Publications
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2025
R. López, O. Mateos, P. M. Martínez, J. J. García-Esteban, A. Ibabe, N. Roca-Giménez, P. Segovia, E. G. Michel, E. J. H. Lee, J. G.Vilhena, J. C. Cuevas and N. Agraït. “Heat transfer in metallic nanometre-sized gaps”. Nat. Coms. 16, 7324 (2025).
P. D’Astolfo, J. G. Vilhena, S. Rothenbuhler, C. Drechsel, O. Gutiérrez, R. Häner, S. Decurtins, S. Liu, G. Prampolini, R. Pawlak and E. Meyer. “On-Surface Synthesis and Cryogenic Exfoliation of Sterically Frustrated Atropisomers”. ACS Nano 19 (14), 13805-13816 (2025).
S. C. Yelishala, Y. Zhu, P. M. Martínez, H. Chen, M. Habibi, G. Prampolini, J. C. Cuevas, W. Zhang, J. G. Vilhena and L. Cui. “Phonon interference in single-molecule junctions”. Nat. Mater. 24, 1258-1264 (2025).
S. Giannini, P. M. Martínez, A. Semmeq, J. P. Galvez, A. Piras, A. Landi, D. Padula, J. G. Vilhena, J. Cerezo and G. Prampolini. “JOYCE3.0: A General Protocol for the Specific Parametrization of Accurate Intramolecular Quantum Mechanically Derived Force Fields““. J. Chem. Theory Comput. 6 (21), 3156-3175 (2025).
2024
E. Ventura, P. M. Martínez, R. Pérez and J. G. Vilhena. “Quantum Mechanical Derived (VdW-DFT) Transferable Lennard–Jones and Morse Potentials to Model Cysteine and Alkanethiol Adsorption on Au(111)”. Adv. Mater. Interfaces 11 (30), 2400369 (2024) — featured in the back cover.
2023
C. Roldán, C. Romero, I. Díez, J. G. Vilhena, R. Pérez, J. C. Cuevas, and L. A. Zotti. “Efficient Electron Hopping Transport through Azurin-Based Junctions”. Journal of Physical Chemistry Letters 14 (49), 11242 (2023) — featured in The Front Cover
Z. Liu, J. G. Vilhena, A. Hinaut, S. Scherb, F. Luo, J. Zhang, T. Glatzel, E. Gnecco, and E. Meyer. “Moiré-Tile Manipulation-Induced Friction Switch of Graphene on a Platinum Surface“. Nano Letters 23 (10), 4693-4697 (2023).
2022
M. Ortega, J. G. Vilhena and R. Pérez. “Hygroscopy of Single‐Stranded DNA Nano‐Brushes: Atomic Workings of its Hydration‐Induced Deformation“. Advanced Materials Interfaces 9 (34), 2201272 (2022).
L. G. da Silveira, P. R. Livotto, D. Padula, J. G. Vilhena, and G. Prampolini. “Predicting Spontaneous Orientational Self-Assembly: In Silico Design of Materials with Quantum Mechanically Derived Force Fields”. The Journal of Physical Chemistry Letters 13 (1), 243 (2022) — featured in the front cover.
J. G. Vilhena, L. G. da Silveira, P. R. Livotto, I. Cacelli and G. Prampolini. “Accurate Quantum-Mechanically Derived Force-Fields through a Fragment-Based Approach: Balancing Specificity and Transferability in the Prediction of Self-Assembly in Soft Matter”. Journal of Chemical Theory and Computation 18 (11), 6905-6919 (2022).
J. G. Vilhena, R. Pawlak, P. D’Astolfo, X. Liu, E. Gnecco, M. Kisiel, T. Glatzel, R. Pérez, R. Häner, S. Decurtins, A. Baratoff, G. Prampolini, S. Liu and E. Meyer. “Flexible Superlubricity Unveiled in Sidewinding Motion of Individual Polymeric Chains“. Physical Review Letters 128 (21), 216102 (2022).
2021
J. G. Vilhena, L. G. da Silveira, P. R. Livotto, I. Cacelli and G. Prampolini. “Automated Parameterization of Quantum Mechanically Derived Force-Fields for Soft Materials and Complex Fluids: development and validation“. Journal of Chemical Theory and Computation 17 (7), 4449 (2021).
J. G. Vilhena, M. Ortega, M. Uhlig, R. García and R. Perez. “A Practical Guide to Single Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls as Unraveled by All-Atom MD Simulations on Immunoglobulin G“. ACS Sensors 6(2), 553 (2021).
C. Romero, M. Ortega, J. G. Vilhena, I.Díez, R. Pérez, J. C. Cuevas and L. A. Zotti. “Can Electron Transport through a Blue-Copper Azurin Be Coherent? An Ab-Initio Study“. The Journal of Physical Chemistry C 125(3), 1693 (2021).
A. Marín, J. G. Vilhena, R. Pérez and F. Moreno. “A molecular view of DNA flexibility“. Quarterly Reviews of Biophysics 54, e8 (2021).
C. Romero, M. Ortega, J. G. Vilhena, R. Pérez, J. C. Cuevas and L. A Zotti. “The Role of Metal Ions in the Electron Transport through Azurin-Based Junctions“. Applied Sciences 11, 3732 (2021).
2020
A. Marín, C. Aicart, Mikel. Marin, A. Martín, M. Suomalainen, A. Kannan, J. G. Vilhena, U. F. Greber, F. Moreno and R. Pérez. “Double-stranded RNA bending by AU-tract sequences“. Nucleic Acids Research 48 (22), 12917 (2020).
A. Marín, C. Pastrana, R. Bocanegra, A. Martín, J. G. Vilhena, R. Perez, B. Ibarra, C. Aicart and F. Moreno. “Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes“. Nucleic Acids Research 48 (9), 5024 (2020).
S. Scherb, A. Hinaut, R. Pawlak, J. G. Vilhena, Y. Liu, S. Freund, Z. Liu, X. Feng, K. Müllen, T. Glatzel, A. Narita, Ernst Meyer. “Giant thermal expansion of a two-dimensional supramolecular network triggered by alkyl chain motion“. Communications Materials 1, 8 (2020).
R. Pawlak, J. G. Vilhena, P. D’Astolfo, X. Liu, G. Prampolini, T. Meier, T. Glatzel, J. A. Lemkul, R. Häner, S. Decurtins, A. Baratoff, R. Pérez, S. Liu and E. Meyer. “Sequential Bending and Twisting around C–C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer“. Nano Letters 20, 652-657 (2020).
2019
M. Ortega, J. G. Vilhena, L. A. Zotti, I. Díez, J. C. Cuevas and R. Pérez. “Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations“. Biomolecules 9, 611 (2019).
M. Vorholzer, J. G. Vilhena, R. Pérez, E. Gnecco, D. Dietzel and A. Schirmeisen. “Temperature Activates Contact Ageing in Silica Nanocontacts“. Physical Review X 9, 041045 (2019).
C. Romero, M. Ortega, J. G. Vilhena, I. Diéz, J. C. Cuevas, R. Pérez and L. A. Zotti. “Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction“. Biomolecules 9, 506 (2019).
M. Ortega, J. G. Vilhena, P. Rubio, P. A. Serena and R. Pérez. “Assessing the accuracy of implicit solvation models to describe the IgG adsorption over a hydrophobic surface“. Journal of Chemical Theory and Computation 15 (4), 2548 (2019).
R. Pawlak, J. G. Vilhena, A. Hinaut, T. Meier, T. Glatzel, A. Baratoff, E. Gnecco, R. Pérez and E. Meyer. “Conformation And Mechanical Response of Spray Deposited Single Strand DNA on Gold“. Nature Communications 10 (1), 685 (2019) — featured in Nature Portfolio Chemistry.
A. Marín, J. G. Vilhena, F. Moreno and R. Pérez. “DNA crookedness regulates DNA mechanical properties at short length scales”. Physical Review Letters 122 (4), 048102 (2019) -– featured in Nature Reviews Physics.
A. Marín, J. G. Vilhena, F. Moreno and R. Pérez. “Sequence-dependent mechanical properties of double-stranded RNA“. Nanoscale 11, 21471 (2019).
2018
C. Romero, M. Ortega, J. G. Vilhena, I. Díez, J. C. Cuevas, R. Pérez and L. A. Zotti. “Ab-initio Electronic Structure Calculations of Entire Blue Copper Azurins“. Physical Chemistry Chemical Physics 20, 30392 (2018).
J. G. Vilhena and R. Pérez. “Slippery in every direction“. Nature Materials 17, 852 (2018).
J. G. Vilhena, E. Gnecco, R. Pawlak, F. Moreno, E. Meyer and R. Pérez. “Stick-Slip motion of ssDNA over graphene“. Journal of Physical Chemistry B 122, 840 (2018).
2017
M. P. Ruiz, A. C. Aragonès, N. Camarero, J. G. Vilhena, M. Ortega, L. A. Zotti, R. Peréz, J. C. Cuevas, P. Gorostiza and I. Díez. “Bioengineering a Single-Protein Junction“. Journal of the American Chemical Society 139 (43), 15337 (2017).
A. Marín, J. G. Vilhena, R. Pérez and F. Moreno. “Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom MD“. Proceedings of the National Academy of Sciences USA 114 (27), 7049 (2017).
J. J. Mazo, D. Dietzel, A. Schirmeisen, J. G. Vilhena and E. Gnecco. “Time strengthening of crystal nanocontacts”. Physical Review Letters 118 (24), 246101 (2017).
P. Rubio, J. G. Vilhena, N. Takeuchi, P. A. Serena amd R Pérez. “Albumin (BSA) adsorption onto graphite stepped surfaces”. The Journal of Chemical Physics 146(21), 214704 (2017).
G. López, M. Ortega, J. G. Vilhena, I. Alda, J. Gomez, P. A. Serena, C. Gomez and R. Pérez. “Tailoring the thermal expansion of graphene via controlled defect creation“. Carbon 116, 670 (2017).
2016
J. G. Vilhena, C. Pimentel, P. Pedraz, F. Luo, P. A. Serena, C. Pina, E. Gnecco and R Pérez. “Atomic-Scale Sliding Friction on Graphene in Water”. ACS Nano 10 (4), 4288 (2016).
J. G. Vilhena, P. Rubio, P. Vellosillo, P. A. Serena and R. Pérez. “Albumin (BSA) Adsorption over Graphene in Aqueous Environment: Influence of Orientation, Adsorption Protocol, and Solvent Treatment”. Langmuir 32 (7), 1742 (2016).
J. G. Vilhena, A. C. Dumitru, E. T. Herruzo, J. I. Mendieta, R. García, P. A. Serena and R. Pérez. “Adsorption orientations and immunological recognition of antibodies on graphene“. Nanoscale 8 (27), 13463 (2016).
2014 – 2009
J. G. Vilhena, E. Räsänen, M. A. L. Marques and S. Pittalis. “Construction of the B88 exchange-energy functional in two dimensions“. Journal of Chemical Theory and Computation 10, 1837 (2014).
J. G. Vilhena, E. Räsänen, L. Lehtovaara and M. A. L. Marques. “Violation of a local form of the Lieb-Oxford bound“. Physical Review A 85 (5), 052514 (2012).
A. Putaja, E. Räsänen, R. van Leeuwen, J. G. Vilhena and M. A. L. Marques. “Kirzhnits gradient expansion in two dimensions“. Physical Review B 85 (16), 165101 (2012).
E. Räsänen, S. Pittalis, J. G. Vilhena and M. A. L. Marques. “Semi‐local density functional for the exchange‐correlation energy of electrons in two dimensions“. International Journal of Quantum Chemistry 110 (12), 2308 (2010).
J. G. Vilhena, S. Botti and M. A. L. Marques. “Excitonic effects in the optical properties of CdSe nanowires”. Applied Physics Letters 96 (12), 123106 (2010).
S. Pittalis, E. Räsänen, J. G. Vilhena and M. A. L. Marques. “Density gradients for the exchange energy of electrons in two dimensions“. Physical Review A 79 (1), 012503 (2009).
