My research focuses mainly on the theory of single molecule charge trasport, mainly using nonequilibrium Green's function theory. In my group, we have implemented a NEGF module in the quantum chemistry software packages of SCM. This was mainly the work of Chris Verzijl (for the fully self-consistent implementation in BAND) and Jos Seldenthuis (in ADF, post-SCF).

We have also worked on interaction with vibrational modes (Jos Seldenthuis) and on including Coulomb effects (Fatemeh Mirjani, Jos Seldenthuis and Jose Celis Gil) on top of density functional theory (DFT).


  • POOT, Menno, et al., Temperature dependence of three-terminal molecular junctions with sulfur end-functionalized tercyclohexylidenes, Nano Letter, 2006, 6.5: 1031-1035.
  • THIJSSEN, Joseph M.; VAN DER ZANT, Herre SJ., Charge transport and single-electron effects in nanoscale systems, Physica Status Solidi (b), 2008, 245.8: 1455-1470.
  • SELDENTHUIS, Johannes S., et al, Vibrational excitations in weakly coupled single-molecule junctions: a computational analysis. ACS Nano, 2008, 2.7:1445-1451.
  • SELDENTHUIS, Johannes S., et al. An all-electric single-molecule motor. ACS Nano, 2010, 4.11: 6681-6686.
  • MIRJANI, Fatemeh; THIJSSEN, Joseph M. Density functional theory based many-body analysis of electron transport through molecules. Physical Review B, 2011, 83.3: 035415.
  • MIRJANI, Fatemeh; THIJSSEN, Joseph M.; VAN DER MOLEN, Sense Jan. Advantages and limitations of transition voltage spectroscopy: a theoretical analysis. Physical Review B, 2011, 84.11: 115402.
  • MIRJANI, Fatemeh; THIJSSEN, Joseph M.; RATNER, Mark A. Probing charge states in molecular junctions using Raman spectroscopy. The Journal of Physical Chemistry C, 2012, 116.43: 23120-23129.
  • MIRJANI, Fatemeh, et al. Charge transport across insulating self-assembled monolayers: Non-equilibrium approaches and modeling to relate current and molecular structure. ACS Nano, 2014, 8.12: 12428-12436.
  • VERZIJL, C. J. O.; THIJSSEN, J. M. DFT-based molecular transport implementation in ADF/BAND.The Journal of Physical Chemistry C, 2012, 116.46: 24393-24412.
  • VERZIJL, C. J. O.; SELDENTHUIS, J. S.; THIJSSEN, J. M. Applicability of the wide-band limit in DFT-basedmolecular transport calculations. The Journal of Chemical Physics, 2013, 138.9: 094102.
  • PERRIN, Mickael L., et al. Large tunable image-charge effects in single-molecule junctions.Nature Nanotechnology, 2013, 8.4: 282.
  • PERRIN, Mickael L., et al. Large negative differential conductance in single-molecule break junctions.Nature nanotechnology, 2014, 9.10: 830.
  • PERRIN, Mickael L., et al. A gate-tunable single-molecule diode.Nanoscale, 2016, 8.16: 8919-8923.
  • CELIS GIL, J. A.; THIJSSEN, J. M. Transport gap renormalization at a metal-molecule interface using DFT-NEGFand spin unrestricted calculations. The Journal of Chemical Physics, 2017, 147.8: 084102. 
  • JACOBSE, Peter H., et al. Electronic components embedded in a single graphene nanoribbon.Nature Communications, 2017, 8.1: 119.
  • ATESCI, Huseyin, et al. Humidity-controlled rectification switching in ruthenium-complex molecular junctions.Nature Nanotechnology, 2018, 13.2: 117.