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Stochastic chemical kinetics : A review of the modelling and simulation approaches.

Biophysical reviews

Lecca P.
PMID: 28510113
Biophys Rev. 2013 Dec;5(4):323-345. doi: 10.1007/s12551-013-0122-2. Epub 2013 Jul 30.

A review of the physical principles that are the ground of the stochastic formulation of chemical kinetics is presented along with a survey of the algorithms currently used to simulate it. This review covers the main literature of the...

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Lecca P. Stochastic chemical kinetics : A review of the modelling and simulation approaches. Biophys Rev. 2013;5(4):323-345doi: 10.1007/s12551-013-0122-2.
Lecca, P. (2013). Stochastic chemical kinetics : A review of the modelling and simulation approaches. Biophysical reviews, 5(4), 323-345. https://doi.org/10.1007/s12551-013-0122-2
Lecca, Paola. "Stochastic chemical kinetics : A review of the modelling and simulation approaches." Biophysical reviews vol. 5,4 (2013): 323-345. doi: https://doi.org/10.1007/s12551-013-0122-2
Lecca P. Stochastic chemical kinetics : A review of the modelling and simulation approaches. Biophys Rev. 2013 Dec;5(4):323-345. doi: 10.1007/s12551-013-0122-2. Epub 2013 Jul 30. PMID: 28510113; PMCID: PMC5425731.
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Life-threatening asthma attack during prolonged fingolimod treatment: case report.

Patient preference and adherence

Zecca C, Caporro M, Györik S, Gobbi C.
PMID: 25053881
Patient Prefer Adherence. 2014 Jul 14;8:987-9. doi: 10.2147/PPA.S65708. eCollection 2014.

BACKGROUND: Fingolimod (FTY) mediates bronchoconstriction by interacting with sphingosine-1-phosphate receptors. The majority of the reported adverse respiratory events occur during the first weeks of treatment.CASE PRESENTATION: A 49-year-old woman developed a life-threatening asthma attack after 6 months of continuous...

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Zecca C, Caporro M, Györik S, et al. Life-threatening asthma attack during prolonged fingolimod treatment: case report. Patient Prefer Adherence. 2014;8:987-9doi: 10.2147/PPA.S65708.
Zecca, C., Caporro, M., Györik, S., & Gobbi, C. (2014). Life-threatening asthma attack during prolonged fingolimod treatment: case report. Patient preference and adherence, 8987-9. https://doi.org/10.2147/PPA.S65708
Zecca, Chiara, et al. "Life-threatening asthma attack during prolonged fingolimod treatment: case report." Patient preference and adherence vol. 8 (2014): 987-9. doi: https://doi.org/10.2147/PPA.S65708
Zecca C, Caporro M, Györik S, Gobbi C. Life-threatening asthma attack during prolonged fingolimod treatment: case report. Patient Prefer Adherence. 2014 Jul 14;8:987-9. doi: 10.2147/PPA.S65708. eCollection 2014. PMID: 25053881; PMCID: PMC4105229.
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Direct evaluation of secondary orbital interactions in the Diels-Alder reaction between cyclopentadiene and maleic anhydride.

The Journal of organic chemistry

Arrieta A, Cossío FP, Lecea B.
PMID: 11529749
J Org Chem. 2001 Sep 07;66(18):6178-80. doi: 10.1021/jo0158478.

No abstract available.

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Arrieta A, Cossío FP, Lecea B. Direct evaluation of secondary orbital interactions in the Diels-Alder reaction between cyclopentadiene and maleic anhydride. J Org Chem. 2001;66(18):6178-80doi: 10.1021/jo0158478.
Arrieta, A., Cossío, F. P., & Lecea, B. (2001). Direct evaluation of secondary orbital interactions in the Diels-Alder reaction between cyclopentadiene and maleic anhydride. The Journal of organic chemistry, 66(18), 6178-80. https://doi.org/10.1021/jo0158478
Arrieta, A, et al. "Direct evaluation of secondary orbital interactions in the Diels-Alder reaction between cyclopentadiene and maleic anhydride." The Journal of organic chemistry vol. 66,18 (2001): 6178-80. doi: https://doi.org/10.1021/jo0158478
Arrieta A, Cossío FP, Lecea B. Direct evaluation of secondary orbital interactions in the Diels-Alder reaction between cyclopentadiene and maleic anhydride. J Org Chem. 2001 Sep 07;66(18):6178-80. doi: 10.1021/jo0158478. PMID: 11529749.
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[Consequences of early failure in kidney transplant].

Minerva nefrologica

Cantaluppi A, Frontini A, Colombo A, Giorgianni V, Mecca G, Ponticelli C.
PMID: 7012688
Minerva Nefrol. 1980 Apr-Jun;27(2):275-7.

No abstract available.

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Cantaluppi A, Frontini A, Colombo A, et al. Consequenze del fallimento porecoce del trapianto remale. [Consequences of early failure in kidney transplant]. Minerva Nefrol. 1980;27(2):275-7
Cantaluppi, A., Frontini, A., Colombo, A., Giorgianni, V., Mecca, G., & Ponticelli, C. (1980). Consequenze del fallimento porecoce del trapianto remale. [Consequences of early failure in kidney transplant]. Minerva nefrologica, 27(2), 275-7.
Cantaluppi, A, et al. "Consequenze del fallimento porecoce del trapianto remale." [Consequences of early failure in kidney transplant]. Minerva nefrologica vol. 27,2 (1980): 275-7.
Cantaluppi A, Frontini A, Colombo A, Giorgianni V, Mecca G, Ponticelli C. Consequenze del fallimento porecoce del trapianto remale. [Consequences of early failure in kidney transplant]. Minerva Nefrol. 1980 Apr-Jun;27(2):275-7. Italian. PMID: 7012688.
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Activity enhancement by the support in the hydrogenation of C=C bonds over polymer-supported palladium catalysts.

Chemistry (Weinheim an der Bergstrasse, Germany)

Zecca M, Fisera R, Palma G, Lora S, Hronec M, Kralik M.
PMID: 10894397
Chemistry. 2000 Jun 02;6(11):1980-6. doi: 10.1002/1521-3765(20000602)6:11<1980::aid-chem1980>3.0.co;2-z.

Four synthetic ion-exchange resins (AH, BH, CH, DH) of different hydrophilic/hydrophobic properties were used as supports for heterogeneous palladium catalysts (A, B, C, D). The resins contained styrene (STY) and 2-(methacryloxy)ethylsulfonic acid (MESA) as the comonomers. Either divinylbenzene (DVB:...

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Zecca M, Fisera R, Palma G, et al. Activity enhancement by the support in the hydrogenation of C=C bonds over polymer-supported palladium catalysts. Chemistry. 2000;6(11):1980-6doi: 10.1002/1521-3765(20000602)6:11<1980::aid-chem1980>3.0.co;2-z.
Zecca, M., Fisera, R., Palma, G., Lora, S., Hronec, M., & Kralik, M. (2000). Activity enhancement by the support in the hydrogenation of C=C bonds over polymer-supported palladium catalysts. Chemistry (Weinheim an der Bergstrasse, Germany), 6(11), 1980-6. https://doi.org/10.1002/1521-3765(20000602)6:11<1980::aid-chem1980>3.0.co;2-z
Zecca, et al. "Activity enhancement by the support in the hydrogenation of C=C bonds over polymer-supported palladium catalysts." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 6,11 (2000): 1980-6. doi: https://doi.org/10.1002/1521-3765(20000602)6:11<1980::aid-chem1980>3.0.co;2-z
Zecca M, Fisera R, Palma G, Lora S, Hronec M, Kralik M. Activity enhancement by the support in the hydrogenation of C=C bonds over polymer-supported palladium catalysts. Chemistry. 2000 Jun 02;6(11):1980-6. doi: 10.1002/1521-3765(20000602)6:11<1980::aid-chem1980>3.0.co;2-z. PMID: 10894397.
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Peierls-like transition induced by frustration in a two-dimensional antiferromagnet.

Physical review letters

Becca F, Mila F.
PMID: 12144417
Phys Rev Lett. 2002 Jul 15;89(3):037204. doi: 10.1103/PhysRevLett.89.037204. Epub 2002 Jul 01.

We show that the introduction of frustration into the spin- 1/2 two-dimensional (2D) antiferromagnetic Heisenberg model on a square lattice via a next-nearest-neighbor exchange interaction can lead to a Peierls-like transition, from a tetragonal to an orthorhombic phase, when...

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Becca F, Mila F. Peierls-like transition induced by frustration in a two-dimensional antiferromagnet. Phys Rev Lett. 2002;89(3):037204doi: 10.1103/PhysRevLett.89.037204.
Becca, F., & Mila, F. (2002). Peierls-like transition induced by frustration in a two-dimensional antiferromagnet. Physical review letters, 89(3), 037204. https://doi.org/10.1103/PhysRevLett.89.037204
Becca, Federico, and Mila, Frédéric. "Peierls-like transition induced by frustration in a two-dimensional antiferromagnet." Physical review letters vol. 89,3 (2002): 037204. doi: https://doi.org/10.1103/PhysRevLett.89.037204
Becca F, Mila F. Peierls-like transition induced by frustration in a two-dimensional antiferromagnet. Phys Rev Lett. 2002 Jul 15;89(3):037204. doi: 10.1103/PhysRevLett.89.037204. Epub 2002 Jul 01. PMID: 12144417.
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Origins of the Stereodivergent Outcome in the Staudinger Reaction between Acyl Chlorides and Imines.

The Journal of organic chemistry

Arrieta A, Lecea B, Cossío FP.
PMID: 11672189
J Org Chem. 1998 Aug 21;63(17):5869-5876. doi: 10.1021/jo9804745.

Calculations using density functional theory (DFT, B3LYP/6-31G level) provide an explanation for the stereodivergent outcome observed in the Staudinger reaction between acyl chlorides and imines to form 2-azetidinones (beta-lactams). When the ketene is formed prior to the cycloaddition stages,...

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Arrieta A, Lecea B, Cossío FP. Origins of the Stereodivergent Outcome in the Staudinger Reaction between Acyl Chlorides and Imines. J Org Chem. 1998;63(17):5869-5876doi: 10.1021/jo9804745.
Arrieta, A., Lecea, B., & Cossío, F. P. (1998). Origins of the Stereodivergent Outcome in the Staudinger Reaction between Acyl Chlorides and Imines. The Journal of organic chemistry, 63(17), 5869-5876. https://doi.org/10.1021/jo9804745
Arrieta, Ana, et al. "Origins of the Stereodivergent Outcome in the Staudinger Reaction between Acyl Chlorides and Imines." The Journal of organic chemistry vol. 63,17 (1998): 5869-5876. doi: https://doi.org/10.1021/jo9804745
Arrieta A, Lecea B, Cossío FP. Origins of the Stereodivergent Outcome in the Staudinger Reaction between Acyl Chlorides and Imines. J Org Chem. 1998 Aug 21;63(17):5869-5876. doi: 10.1021/jo9804745. PMID: 11672189.
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On the mechanism of conversion of N-acyl-4-acyloxy-beta-lactams into 2-substituted 1,3-oxazin-6-ones. Can a low-barrier transition state be antiaromatic?.

The Journal of organic chemistry

Alajarín M, Sánchez-Andrada P, Cossío FP, Arrieta A, Lecea B.
PMID: 11735527
J Org Chem. 2001 Dec 14;66(25):8470-7. doi: 10.1021/jo015922e.

The mechanism of the conversion of N-acyl-4-acyloxy-beta-lactams into 1,3-oxazin-6-ones has been investigated using ab initio and density functional theories. It has been found that two pseudopericyclic reactions are involved in the whole process. The first key reaction is a...

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Alajarín M, Sánchez-Andrada P, Cossío FP, et al. On the mechanism of conversion of N-acyl-4-acyloxy-beta-lactams into 2-substituted 1,3-oxazin-6-ones. Can a low-barrier transition state be antiaromatic?. J Org Chem. 2001;66(25):8470-7doi: 10.1021/jo015922e.
Alajarín, M., Sánchez-Andrada, P., Cossío, F. P., Arrieta, A., & Lecea, B. (2001). On the mechanism of conversion of N-acyl-4-acyloxy-beta-lactams into 2-substituted 1,3-oxazin-6-ones. Can a low-barrier transition state be antiaromatic?. The Journal of organic chemistry, 66(25), 8470-7. https://doi.org/10.1021/jo015922e
Alajarín, M, et al. "On the mechanism of conversion of N-acyl-4-acyloxy-beta-lactams into 2-substituted 1,3-oxazin-6-ones. Can a low-barrier transition state be antiaromatic?." The Journal of organic chemistry vol. 66,25 (2001): 8470-7. doi: https://doi.org/10.1021/jo015922e
Alajarín M, Sánchez-Andrada P, Cossío FP, Arrieta A, Lecea B. On the mechanism of conversion of N-acyl-4-acyloxy-beta-lactams into 2-substituted 1,3-oxazin-6-ones. Can a low-barrier transition state be antiaromatic?. J Org Chem. 2001 Dec 14;66(25):8470-7. doi: 10.1021/jo015922e. PMID: 11735527.
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Determination of the total content and binding pattern of elements in human milk by high performance liquid chromatography-inductively coupled plasma atomic emission spectrometry.

Talanta

Bocca B, Alimonti A, Coni E, Di Pasquale M, Giglio L, Piccioli Bocca A, Caroli S.
PMID: 18968115
Talanta. 2000 Nov 01;53(2):295-303. doi: 10.1016/s0039-9140(00)00473-2.

Evidence of element speciation in biological fluids is scarce and fragmentary in the literature. On the other hand, it is well known that chemical speciation analysis is prone to error due to contamination, modification or breaking up of the...

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Bocca B, Alimonti A, Coni E, et al. Determination of the total content and binding pattern of elements in human milk by high performance liquid chromatography-inductively coupled plasma atomic emission spectrometry. Talanta. 2000;53(2):295-303doi: 10.1016/s0039-9140(00)00473-2.
Bocca, B., Alimonti, A., Coni, E., Di Pasquale, M., Giglio, L., Piccioli Bocca, A., & Caroli, S. (2000). Determination of the total content and binding pattern of elements in human milk by high performance liquid chromatography-inductively coupled plasma atomic emission spectrometry. Talanta, 53(2), 295-303. https://doi.org/10.1016/s0039-9140(00)00473-2
Bocca, B, et al. "Determination of the total content and binding pattern of elements in human milk by high performance liquid chromatography-inductively coupled plasma atomic emission spectrometry." Talanta vol. 53,2 (2000): 295-303. doi: https://doi.org/10.1016/s0039-9140(00)00473-2
Bocca B, Alimonti A, Coni E, Di Pasquale M, Giglio L, Piccioli Bocca A, Caroli S. Determination of the total content and binding pattern of elements in human milk by high performance liquid chromatography-inductively coupled plasma atomic emission spectrometry. Talanta. 2000 Nov 01;53(2):295-303. doi: 10.1016/s0039-9140(00)00473-2. PMID: 18968115.
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Variational description of Mott insulators.

Physical review letters

Capello M, Becca F, Fabrizio M, Sorella S, Tosatti E.
PMID: 15698205
Phys Rev Lett. 2005 Jan 21;94(2):026406. doi: 10.1103/PhysRevLett.94.026406. Epub 2005 Jan 20.

The Gutzwiller wave function for a strongly correlated model can, if supplemented with a long-range Jastrow factor, provide a proper variational description of Mott insulators, so far unavailable. We demonstrate this concept in the prototypical one-dimensional t-t(') Hubbard model,...

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Capello M, Becca F, Fabrizio M, et al. Variational description of Mott insulators. Phys Rev Lett. 2005;94(2):026406doi: 10.1103/PhysRevLett.94.026406.
Capello, M., Becca, F., Fabrizio, M., Sorella, S., & Tosatti, E. (2005). Variational description of Mott insulators. Physical review letters, 94(2), 026406. https://doi.org/10.1103/PhysRevLett.94.026406
Capello, Manuela, et al. "Variational description of Mott insulators." Physical review letters vol. 94,2 (2005): 026406. doi: https://doi.org/10.1103/PhysRevLett.94.026406
Capello M, Becca F, Fabrizio M, Sorella S, Tosatti E. Variational description of Mott insulators. Phys Rev Lett. 2005 Jan 21;94(2):026406. doi: 10.1103/PhysRevLett.94.026406. Epub 2005 Jan 20. PMID: 15698205.
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Highly hydrophilic copolymers of N,N-dimethylacrylamide, acrylamido-2-methylpropanesulfonic acid, and ethylenedimethacrylate: nanoscale morphology in the swollen state and use as exotemplates for synthesis of nanostructured ferric oxide.

Chemistry (Weinheim an der Bergstrasse, Germany)

Centomo P, Jeřábek K, Canova D, Zoleo A, Maniero AL, Sassi A, Canton P, Corain B, Zecca M.
PMID: 22461082
Chemistry. 2012 May 21;18(21):6632-43. doi: 10.1002/chem.201102359. Epub 2012 Mar 29.

The polymer framework of water-swollen copolymers of N,N-dimethylacrylamide, acrylamido-2-methylpropanesulfonic acid, and ethylenedimethacrylate (nominal cross-linking degrees of 4, 8, and 20 mol %) is composed of highly expanded domains, with "pores" not less than 6 nm in diameter. When the...

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Centomo P, Jeřábek K, Canova D, et al. Highly hydrophilic copolymers of N,N-dimethylacrylamide, acrylamido-2-methylpropanesulfonic acid, and ethylenedimethacrylate: nanoscale morphology in the swollen state and use as exotemplates for synthesis of nanostructured ferric oxide. Chemistry. 2012;18(21):6632-43doi: 10.1002/chem.201102359.
Centomo, P., Jeřábek, K., Canova, D., Zoleo, A., Maniero, A. L., Sassi, A., Canton, P., Corain, B., & Zecca, M. (2012). Highly hydrophilic copolymers of N,N-dimethylacrylamide, acrylamido-2-methylpropanesulfonic acid, and ethylenedimethacrylate: nanoscale morphology in the swollen state and use as exotemplates for synthesis of nanostructured ferric oxide. Chemistry (Weinheim an der Bergstrasse, Germany), 18(21), 6632-43. https://doi.org/10.1002/chem.201102359
Centomo, Paolo, et al. "Highly hydrophilic copolymers of N,N-dimethylacrylamide, acrylamido-2-methylpropanesulfonic acid, and ethylenedimethacrylate: nanoscale morphology in the swollen state and use as exotemplates for synthesis of nanostructured ferric oxide." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 18,21 (2012): 6632-43. doi: https://doi.org/10.1002/chem.201102359
Centomo P, Jeřábek K, Canova D, Zoleo A, Maniero AL, Sassi A, Canton P, Corain B, Zecca M. Highly hydrophilic copolymers of N,N-dimethylacrylamide, acrylamido-2-methylpropanesulfonic acid, and ethylenedimethacrylate: nanoscale morphology in the swollen state and use as exotemplates for synthesis of nanostructured ferric oxide. Chemistry. 2012 May 21;18(21):6632-43. doi: 10.1002/chem.201102359. Epub 2012 Mar 29. PMID: 22461082.
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Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks.

Computational biology and chemistry

Damiani C, Filisetti A, Graudenzi A, Lecca P.
PMID: 23246776
Comput Biol Chem. 2013 Feb;42:5-17. doi: 10.1016/j.compbiolchem.2012.10.007. Epub 2012 Nov 07.

A general numerical methodology for parametric sensitivity analysis is proposed, which allows to determine the parameters exerting the greatest influence on the output of a stochastic computational model, especially when the knowledge about the actual value of a parameter...

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Damiani C, Filisetti A, Graudenzi A, et al. Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Comput Biol Chem. 2012;42:5-17doi: 10.1016/j.compbiolchem.2012.10.007.
Damiani, C., Filisetti, A., Graudenzi, A., & Lecca, P. (2013). Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Computational biology and chemistry, 425-17. https://doi.org/10.1016/j.compbiolchem.2012.10.007
Damiani, Chiara, et al. "Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks." Computational biology and chemistry vol. 42 (2013): 5-17. doi: https://doi.org/10.1016/j.compbiolchem.2012.10.007
Damiani C, Filisetti A, Graudenzi A, Lecca P. Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Comput Biol Chem. 2013 Feb;42:5-17. doi: 10.1016/j.compbiolchem.2012.10.007. Epub 2012 Nov 07. PMID: 23246776.
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Showing 1 to 12 of 294 entries