TransSim Simulation Research Group

66.	Disorder information from conductance: A quantum inverse problem, S. Mukim, F. P. Amorim, A. R. Rocha, R. B. Muniz, C. Lewenkopf, M. S. Ferreira, Physical Review B 102 (7), 075409 (2020). [ Download ]
65.	Hydration dependent band gap tunability of self-assembled phenylalanine-tryptophan nanotubes, H. Souza, A. Chaves Neto, F. Sousa, R. G. Amorim, A. R. Rocha, T. A. Filho, (2020) [ ChemRxiv ]
64.	Enhanced near-Infrared Photoresponse from Nanoscale Ag-Au Alloyed Films, L. J. Krayer, K. J. Palm, C. Gong, A. Torres, C. E. P. Villegas, A. R. Rocha, M. S. Leite, J. Munday, ACS Photonics 7 (7), 1689-1698 (2020). [ Download ]
63.	Electronic mechanism for resistive switching in metal/insulator/metal nanodevices, H. Raebiger, A. C. M. Padilha, A. R. Rocha, G. M. Dalpian, Journal of Physics D: Applied Physics 53 (29), 295302 (2020). [ Download ]
62.	First-principles calculation of hot carriers in black phosphorus, C. E. P. Villegas, A. R. Rocha, Journal of Physics: Conference Series 1558 (1), 012002 (2020). [ Download ]
61.	The role of water on the electronic transport in graphene nanogap devices designed for DNA sequencing, E. de Freitas Martins, R. G. Amorim, G. T. Feliciano, R. H. Scheicher, A. R. Rocha, Carbon 158, 314-319 (2020). [ Download ]

60.	Ab Initio Simulations and Materials Chemistry in the Age of Big Data, G.R. Schleder, A.C.M. Padilha, A. R. Rocha, G. M. Dalpian, A. Fazzio, Journal of Chemical Information and Modeling 60 (2), 452-459, (2019). \| [Download]
59.	Phase transition and electronic structure investigation of MoS2-reduced graphene oxide nanocomposite decorated with Au nanoparticles, Y. Garcia-Basabe, G. F. Peixoto, D. Grasseschi, E. C. Romani, F. C. Vicentin, C. E. P. Villegas, A. R. Rocha and D. G. Larrude, Nanotechnology 30 (47), 475707 2 2019. \| [ Download ]
58.	Quantitative comparison of Anderson impurity solvers applied to transport in quantum dots, B. M. de Souza Melo, L. G. G. V. D. da Silva, A. R. Rocha, C. Lewenkopf, Journal of Physics: Condensed Matter 32 (9), 095602, (2019). \| [ Download ]
57.	Ab initio modelling of spin relaxation lengths in disordered graphene nanoribbons, W. Y. Rojas, C. E. P. Villegas, A. R. Rocha, arXiv preprint arXiv:1907.05979 (2019).
56.	Structure-Property-Performance Relationship of Ultrathin Pd-Au Alloy Catalyst Layers for Low-Temperature Ethanol Oxidation in Alkaline Media, Joshua P. McClure, Jonathan Boltersdorf, David R. Baker, Thomas G. Farinha, Nicholas Dzuricky, Cesar E. P. Villegas, Alexandre R. Rocha, Marina S. Leite, ACS Applied Materials and Interfacdes, 11, 24919 (2019). \| [ACS]
55.	Simulating DNA chip design using all-electronic graphene-based substrates, E. de Freitas Martins, G. Troiano Feliciano, R. Hendrik Scheicher and Alexandre Reily Rocha, Molecules, 24, 951 (2019)

54.	Spin-orbit coupling prevents spin channel suppression of transition metal atoms on armchair graphene nanoribbons, W. Y. Rojas, C. E. P. Villegas and A. R. Rocha, Physical Chemistry Chemical Physics, 20, 085413 (2018).

53.

Band Structure Engineering by Alloying for Photonics, Chen Gong, Alan Kaplan, Zackery A. Benson, David R. Baker, Joshua P. McClure, Alexandre A. Rocha, and Marina S. Leite, Advanced Optical Materials, 6, 1800218 (2018). | [Download]

52.	Finite-size correction scheme for supercell calculations in two-dimensional Dirac-point two-dimensional materials, C. G. da Rocha, P. Venezuela, A. R. Rocha, M. S. Ferreira, Scientiffc Reports, 8, 9348 (2018). \| [Download]
51.	J. Prasongkit, E. F. Martins, F. A. L. de Souza, W. L. Scopel, R. G. Amorim, V. Amornkibamrung, Alexandre R. Rocha, R. H. Scheicher, Topological Line Defects around Graphene Nanopores for DNA sequencing, The Journal of Physical Chemistry C, 122, 7094 (2018) \| [arxiv]
50.	Tarik P. Cysne, Tatiana G. Rappoport, Jose H. Garcia, Alexandre R. Rocha, Quantum Hall Effect in Graphene with Interface-Induced Spin-Orbit Coupling \| [arxiv]
49.	Fábio A. L. de Souza, Rodrigo G. Amorim, Jariyanee Prasongkit, Wanderlã L. Scopel, Ralph H. Scheicher, Alexandre R. Rocha, Topological Line Defects in Graphene for Applications as Gas Sensing, Carbon, 129, 803 (2018).

48.

Luana Pedroza, P. B. Mendonca, A. R. Rocha, Marivi Fernandez-Serra, Bias-dependent local structure of water molecule at a metallic interface, Chemical Science, 9, 62 (2018) | [arxiv | DOI]

47.	Yunier Garcia Basabe, Alexandre R. Rocha, Flavio Vicentin, Cesar E. Villegas, Regiane Nascimento, Eric C. Romani, Emerson C. de Oliveira, Guilhermino Fechine, Goki Eda, Shisheng Li and Dunieskys Gonzalez Larrude, Ultrafast Charge Transfer Dynamics Pathways in Two Dimensional MoS2-Graphene Heterostructures: A Core Hole Clock Approach, Physical Chemistry Chemical Physics, 19, 29954 (2017) \| [PCCP]
46.	M. S. Ferreira, C. G. Rocha, J. A. Lawlor, P. Venezuela, R. G. Amorim4 and A. R. Rocha, Commensurability effect on the electronic structure of carbon nanostructures: Impact on supercell calculations in nanotubes, European Physics Letters, 117, 27005 (2017) \| [DOI]
45.	G. T. Feliciano, C. Sanz-Navarro, M. D. Coutinho-Neto, P. Ordejon, R. H. Scheicher, Alexandre Reily Rocha, Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach, J. Phys. Chem. Phys. (ASAP) (2017) \| [DOI]

44.	Cesar E.P. Villegas, A.R. Rocha, Andrea Marini, Electron-phonon scattering effects on electronic and optical properties of orthorhombic GeS, Phys. Rev. B 94, 134306 (2016) \| [DOI]
43.	Cesar Perez Villegas, Aleksandr Rodin, Alexandra Carvalho and Alexandre R. Rocha, Two-dimensional exciton properties in monolayer semiconducting phosphorus allotropes, Physical Chemistry Chemical Physics (2016). \| [DOI]
42.	Rodrigo Garcia Amorim, Alexandre Reily and Ralph H. Scheicher, Boosting DNA Recognition Sensitivity of Graphene Nanogaps through Nitrogen Edge Functionalization, Journal of Physical Chemistry C, 120,19384 (2016). \| [DOI]

41.

H. B. Ribeiro, C. E. P. Villegas, D. A. Bahamon, D. Muraca, A. H. Castro Neto, E. A. T. de Souza, A. R. Rocha, M. A. Pimenta and C. J. S. de Matos; Edge Phonons in Black Phoshorus, Nature Communications, 7, 12191, 2016. [DOI] | arxiv:1605.00032 | arxiv

40.	Cesar E.P. Villegas, A.R. Rocha, Andrea Marini, The origin of the anomalous thermal dependence of the band-gap in Black Phosphorus, Nano Letters (accepted) \| [DOI] \| arxiv:1605.03442 \| arxiv
39.	A. C. M. Padilha, H. Raebiger, A. R. Rocha, G. M. Dalpian, Charge storage in oxygen deficient phases of TiO2: defect Physics without defects. Scientific Reports, v. 6, p. 28871, 2016.[DOI]
38.	Jariyanee Prasongkit, A. R. Rocha, Quantum Interference Effects in Biphenyl Dithiol for Gas Detection. RSC Advances, v. 6, p. 1, 2016.[DOI]
37.	J. Soumayajyoti Haldar, Rodrigo Garcia Amorim, Biplab Sanyal, Ralph H. Scheicher and Alexandre Reily Rocha; Energetic stability, STM fingerprints and electronic transport properties of defects in graphene and silicene. RSC Advances, v. 6, p. 6702, (2016). \| [DOI]
36.	S. Kogikoski, C. P. Sousa, M. S. Liberato, T. Andrade-Filho, T. Prieto, F. F. Ferreira, F. Furlan, A. R. Rocha, S. Guha, W. A. Alves, Multifunctional biosensors based on peptide-polyelectrolyte conjugates. PCCP. Physical Chemistry Chemical Physics, v. 18, p. 3223-3233, 2016. \| [DOI]
35.	T. Andrade-Filho, T. C. Martins, F. F. Ferreira, W. A. Alves, Alesandre Reily Rocha. Water-driven stabilization of diphenylalanine nanotube structures. Theoretical Chemistry Accounts, v. 135, p. 1, 2016. \| [DOI]

34.	Jariyanee Prasongkit, Gustavo T. Feliciano, Alexandre R. Rocha, Yuhui He, Tanakorn Osotchan, Rajeev Ahuja & Ralph H. Scheicher, Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene, Scientific Reports, v. 5, p. 17560 (2015) \| [DOI].
33.	G. T. Feliciano, C. Sanz-Navarro, M. D. Coutinho-Neto, P. Ordejon, R. H. Scheicher, Alexandre Reily Rocha, Capacitive DNA Detection Driven by Electronic Charge Fluctuations in a Graphene Nanopore, Physical Review Applied, v.3, p.034003 (2015) \| [DOI].
32.	E. T. Sato, Alexandre Reily Rocha, L. F. C. S. Carvalho, J. D. Almeida, H. Martinho, A microscopic model for hydrated biological tissues, Phys. Rev. E link.
	Figure chosen for Physical Review E's kaleidoscope
31.	C. Perez-Villegas, Alexandre Reily Rocha, Elucidating the Optical Properties of Novel Hetero-Layered Materials Based on MoTe₂-InN for Photovoltaic Applications, Journal of Physical Chemistry C (accepted) [DOI]..

Nanosensores de gas baseados em nanotubos de carbono , Amaury Melo Souza, Alexandre Reily Rocha and Antonio Jose Roque da Silva

30.	G. T. Feliciano, C. Sanz-Navarro, M. D. Coutinho-Neto, P. Ordejon, R. H. Scheicher, Alexandre Reily Rocha, Capacitive DNA Detection Driven by Electronic Charge Fluctuations in a Graphene Nanopore, Physical Review Applied, v.3, p.034003 (2015) \| [DOI].
29.	C. M. Padilha, Alexandre R. Rocha and G. M. Dalpian, DTF+U Simulation of the Ti4O7-TiO2 Interface, Physical Review Applied, v. 3, p. 024009 (2015) \| [DOI].

28.	C. E. P Villegas, P. B. Mendonça, Alexandre R. Rocha, Optical spectrum of bottom-up graphene nanoribbons: towards efficient atom-thick excitonic solar cells. Scientific Reports, v. 4, p. 6579, (2014) \| [DOI].
27.	A. Dominguez, M. Lorke, A. L. Schoenhalz, A. L. Rosa, Frauenheim, T H., A. R. Rocha, G. M. Dalpian, First principles investigations on the electronic structure of anchor groups on ZnO nanowires and surfaces. Journal of Applied Physics, v. 115, p. 203720 (2014) \| [DOI].
26.	V. M. Prado, R. C. Seiceira, A. Pitaluga-Junior, T. Andrade-Filho, W. A. Alves, A. R. Rocha, F. F. Ferreira, Elucidating the crystal structure of the antimalarial drug (±)-mefloquine hydrochloride: a tetragonal hydrated species. Journal of Applied Crystallography, v. 47, p. 1380-1386 (2014) \| [DOI].
25.	X. Zhong, R. G. Amorim, A. Reily Rocha, R. Pandey, Hybridization effects on the out-of-plane electron tunneling properties of monolayers: is h-BN more conductive than graphene?. Nanotechnology (Bristol. Print), v. 25, p. 345703, (2014) [DOI].
24.	A. C. M. Padilha, J. M. Osorio-Guillen, A. R. Rocha, G. M. Dalpian, Ti_nO_2n-1 Magnéli phases studied using density functional theory. Physical Review. B, Condensed Matter and Materials Physics, v. 90, p. 035213 (2014) [DOI].

23.	Rocha, A R . Physics (Viewpoint), 6, 96 (2013) \| DOI: 10.1103/Physics.6.96
22.	J M de Almeida, A R Rocha, Abhshek K Singh, A Fazzio and Ant�nio J R da Silva, Electronic transport in patterned graphene nanoroads, Nanotechnology, v. 24, p. 495201 (2013). [DOI]
20.	ANDRADE FILHO, T. ; ALVES, W. A. ; FERREIRA, F. F. ; Rocha, A R . The effects of water molecules on the electronic and structural properties of peptide nanotubes. PCCP. Physical Chemistry Chemical Physics (Print), v. 15, p. 1, 2013.[DOI]
19.	Amorim, Rodrigo G ; Zhong, Xiaoliang ; MUKHOPADHYAY, SAIKAT ; Pandey, Ravindra ; ROCHA, ALEXANDRE R ; KARNA, SHASHI P . Strain- and electric field-induced band gap modulation in nitride nanomembranes. Journal of Physics. Condensed Matter (Online), v. 25, p. 195801-195808, 2013.[DOI]
18.	Amorim, R. G. ; Da Silva, A. J. R. ; Fazzio, A.; A. R. Rocha.Confinement effects and why carbon nanotubes bundles can work as gas sensors. Nanoscale (Print), v. 1, p. 1, 2013. [DOI]

17.	Souza, A. M. ; Rocha, A. R. ; FAZZIO, A. ; da Silva, A. J. R. . Ab-initio calculations for a realistic sensor: A study of CO sensors based on nitrogen-rich carbon nanotubes. AIP Advances, 2, 032115 (2012).

16.	Autreto, P. ; Lagos, M. ; Sato, F. ; Bettini, J. ; Rocha, A. ; Rodrigues, V. ; Ugarte, D. ; Galvao, D., Intrinsic Stability of the Smallest Possible Silver Nanotube, Physical Review Letters, 106, 065501 (2011).
15.	J. E. Padilha, R. G. Amorim, A. R. Rocha, A. J. R. da Silva, A. Fazzio, Energetics and stability of vacancies in carbon nanotubes, Solid State Communications, 151, 482-486 (2011).
14.	R. B. Pontes, A. R. Rocha, S. Sanvito, A. Fazzio, A. J. R. da Silva, Calculations of Structural Evolution and Conductance of Benzene-1,4-dithiol on Gold Leads ACS Nano, 5, 795-804, (2011).

Electronic transport at the nanoscale: Theoretical and computational aspects, Alexandre Reily Rocha and Stefano Sanvito

13.	A. R. Rocha, M. Rossi, A. Fazzio and A. J. R. da Silva, Designing reallistic nanotube gas sensors, J. Physics D: Applied Physics, 43, 374002 (2010).
12.	A. R. Rocha, T. B. Martins, A. Fazzio, A. J. R. da Silva, Spintronics in disordered graphene-based systems, Nanotechnology, 21, 345202 (2010).
11.	Zhong, Xiaoliang; Pandey, Ravindra; Rocha, Alexandre Reily; Karna, Shashi P., Can Single-Atom Change Affect Electron Transport Properties of Molecular Nanostructures such as C Fullerene?, The Journal of Physical Chemistry Letters, p. 100429122821010-1589, (2010).
10.	Pemmaraju, C. ; Rungger, I.; Chen, X.; Sanvito, S.; Rocha, A.R. . Ab initio study of electron transport in dry poly(G)-poly(C) A-DNA strands. Physical Review. B, Condensed Matter and Materials Physics, v. 82, p. 125426, 2010.
9.	Lima, Matheus; Rocha, A. R.; da Silva, Ant�nio J. R.; Fazzio, A.; Mimicking nanoribbon behavior using a graphene layer on SiC. Physical Review. B, Condensed Matter and Materials Physics, v. 82, p. 153402, 2010.

8.	Cao, Chao; Kemper, A. F.; Agapito, Luis; Zhang, Jian-Wei; He, Yao; Rinzler, Andrew; Cheng, Hai-Ping; Zhang, X.-G.; Rocha, Alexandre Reily; Sanvito, Stefano. Nonequilibrium Green s function study of Pd_{4}-cluster-functionalized carbon nanotubes as hydrogen sensors. Physical Review. B, Condensed Matter and Materials Physics, v. 79, p. 075127, (2009).
7.	Morari, Cristian; Rungger, Ivan; Rocha, Alexandre R.; Sanvito, Stefano; Melinte, Sorin; Rignanese, Gian-Marco. Electronic Transport Properties of 1,1?-Ferrocene Dicarboxylic Acid Linked to Al(111) Electrodes. ACS Nano, v. 3, p. 4137-4143, (2009).
6.	ROCHA, A. R.; Rossi, M. A.; FAZZIO, A.; da SILVA, A. J. R.. Designing Real Nanotube-Based Gas Sensors. Physical Review Letters, v. 100, p. 176803, (2008).

5.	ROCHA, A. R.; PADILHA, J. E.; FAZZIO, A.; da SILVA, A. J. R.. Transport properties of single vacancies in nanotubes. Physical Review B - Solid State, v. 77, p. 153406, (2008).
4.	Fan, Wei; Zhang, R. Q.; ROCHA, A. R.; Sanvito, Stefano. Energy alignment induced negative differential resistance: The role of hybrid states in aromatic molecular devices. Journal of Chemical Physics, v. 129, p. 074710, (2008).
3.	Li, G. Q.; Cai, J.; Deng, J. K.; ROCHA, A. R.; Sanvito, S.. The difference of the transport properties of graphene with corrugation structure and with flat structure. Applied Physics Letters, v. 92, p. 163104, (2008).
2.	Nakamura, Hisao; Yamashita, Koich; ROCHA, A. R.. Efficient ab initio method for inelastic transport in nanoscale devices: Analysis of inelastic electron tunneling spectroscopy. Physical Review. B, Condensed Matter and Materials Physics, v. 78, p. 235420, (2008).
1.	He, H.; Scheicher, R.H.; Pandey, R.; Rocha, A.R.; Sanvito, S.; Grigoriev, A.; Ahuja, R.; Karna, S.P.. Functionalized Nanopore-Embedded Electrodes for Rapid DNA Sequencing. Journal of Physical Chemistry. C, v. 112, p. 3456-3459, (2008).

6.	Dissertation Title: Excitons in monolayer Tellurium studied wiht QPMBPT [pdf] Student: Kevin Angello Lizarraga Olivares (M.Sc.) Address: Instituto de Física Teórica (IFT), São Paulo State University Year: 2019
5.	Thesis Title: QM/MM simulations of electronic transport properties for DNA sensing devices based on graphene [pdf] Student: Ernane de Freitas Martins (Ph.D.) Address: Instituto de Física Teórica (IFT), São Paulo State University Year: 2018
4.	Dissertation Title: Electronic structure of two-dimensional systems with spin-orbit interaction [pdf] Student: Armando Pezo Lopez (M.Sc.) Address: Instituto de Física Teórica (IFT), São Paulo State University Year: 2016
3.	Thesis Title: Simulacões Computacionais de Efeitos de Solvente em Sistemas Nanoscópicos Student: Tarciso Silva de Andrade Filho (Ph.D.) Address: Universidade Federal do ABC Year: 2014
2.	Dissertation Title: QM/MM simulations of electronic transport properties for DNA sensing devices based on graphene Student: Wudmir Verastegui Rojas (M.Sc.) Address: Universidade Federal do ABC Year: 2013
1.	Dissertation Title: QM/MM simulations of electronic transport properties for DNA sensing devices based on graphene Student: Ekaterina Filatova (M.Sc.) Address: Universidade Federal do ABC Year: 2012