Anal. Bioanal. Chem. 384, 2006, pp 601–619.
[3] G. Maino, D. Meroni, V. Pifferi, L. Falciola, G. Soliveri, G. Cappelletti, S. Ardizzone, J. Nanoparticle Res. 15, 2013, pp 2087.
[4] G. Soliveri, V. Pifferi, G. Panzarasa, S. Ardizzone, G. Cappelletti, D. Meroni, K. Sparnacci, L. Falciola, Analyst 140, 2015, 1486-1494.
[5] V. Pifferi, G. Soliveri, G. Panzarasa, S. Ardizzone, G. Cappelletti, D. Meroni, L. Falciola, RSC Advances, 5, 2015, 71210-71214
Self-cleaning properties of a silica/silver nanoparticles/titania sandwich sensor
No full textOne of the main challenges faced during electroanalysis of complex matrices is represented by fouling and passivation of the electrode surface, especially in the fields of biomedical and environmental trace analysis [1], where sophisticated and highly engineered sensors have to be used in order to increase sensitivity and lower detection limits. These sensors can not be cleaned by conventional mechanical or electrochemical procedures, since these methods could affect the integrity of the active layer. In order to overcome these problems, the production of highly engineered reliable and reusable devices, designed ad hoc for specific applications, which could be simply cleaned by irradiation with UV light, would be an interesting step beyond the current state of the art.
In this context, a three-layered transparent electrode, in which silver nanoparticles are embedded between a bottom silica and a top titania layer [2, 3] was designed, prepared and characterized. The device structure is meant to confer multifunctional properties for a complex biomedical challenge: the detection and quantification of catecholamine neurotransmitters. The key role of each component of the device was thoroughly investigated to demonstrate the robustness and efficiency of the final sensor. In particular, the size distribution of silver nanoparticles, the device architecture and surface homogeneity were inspected by electron microscopy. The cleaning overlayer was made of the active polymorph of titanium dioxide (anatase), as confirmed by X-ray diffraction and by model contaminants photodegradation measurements. Electrochemical techniques (cyclic voltammetry and electrochemical impedance spectroscopy) revealed that an highly ordered distribution of silver nanoparticles is the active core of the device, allowing easier electron transfer and better quantification of the analytes even in the presence of conventional interferents, e.g. ascorbic acid and uric acid in human fluids.
The high photoactivity of titania top layer allowed total recovery of the device performance in terms of sensitivity after a fast (less than 20 min) UV cleaning step, affordable with different UV-A sources. This self-cleaning property, combined with a remarkable resistance against ageing, allows to employ the sensor also in on-field and remote applications.
References
[1] C. M. Welch and R. G. Compton, Anal. Bioanal. Chem. 2006, 384, 601–619.
[2] G. Maino, D. Meroni, V. Pifferi, L. Falciola, G. Soliveri, G. Cappelletti, S. Ardizzone, J. Nanoparticle Res. 2013, 15, 2087.
[3] G. Soliveri, V. Pifferi, G. Panzarasa, S. Ardizzone, G. Cappelletti, D. Meroni, K. Sparnacci, L. Falciola, Analyst 2015, 140, 1486
Self-cleaning features of an innovative engineered sensor based on silica, silver nanoparticles and titania
No full textPassivation of the electrode surface and fouling are important challenges in electroanalysis during the use of modified electrodes in complex matrices, especially in the biomedical and environmental fields [1-2].
In order to overcome such problems, the production of highly engineered ad hoc designed devices could access really effective sensors [2]. In particular, a performing, reliable and reusable sensor, that could be cleaned by a simple irradiation with UV or solar light, would be perfect for this purpose.
In this context, a three-layered transparent electrode, in which silver nanoparticles are embedded between a bottom silica and a top titania layer was developed [3-4]. Such structure confers to the device multifunctional properties for a complex biomedical challenge: the detection and quantification of catecholamine neurotransmitters. The sensor was thoroughly investigated by structural, morphological and electrochemical characterizations in order to understand the role of each component with the aim to improve the robustness and efficiency of the electroanalytical system.
The overlayer was made of anatase (the active polymorph of titanium dioxide) as confirmed by X-ray diffraction and by measuring the photodegradation of model contaminants. The size distribution of silver nanoparticles, the device architecture and surface homogeneity were inspected by electron microscopy. Electrochemical techniques (cyclic voltammetry and electrochemical impedance spectroscopy) revealed that a highly ordered distribution of silver nanoparticles constitutes the active core of the device, allowing easier electron transfer and better quantification of the analytes even in the presence of conventional interferents, e.g. ascorbic and uric acid. Titania photoactive top layer allowed total recovery of the device performance in terms of sensitivity after a fast and simple UV-A cleaning step, affordable with different UV sources. This self-cleaning property, combined with a remarkable resistance against aging and ease of use, allows to employ the sensor also in on-field and remote applications.
References
1. C.M.A. Brett, Pure Appl. Chem. 73, 2001, pp 1969–1977.
2. C.M. Welch, R.G. Compton, Anal. Bioanal. Chem. 384, 2006, pp 601–619.
3. G. Maino, D. Meroni, V. Pifferi, L. Falciola, G. Soliveri, G. Cappelletti, S. Ardizzone, J. Nanoparticle Res. 15, 2013, pp 2087.
4. G. Soliveri, V. Pifferi, G. Panzarasa, S. Ardizzone, G. Cappelletti, D. Meroni, K. Sparnacci, L. Falciola, Analyst 140, 2015, 1486-1494
Innovative engineered sensors based on silica, silver nanoparticles and titania with self-cleaning features
No full textPassivation of the electrode surface and fouling are important challenges in electroanalysis during the use of modified electrodes in complex matrices, especially in the biomedical and environmental fields (Soliveri et al., 2015). The production of highly engineered devices, ad hoc designed for specific applications, could overcome such problems, accessing really effective sensors. A performing, reliable and reusable sensor, that could be cleaned by a simple irradiation with UV or solar light, would perfectly match this goal.
In this context, a three-layered transparent electrode, in which silver nanoparticles are embedded between a bottom silica and a top titania layer (Maino et al., 2013 and Welch and Compton, 2006), was developed. Such structure confers to the device multifunctional properties for a complex biomedical challenge: the detection and quantification of catecholamine neurotransmitters. The sensor was thoroughly investigated in order to understand the role of each component with the aim of making the device a robust and efficient electroanalytical system.
The overlayer was made of anatase (the active polymorph of titanium dioxide) as confirmed by X-ray diffraction and by measuring the photodegradation of model contaminants. The size distribution of silver nanoparticles, the device architecture and surface homogeneity were inspected by electron microscopy. Electrochemical techniques (cyclic voltammetry and electrochemical impedance spectroscopy) revealed that a highly ordered distribution of silver nanoparticles constitutes the active core of the device, allowing easier electron transfer and better quantification of the analytes even in the presence of conventional interferents, e.g. ascorbic and uric acid. Titania photoactive top layer allowed total recovery of the device performance in terms of sensitivity after a fast and simple UV-A cleaning step, affordable with different UV sources. This self-cleaning property, combined with a remarkable resistance against aging and ease of use, allows to employ the sensor also in on-field and remote applications.
Maino G., Meroni D., Pifferi V., Falciola L., Soliveri G., Cappelletti G., Ardizzone S. (2013). Electrochemically assisted deposition of transparent, mechanically robust TiO2 films for advanced applications. J. Nanoparticle Res., 15, 2087.
Soliveri G., Pifferi V., Panzarasa G., Ardizzone S., Cappelletti G., Meroni D., Sparnacci K., Falciola L. (2015). Self-cleaning properties in engineered sensors fordopamine electroanalytical detection. Analyst, 140, 1486-1494.
Welch C. M., Compton R. G. (2006). The use of nanoparticles in electroanalysis: a review. Anal. Bioanal. Chem., 384, 601–619
Discrepancies between extinction events and boundary equilibria in reaction networks
No full textReaction networks are mathematical models of interacting chemical species that are primarily used in biochemistry. There are two modeling regimes that are typically used, one of which is deterministic and one that is stochastic. In particular, the deterministic model consists of an autonomous system of differential equations, whereas the stochastic system is a continuous-time Markov chain. Connections between the two modeling regimes have been studied since the seminal paper by Kurtz (J Chem Phys 57(7):2976–2978, 1972), where the deterministic model is shown to be a limit of a properly rescaled stochastic model over compact time intervals. Further, more recent studies have connected the long-term behaviors of the two models when the reaction network satisfies certain graphical properties, such as weak reversibility and a deficiency of zero. These connections have led some to conjecture a link between the long-term behavior of the two models exists, in some sense. In particular, one is tempted to believe that positive recurrence of all states for the stochastic model implies the existence of positive equilibria in the deterministic setting, and that boundary equilibria of the deterministic model imply the occurrence of an extinction event in the stochastic setting. We prove in this paper that these implications do not hold in general, even if restricting the analysis to networks that are bimolecular and that conserve the total mass. In particular, we disprove the implications in the special case of models that have absolute concentration robustness, thus answering in the negative a conjecture stated in the literature in 2014
Uniform approximation of solutions by elimination of intermediate species in deterministic reaction networks
No full textChemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a setting, based on ordinary differential equations, in which the presence of intermediate species has little effect on the overall dynamics of a biological system. The result provides a method to perform model reduction by elimination of intermediate species. We study the problem in a multiscale setting, where the species abundances as well as the reaction rates scale to different orders of magnitudes. The different time and concentration scales are parameterized by a single parameter N. We show that a solution to the original reaction system is uniformly approximated on compact time intervals to a solution of a reduced reaction system without intermediates and to a solution of a certain limiting reaction systems, which does not depend on N. Known approximation techniques such as the theorems by Tikhonov and Fenichel cannot readily be used in this framework
Insight into microtubule dynamics: from purified protein to cell
No full textMicrotubule-targeting agents have received considerable interest as potential tumour-selective anti-angiogenic and vascular-disrupting agents. To improve targeting of these agents, a detailed characterization of their interaction with tubulin/microtubule system is required and includes the analysis of stabilisation and depolymerisation of microtubules as well as imbalance in microtubule dynamics. We performed in vitro assays using purified tubulin to investigate the effects of microtubule-targeting agents on microtubule assembly in terms of polymer mass, polymerization kinetics, microtubule structure.and dynamics1. Moving from purified protein to cultured cells, we investigated the effects of microtubule-targeting agents on microtubule network by immunofluorescence and confocal analyses. Finally, microtubule dynamics in live cell was investigated by time lapse imaging of cells expressing the microtubule-associated protein EB3-GFP, a protein that binds specifically to the plus end of growing microtubules
Elimination of intermediate species in multiscale stochastic reaction networks
No full textWe study networks of biochemical reactions modelled by continuous time Markov processes. Such networks typically contain many molecular species and reactions and are hard to study analytically as well as by simulation. Particularly, we are interested in reaction networks with intermediate species such as the substrate-enzyme complex in the Michaelis-Menten mechanism. Such species are virtually in all real-world networks, they are typically short-lived, degraded at a fast rate and hard to observe experimentally. We provide conditions under which the Markov process of a multiscale reaction network with intermediate species is approximated by the Markov process of a simpler reduced reaction network without intermediate species. We do so by embedding the Markov processes into a one-parameter family of processes, where reaction rates and species abundances are scaled in the parameter. Further, we show that there are close links between these stochastic models and deterministic ODE models of the same networks
Product-form poisson-like distributions and complex balanced reaction systems
No full textStochastic reaction networks are dynamical models of biochemical reaction systems and form a particular class of continuous-time Markov chains on Nn. Here we provide a fundamental characterization that connects structural properties of a network to its dynamical features. Specifically, we define the notion of "stochastically complex balanced systems" in terms of the network's stationary distribution and provide a characterization of stochastically complex balanced systems, parallel to that established in the 1970s and 1980s for deterministic reaction networks. Additionally, we establish that a network is stochastically complex balanced if and only if an associated deterministic network is complex balanced (in the deterministic sense), thereby proving a strong link between the theory of stochastic and deterministic networks. Further, we prove a stochastic version of the "deficiency zero theorem" and show that any (not only complex balanced) deficiency zero reaction network has a product-form Poisson-like stationary distribution on all irreducible components. Finally, we provide sufficient conditions for when a product-form Poisson-like distribution on a single (or all) component(s) implies the network is complex balanced, and we explore the possibility to characterize complex balanced systems in terms of product-form Poisson-like stationary distributions
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