Subproject C.9

Duration

since 1-1-2015

Publications

Maier, F. C. ; Fyta, M.: Influence of dynamics on the conductance across functionalized electrodes for biodetection. (2019)
- BibTeX
BibTeX
@article{maier2019influence, author = {Maier, F. C. and Fyta, M.}, title = {Influence of dynamics on the conductance across functionalized electrodes for biodetection.}, year = 2019 }
Maier, F. C. ; Sarap, C. S. ; Dou, M. ; Sivaraman, G. ; Fyta, M.: Diamondoid-functionalized nanogaps: From small molecules to electronic biosensing. In: Holm, C. ; Ertl, T. ; Schmauder, S. ; Kästner, J. ; Groß, J. (Hrsg.) The European Physical Journal (Special Topics), The European Physical Journal (Special Topics). Bd. 227: Particle Methods in Natural Science and Engineering (2019b), Nr. 14, S. 1681--1692
- BibTeX
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@article{maier2019diamondoidfunctionalized, author = {Maier, F. C. and Sarap, C. S. and Dou, M. and Sivaraman, G. and Fyta, M.}, editor = {Holm, C. and Ertl, T. and Schmauder, S. and Kästner, J. and Groß, J.}, journal = {The European Physical Journal (Special Topics)}, number = 14, pages = {1681--1692}, title = {Diamondoid-functionalized nanogaps: From small molecules to electronic biosensing.}, volume = {227: Particle Methods in Natural Science and Engineering}, year = 2019 }
Maier, F. C. ; Dou, M. ; Fyta, M.: Solvent effects in the transmission across diamondoid-functionalized gaps reading-out DANN. (2019a)
- BibTeX
BibTeX
@article{maier2019solvent, author = {Maier, F. C. and Dou, M. and Fyta, M.}, title = {Solvent effects in the transmission across diamondoid-functionalized gaps reading-out DANN.}, year = 2019 }
Sarap, C.S. ; Adhikari, B. ; Meng, S. ; Uhlig, F. ; Fyta, M.: Optical Properties of Single- and Double-Functionalized Small Diamondoids. In: The Journal of Physical Chemistry A, The Journal of Physical Chemistry A. Bd. 2018 122 (2018b), Nr. 14, S. 3583–3593
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- Link
BibTeX
@article{sarap2018optical, author = {Sarap, C.S. and Adhikari, B. and Meng, S. and Uhlig, F. and Fyta, M.}, doi = {10.1021/acs.jpca.7b12519}, journal = {The Journal of Physical Chemistry A}, language = {en}, month = {February 2018}, number = 14, pages = {3583-3593}, title = {Optical Properties of Single- and Double-Functionalized Small Diamondoids}, url = {https://doi.org/10.1021/acs.jpca.7b12519}, volume = {2018 122}, year = 2018 }
Link
https://doi.org/10.1021/acs.jpca.7b12519
Sarap, C. S. ; Partov-Azar, P. ; Fyta, M.: Optoelectronic properties of diamondoid-DNA complexes. In: ACS Applied Bio Materials, ACS Applied Bio Materials. Bd. 1 (2018a), Nr. 1, S. 59–69
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@article{sarap2018optoelectronic, author = {Sarap, C. S. and Partov-Azar, P. and Fyta, M.}, journal = {ACS Applied Bio Materials}, number = 1, pages = {59-69}, title = {Optoelectronic properties of diamondoid-DNA complexes.}, volume = 1, year = 2018 }
Cruz-Leon, Sergio ; Vazquez-Mayagoitia, Alvaro ; Melchionna, Simone ; Schwierz, Nadine ; Fyta, Maria: Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations. In: The Journal of Physical Chemistry B, The Journal of Physical Chemistry B. Bd. 122 (2018), Nr. 32, S. 7915--7928
- BibTeX
BibTeX
@article{cruzleon2018coarsegrained, affiliation = {Fyta, M (Reprint Author), Univ Stuttgart, Inst Computat Phys, Allmandring 3, D-70569 Stuttgart, Germany. Cruz-Leon, Sergio; Fyta, Maria, Univ Stuttgart, Inst Computat Phys, Allmandring 3, D-70569 Stuttgart, Germany. Cruz-Leon, Sergio; Schwierz, Nadine, Max Planck Inst Biophys, Dept Theoret Biophys, Max von Laue Str 3, D-60438 Frankfurt, Germany. Vazquez-Mayagoitia, Alvaro, Argonne Natl Lab, 9700 S Cass Ave,Bldg 240, Argonne, IL USA. Melchionna, Simone, Univ Sapienza, Dipartimento Fis, ISC CNR, Ist Sistemi Complessi, Ple A Moro 2, I-00185 Rome, Italy.}, author = {Cruz-Leon, Sergio and Vazquez-Mayagoitia, Alvaro and Melchionna, Simone and Schwierz, Nadine and Fyta, Maria}, da = {2019-03-13}, doi = {10.1021/acs.jpcb.8b03566}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, language = {English}, number = 32, orcid-numbers = {Fyta, Maria/0000-0002-5425-7907 Cruz-Leon, Sergio/0000-0003-1256-2206}, pages = {7915--7928}, research-areas = {Chemistry}, title = {Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations.}, type = {Article}, unique-id = {ISI:000442437700012}, volume = 122, year = 2018 }
Sivaraman, Ganesh ; Amorim, Rodrigo G. ; Scheicherb, Ralph H. ; Fyta, Maria: Insights into the detection of mutations and epigenetic markers using diamondoidfunctionalized sensors. In: RSC Advances, RSC Advances. Bd. 7 (2017), Nr. 68, S. 43064–43072
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@article{sivaraman17b, abstract = {Nanogaps functionalized with small diamond-like particles, diamondoids, have been shown to effectively distinguish between different DNA nucleotides. Here, we focus on the detection of mutations and epigenetic markers using such devices. Based on quantum mechanical simulations within the density functional theory approach coupled with the non-equilibrium Green’s function scheme, we provide deeper insight into the inherent differences in detecting modified nucleotides. Our results strongly underline the influence of the type of functionalization molecule of the nanogap, as well its conformational details within the nanogap, on the sensing efficiency of the device. The electronic features for the mutations and epigenetic markers are compared to those for the respective canonical nucleotides that are detected by different devices. The calculations directly correlate the structural and electronic properties of the different nucleotides with the electronic transmission across the diamondoid-based device. The latter was found to be controlled by the functionalizing molecule and its binding to the nucleotides. We report on the direct connection of these characteristics to the sensitivity of the diamondoid-functionalized nanogaps, which could eventually be embedded in a nanopore device, and discuss the implications for DNA sensing.}, author = {Sivaraman, Ganesh and Amorim, Rodrigo G. and Scheicherb, Ralph H. and Fyta, Maria}, doi = {10.1039/C7RA06889A}, file = {sivaraman17b.pdf:sivaraman17b.pdf:PDF}, journal = {RSC Advances}, number = 68, owner = {tkobayashi}, pages = {43064-43072}, title = {Insights into the detection of mutations and epigenetic markers using diamondoidfunctionalized sensors}, volume = 7, year = 2017 }
Datar, Adwait V. ; Fyta, Maria ; Marconi, Umberto Marini Bettolo ; Melchionna, Simone: Electrokinetic Lattice Boltzmann Solver Coupled to Molecular Dynamics: Application to Polymer Translocation. In: Langmuir, Langmuir. Bd. 33 (2017), Nr. 42, S. 11635–11645
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BibTeX
@article{datar2017electrokinetic, affiliation = {Marconi, UMB (Reprint Author), Univ Camerino, Scuola Sci \& Tecnol, Via Madonna Carceri, I-62032 Camerino, Italy. Datar, Adwait V.; Fyta, Maria, Univ Stuttgart, Inst Computat Phys, Allmandring 3, D-70569 Stuttgart, Germany. Marconi, Umberto Marini Bettolo, Univ Camerino, Scuola Sci \& Tecnol, Via Madonna Carceri, I-62032 Camerino, Italy. Melchionna, Simone, Univ Sapienza, Dipartimento Fis, ISC, CNR, Ple A Moro 2, I-00185 Rome, Italy.}, author = {Datar, Adwait V. and Fyta, Maria and Marconi, Umberto Marini Bettolo and Melchionna, Simone}, da = {2018-02-09}, doi = {10.1021/acs.langmuir.7601997}, issn = {0743-7463}, journal = {Langmuir}, language = {English}, number = 42, orcid-numbers = {Marini Bettolo Marconi, Umberto/0000-0002-2764-8259 Fyta, Maria/0000-0002-5425-7907}, pages = {11635-11645}, research-areas = {Chemistry; Materials Science}, researcherid-numbers = {Marini Bettolo Marconi, Umberto/B-7123-2011 Fyta, Maria/F-8562-2013}, title = {Electrokinetic Lattice Boltzmann Solver Coupled to Molecular Dynamics: Application to Polymer Translocation}, type = {Article}, unique-id = {ISI:000413992700055}, volume = 33, year = 2017 }
Natterer, Andreas ; Adhikari, Bibek ; Fyta, Maria: Complexes of carbene-functionalized diamondoids and metal atoms: Electronic properties. In: Journal of Organometallic Chemistry, Journal of Organometallic Chemistry. Bd. 815–816 (2016), S. 8–15
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BibTeX
@article{natterer16a, author = {Natterer, Andreas and Adhikari, Bibek and Fyta, Maria}, doi = {10.1016/j.jorganchem.2016.04.024}, file = {natterer16a.pdf:natterer16a.pdf:PDF}, journal = {Journal of Organometallic Chemistry}, owner = {tkobayashi}, pages = {8-15}, title = {Complexes of carbene-functionalized diamondoids and metal atoms: Electronic properties}, volume = {815-816}, year = 2016 }
Sivaraman, Ganesh ; de Souza, Fabio A. L. ; Amorim, Rodrigo G. ; Scopela, Wanderla L. ; Fyta, Maria ; Scheicher, Ralph H.: Electronic Transport along Hybrid MoS2 Monolayers. In: The Journal of Physical Chemistry C, The Journal of Physical Chemistry C. Bd. 120 (2016c), Nr. 41, S. 23389--3396
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BibTeX
@article{sivaraman16c, author = {Sivaraman, Ganesh and de Souza, Fabio A. L. and Amorim, Rodrigo G. and Scopela, Wanderla L. and Fyta, Maria and Scheicher, Ralph H.}, doi = {10.1021/acs.jpcc.6b07917}, file = {sivaraman16c.pdf:sivaraman16c.pdf:PDF}, journal = {The Journal of Physical Chemistry C}, number = 41, owner = {tkobayashi}, pages = {23389--3396}, title = {Electronic Transport along Hybrid MoS2 Monolayers.}, volume = 120, year = 2016 }
Sivaraman, Ganesh ; Amorim, Rodrigo G. ; Scheicher, Ralph H. ; Fyta, Maria: Benchmark investigation of diamondoid-functionalized electrodes for nanopore DNA sequencing. In: NANOTECHNOLOGY, NANOTECHNOLOGY. Bd. 27, IOP PUBLISHING LTD (2016a), Nr. 41
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BibTeX
@article{sivaraman2016benchmark, affiliation = {Fyta, M (Reprint Author), Univ Stuttgart, Inst Computat Phys, Stuttgart, Germany. Sivaraman, Ganesh; Fyta, Maria, Univ Stuttgart, Inst Computat Phys, Stuttgart, Germany. Amorim, Rodrigo G.; Scheicher, Ralph H., Uppsala Univ, Dept Phys \& Astron, Div Mat Theory, Uppsala, Sweden. Amorim, Rodrigo G., Univ Fed Fluminense, Dept Fis, ICEx, Volta Redonda, RJ, Brazil.}, article-number = {414002}, author = {Sivaraman, Ganesh and Amorim, Rodrigo G. and Scheicher, Ralph H. and Fyta, Maria}, da = {2017-07-13}, doi = {10.1088/0957-4484/27/41/414002}, eissn = {1361-6528}, issn = {0957-4484}, journal = {NANOTECHNOLOGY}, language = {English}, month = {OCT 14}, number = 41, oa = {No}, orcid-numbers = {Scheicher, Ralph/0000-0001-5397-7753 Amorim, Rodrigo/0000-0001-9611-8772}, publisher = {IOP PUBLISHING LTD}, research-areas = {Science \& Technology - Other Topics; Materials Science; Physics}, researcherid-numbers = {Scheicher, Ralph/G-1740-2012}, title = {Benchmark investigation of diamondoid-functionalized electrodes for nanopore DNA sequencing}, type = {Article}, unique-id = {ISI:000394367200001}, volume = 27, year = 2016 }
Adhikari, Bibek ; Sivaraman, Ganesh ; Fyta, Maria: Diamondoid-based molecular junctions: a computational study. In: NANOTECHNOLOGY, NANOTECHNOLOGY. Bd. 27. TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND, IOP PUBLISHING LTD (2016b), Nr. 48
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@article{ISI:000388006400001, abstract = {{In this work, we deal with the computational investigation of diamondoid-based molecular conductance junctions and their electronic transport properties. A small diamondoid is placed between the two gold electrodes of the nanogap and is covalently bonded to the gold electrodes through two different molecules, a thiol group and a N-heterocyclic carbene molecule. We have shown that the thiol linker is more efficient as it introduces additional electron paths for transport at lower energies. The influence of doping the diamondoid on the properties of the molecular junctions has been investigated. We find that using a nitrogen atom to dope the diamondoids leads to a considerable increase of the zero bias conductance. For the N-doped system we show an asymmetric feature of the I-V curve of the junctions resulting in rectification within a very small range of bias voltages. The rectifying nature is the result of the characteristic shift in the bias-dependent highest occupied molecular orbital state. In all cases, the efficiency of the device is manifested and is discussed in view of novel nanotechnological applications.}}, address = {{TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND}}, affiliation = {{Fyta, M (Reprint Author), Univ Stuttgart, Inst Computat Phys, Allmandring 3, D-70569 Stuttgart, Germany. Adhikari, Bibek; Sivaraman, Ganesh; Fyta, Maria, Univ Stuttgart, Inst Computat Phys, Allmandring 3, D-70569 Stuttgart, Germany.}}, article-number = {{485207}}, author = {Adhikari, Bibek and Sivaraman, Ganesh and Fyta, Maria}, author-email = {{mfyta@icp.uni-stuttgart.de}}, doi = {{10.1088/0957-4484/27/48/485207}}, eissn = {{1361-6528}}, funding-acknowledgement = {{Junior-professorenprogramm - Ministry of Science, Research and the Arts Baden-Wurttemberg (MWK); German Funding Agency (Deutsche Forschungsgemeinschaft-DFG) {[}SFB 716]; Ministry of Science, Research and the Arts Baden-Wurrttenberg (MWK); German Research Foundation (DFG); DFG; bwHPC initiative}}, funding-text = {{The authors acknowledge financial support from the Junior-professorenprogramm funded by the Ministry of Science, Research and the Arts Baden-Wurttemberg (MWK) and from the collaborative network SFB 716 `Dynamic simulations of systems with large particle numbers' funded by the German Funding Agency (Deutsche Forschungsgemeinschaft-DFG). This research was supported in part by the bwHPC initiative and the bwHPC-C5 project provided through associated compute services of the JUSTUS HPC facility at the University of Ulm. The bwHPC and bwHPC-C5 (http://www.bwhpc-c5.de) are funded by the Ministry of Science, Research and the Arts Baden-Wurrttenberg (MWK) and the German Research Foundation (DFG). Part of this work was performed on the computational resource ForHLR Phase I funded by the Ministry of Science, Research and the Arts Baden-Wurttemberg and DFG.}}, issn = {{0957-4484}}, journal = {{NANOTECHNOLOGY}}, keywords-plus = {{SELF-ASSEMBLED MONOLAYERS; N-HETEROCYCLIC CARBENES; ELECTRONIC TRANSPORT; RECTIFICATION; PHOTOEMISSION; CONDUCTANCE; SIMULATION; RECTIFIERS; METALS}}, language = {{English}}, month = {{DEC 2}}, number = {{48}}, number-of-cited-references = {{65}}, publisher = {{IOP PUBLISHING LTD}}, research-areas = {{Science \& Technology - Other Topics; Materials Science; Physics}}, times-cited = {{0}}, title = {{Diamondoid-based molecular junctions: a computational study}}, type = {{Article}}, volume = {{27}}, web-of-science-categories = {{Nanoscience \& Nanotechnology; Materials Science, Multidisciplinary; Physics, Applied}}, year = {{2016}} }
León, Sergio Cruz ; Prentiss, Mara ; Fyta, Maria: Binding energies of nucleobase complexes: Relevance to homology recognition of DNA. In: Physical Review E, Physical Review E. Bd. 93 (2016), Nr. 62410
- BibTeX
BibTeX
@article{cruzleon16a, author = {Le{\'o}n, Sergio Cruz and Prentiss, Mara and Fyta, Maria}, doi = {10.1103/PhysRevE.93.062410}, file = {cruzleon16a.pdf:cruzleon16a.pdf:PDF}, journal = {Physical Review E}, number = 62410, owner = {tkobayashi}, title = {Binding energies of nucleobase complexes: Relevance to homology recognition of DNA}, volume = 93, year = 2016 }
Adhikari, Bibek ; Meng, Sheng ; Fyta, Maria: Carbene-mediated self-assembly of diamondoids on metal surfaces. In: Nanoscale, Nanoscale. Bd. 8 (2016a), S. 8966--8975
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@article{adhikari16a, author = {Adhikari, Bibek and Meng, Sheng and Fyta, Maria}, doi = {10.1039/C5NR08709K}, file = {:adhikari16a.pdf:PDF}, journal = {Nanoscale}, owner = {tkobayashi}, pages = {8966--8975}, title = {Carbene-mediated self-assembly of diamondoids on metal surfaces.}, volume = 8, year = 2016 }
Sivaraman, Ganesh ; Amorim, Rodrigo G. ; Scheicher, Ralph H. ; Fyta, Maria: Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides. In: Nanoscale, Nanoscale. Bd. 8 (2016b), S. 10105–10112
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@article{sivaraman16a, author = {Sivaraman, Ganesh and Amorim, Rodrigo G. and Scheicher, Ralph H. and Fyta, Maria}, doi = {10.1039/C6NR00500D}, file = {sivaraman16a.pdf:sivaraman16a.pdf:PDF}, journal = {Nanoscale}, owner = {tkobayashi}, pages = {10105-10112}, title = {Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides}, volume = 8, year = 2016 }
Fyta, Maria: Threading DNA through nanopores for biosensing applications. In: JOURNAL OF PHYSICS-CONDENSED MATTER, JOURNAL OF PHYSICS-CONDENSED MATTER. Bd. 27, IOP PUBLISHING LTD (2015), Nr. 27
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@article{fyta2015threading, affiliation = {Fyta, M (Reprint Author), Univ Stuttgart, Inst Computat Phys, Allmandring 3, Stuttgart, Germany. Univ Stuttgart, Inst Computat Phys, Stuttgart, Germany.}, article-number = {273101}, author = {Fyta, Maria}, doi = {10.1088/0953-8984/27/27/273101}, eissn = {1361-648X}, issn = {0953-8984}, journal = {JOURNAL OF PHYSICS-CONDENSED MATTER}, language = {English}, month = {JUL 15}, number = 27, publisher = {IOP PUBLISHING LTD}, research-areas = {Physics}, title = {Threading DNA through nanopores for biosensing applications}, type = {Review}, unique-id = {ISI:000357121900001}, volume = 27, year = 2015 }
Adhikari, Bibek ; Fyta, Maria: Towards double-functionalized small diamondoids: selective electronic band-gap tuning. In: Nanotechnology, Nanotechnology. Bd. 26 (2015), Nr. 35701
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@article{764bbc0c32b6464087820da661ab1299, author = {Adhikari, Bibek and Fyta, Maria}, journal = {Nanotechnology}, number = 35701, title = {Towards double-functionalized small diamondoids: selective electronic band-gap tuning}, volume = 26, year = 2015 }
Sivaraman, Ganesh ; Fyta, Maria: Diamondoids as DNA methylation and mutation probes. In: Europhysics Letters, Europhysics Letters. Bd. 108 (2014b), Nr. 17005
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@article{4faf9e5205aa4c7589f59e6137366691, abstract = {In a recent study we proposed derivatives of lower diamondoids as novel biosensors, as well as possible functionalisation candidates of solid-state nanopores for DNA sequencing. A qualitative analysis has shown the abilities of these molecules to distinguish among different DNA nucleobases. In this letter, we extend the analysis and consider also methylated and mutated nucleobases, often being an indication of genetic diseases. Based on the bonding characteristics of these modified nucleobases to a diamondoid derivative, as well as their electronic properties we could reveal the ability of the diamondoid to clearly distinguish the regular from the modified nucleobases. The results show a clear indication that transport properties along these molecules would give distinct current signals.}, author = {Sivaraman, Ganesh and Fyta, Maria}, doi = {10.1209/0295-5075/108/17005}, journal = {Europhysics Letters}, number = 17005, title = {Diamondoids as DNA methylation and mutation probes}, url = {http://iopscience.iop.org/article/10.1209/0295-5075/108/17005/meta}, volume = 108, year = 2014 }
Link
http://iopscience.iop.org/article/10.1209/0295-5075/108/17005/meta
Maier, Frank C. ; Fyta, Dr. Maria: Type-Dependent Identification of DNA Nucleobases by Using Diamondoids. In: ChemPhysChem, ChemPhysChem. Bd. 15 (2014b), S. 3466–3475
- BibTeX
BibTeX
@article{maier14a, author = {Maier, Frank C. and Fyta, Dr. Maria}, doi = {10.1002/cphc.201402335}, file = {maier14a.pdf:maier14a.pdf:PDF}, journal = {ChemPhysChem}, owner = {tkobayashi}, pages = {3466-3475}, title = {Type-Dependent Identification of DNA Nucleobases by Using Diamondoids}, volume = 15, year = 2014 }
Sivaraman, Ganesh ; Fyta, Maria: Derivatives of small diamondoids as biosensors for DNA nucleobases. In: Nanoscale, Nanoscale. Bd. 6 (2014a), Nr. 4225
- BibTeX
BibTeX
@article{825c16d9ec2e444ab79770f8114265de, author = {Sivaraman, Ganesh and Fyta, Maria}, doi = {10.1002/cphc.201402335}, journal = {Nanoscale}, number = 4225, title = {Derivatives of small diamondoids as biosensors for DNA nucleobases}, volume = 6, year = 2014 }
Maier, F.C. ; Sivaraman, Ganesh ; Fyta, Maria: The role of a diamondoid as a hydrogen donor or acceptor in probing DNA nucleobases. In: European Physical Journal E 37, European Physical Journal E 37. Bd. 95 (2014)
- BibTeX
- Link
BibTeX
@article{799683971a22408b8195d75e584b01bb, author = {Maier, F.C. and Sivaraman, Ganesh and Fyta, Maria}, doi = {https://doi.org/10.1140/epje/i2014-14095-0}, journal = {European Physical Journal E 37}, title = {The role of a diamondoid as a hydrogen donor or acceptor in probing DNA nucleobases}, url = {https://link.springer.com/article/10.1140/epje/i2014-14095-0}, volume = 95, year = 2014 }
Link
https://link.springer.com/article/10.1140/epje/i2014-14095-0
Maier, F.C. ; Fyta, Maria: Type-dependent identification of DNA nucleobases using diamondoids. In: ChemPhysChem, ChemPhysChem. (2014a)
- BibTeX
- Link
BibTeX
@article{fcd1d0831eb44296a2d680b9150a0e20, author = {Maier, F.C. and Fyta, Maria}, journal = {ChemPhysChem}, title = {Type-dependent identification of DNA nucleobases using diamondoids}, url = {http://dx.doi.org/10.1002/cphc.201402335}, year = 2014 }
Link
http://dx.doi.org/10.1002/cphc.201402335

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