# Recent Publications

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1. Title: Electric Field Effects on Graphene Materials

Author(s): Santos E.J.G.

Carbon Materials: Chemistry and Physics , 8, pp. 383-391 (8 March 2015)

Understanding the effect of electric fields on the physical and chemical properties of two-dimensional (2D) nanostructures is instrumental in the design of novel electronic and optoelectronic devices. Several of those properties are characterized in terms of the dielectric constant which play an important role on capacitance, conductivity, screening, dielectric losses and refractive index. Here we review our recent theoretical studies using density functional calculations including van der Waals interactions on two types of layered materials of similar two-dimensional molecular geometry but remarkably different electronic structures, that is, graphene and molybdenum disulphide (MoS2). We focus on such two-dimensional crystals because of they complementary physical and chemical properties, and the appealing interest to incorporate them in the next generation of electronic and optoelectronic devices. We predict that the effective dielectric constant (ε) of few-layer graphene and MoS2 is tunable by external electric fields (E ext). We show that at low fields (E ext < 0.01 V/Å) ε assumes a nearly constant value ∼4 for both materials, but increases at higher fields to values that depend on the layer thickness. The thicker the structure the stronger is the modulation of ε with the electric field. Increasing of the external field perpendicular to the layer surface above a critical value can drive the systems to an unstable state where the layers are weakly coupled and can be easily separated. The observed dependence of ε on the external field is due to charge polarization driven by the bias, which show several similar characteristics despite of the layer considered. All these results provide key information about control and understanding of the screening properties in two-dimensional crystals beyond graphene and MoS2.

2. Title: Epitaxially Grown Strained Pentacene Thin Film on Graphene Membrane

Author(s): Kim K., Santos E.J.G., Lee T.H., Nishi Y., Bao Z.

Small, 11, No. 17, pp. 2037-2043 (7 January 2015)

Organic-graphene system has emerged as a new platform for various applications such as flexible organic photovoltaics and organic light emitting diodes. Due to its important implication in charge transport, the study and reliable control of molecular packing structures at the graphene–molecule interface are of great importance for successful incorporation of graphene in related organic devices. Here, an ideal membrane of suspended graphene as a molecular assembly template is utilized to investigate thin-film epitaxial behaviors. Using transmission electron microscopy, two distinct molecular packing structures of pentacene on graphene are found. One observed packing structure is similar to the well-known bulk-phase, which adapts a face-on molecular orientation on graphene substrate. On the other hand, a rare polymorph of pentacene crystal, which shows significant strain along the c-axis, is identified. In particular, the strained film exhibits a specific molecular orientation and a strong azimuthal correlation with underlying graphene. Through ab initio electronic structure calculations, including van der Waals interactions, the unusual polymorph is attributed to the strong graphene–pentacene interaction. The observed strained organic film growth on graphene demonstrates the possibility to tune molecular packing via graphene–molecule interactions.

3. Title: Understanding the Interaction between Low-Energy Electrons and DNA Nucleotides in Aqueous Solution

Author(s): McAllister M., Smyth, M., Gu B., Tribello G.A., Kohanoff J.,

Journal of Physical Chemistry Letters, 6, No. 15, pp. 3091-3097 (6 August 2015)

Full Text

Reactions that can damage DNA have been simulated using a combination of molecular dynamics and density functional theory. In particular, the damage caused by the attachment of a low energy electron to the nucleobase. Simulations of anionic single nucleotides of DNA in an aqueous environment that was modeled explicitly have been performed. This has allowed us to examine the role played by the water molecules that surround the DNA in radiation damage mechanisms. Our simulations show that hydrogen bonding and protonation of the nucleotide by the water can have a significant effect on the barriers to strand breaking reactions. Furthermore, these effects are not the same for all four of the bases.

4. Title: Applications of the generalized Langevin equation: Towards a realistic description of the baths

Author(s): Ness H., Stella L., Lorenz c.D., Kantorovich L.

Physical Review B, 91, pp. 014301- (5 January 2015)

The generalized Langevin equation (GLE) method, as developed previously [L. Stella et al., Phys. Rev. B 89, 134303 (2014)], is used to calculate the dissipative dynamics of systems described at the atomic level. The GLE scheme goes beyond the commonly used bilinear coupling between the central system and the bath, and permits us to have a realistic description of both the dissipative central system and its surrounding bath. We show how to obtain the vibrational properties of a realistic bath and how to convey such properties into an extended Langevin dynamics by the use of the mapping of the bath vibrational properties onto a set of auxiliary variables. Our calculations for a model of a Lennard-Jones solid show that our GLE scheme provides a stable dynamics, with the dissipative/relaxation processes properly described. The total kinetic energy of the central system always thermalizes toward the expected bath temperature, with appropriate fluctuation around the mean value. More importantly, we obtain a velocity distribution for the individual atoms in the central system which follows the expected canonical distribution at the corresponding temperature. This confirms that both our GLE scheme and our mapping procedure onto an extended Langevin dynamics provide the correct thermostat. We also examined the velocity autocorrelation functions and compare our results with more conventional Langevin dynamics.

5. Title: Toward Controlled Growth of Helicity-Specific Carbon Nanotubes

Author(s): Santos E.J.G., Nørskov J.K., Harutyunyan A.R., Abild-Pedersen F.

The Journal of Physical Chemistry Letters, 6, pp. 2232-2237 (28 May 2015)

The underlying mechanisms for the nucleation of carbon nanotubes as well as their helicity, remain elusive. Here, using van der Waals dispersion force calculations implemented within density functional theory, we study the cap formation, believed to be responsible for the chirality of surface-catalyzed carbon nanotubes. We find the energetics associated with growth along different facets to be independent of the surface orientation and that the growth across an edge along the axis of the metal particle leads to a perfect honeycomb lattice in a curved geometry. The formation of defects in the graphene matrix, which bend the carbon plane, requires that two or more graphene embryos with significantly different growth axis merge. Such scenario is only possible at the front- or back-end of the metal particle where growth symmetry is broken. The graphene embryos reconstruct their hexagonal structure into pentagons, heptagons, and octagons counterpart to accommodate the tube curvature.

6. Title: Strong second harmonic generation in SiC, ZnO, GaN two-dimensional hexagonal crystals from first-principles many-body calculations

Author(s): Attaccalite C., Nguer A., Cannuccia E., Gruning M.

Physical Chemistry Chemical Physics (25 February 2015)

The second harmonic generation (SHG) intensity spectrum of SiC, ZnO, GaN two-dimensional hexagonal crystals is calculated by using a real-time first-principles approach based on Green's function theory [Attaccalite \textit{et al.,Phys Rev B} 2013 \textbf{88}, 235113 ]. This approach allows one to go beyond the independent particle description used in standard first-principles nonlinear optics calculations by including quasiparticle corrections (by means of the $GW$ approximations), crystal local field effects and excitonic effects. Our results show that the SHG spectra obtained by the latter approach differ significantly from their independent particle counterparts. In particular they show strong excitonic resonances at which the SHG intensity is about two times stronger than within the independent particle approximation. All the systems studied (whose stability have been predicted theoretically) are transparent and at the same time exhibit a remarkable SHG intensity in the range of frequencies at which Ti:Sapphire and Nd:YAG lasers operates thus they can be of interest for nanoscale nonlinear frequency conversion devices. Specifically the SHG intensity at 800 nm (1.55 eV) ranges from about 40-80 pm/V in ZnO and GaN to 0.6 nm/V in SiC. The latter value in particular is 1 order of magnitude larger than values in standard nonlinear crystals.

7. Title: Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

Author(s): Andrade X., Strubbe D., De Giovannini U., Larsen A.H., Oliveira M.J.T., Alberdi-Rodriguez J., Varas A., Theophilou I., Helbig N., Verstraete M.J., Stella L., Nogueira F., Aspuru-Guzik A., Castro A., Marques M.A.L., Rubio A.

Physical Chemistry Chemical Physics (20 February 2015)

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

8. Title: Thermochromism and switchable paramagnetism of cobalt(II) in thiocyanate ionic liquids

Author(s): Osborne S.J., Wellens S., Ward C., Felton S., Bowman R.M., Binnemans K., Swadźba-Kwaśny M., Gunaratnea H.Q.N., Nockemann P.

Dalton Transactions, 44, No. 25, pp. 11286-11289 (2 June 2015)

Temperature-dependent switching of paramagnetism of a cobalt(II) complex is observed in an ionic liquid solution. Paramagnetic and thermochromic switching occur simultaneously due to a reversible change in coordination. This reversible switching is possible in the ionic liquid solution, which enables mobility of thiocyanate anions by remaining mobile at low temperatures and acts as an anion reservoir.

9. Title: Dielectric Screening in Atomically Thin Boron Nitride Nanosheets

Author(s): Li L.H., Santos E.J.G., Xing T., Cappelluti E., Roldán R., Chen Y., Watanabe K., Taniguchi T.

Nano Letters, 15, No. 1, pp. 218-223 (2 December 2015)

Two-dimensional (2D) hexagonal boron nitride (BN) nanosheets are excellent dielectric substrate for graphene, molybdenum disulfide, and many other 2D nanomaterial-based electronic and photonic devices. To optimize the performance of these 2D devices, it is essential to understand the dielectric screening properties of BN nanosheets as a function of the thickness. Here, electric force microscopy along with theoretical calculations based on both state-of-the-art first-principles calculations with van der Waals interactions under consideration, and nonlinear Thomas–Fermi theory models are used to investigate the dielectric screening in high-quality BN nanosheets of different thicknesses. It is found that atomically thin BN nanosheets are less effective in electric field screening, but the screening capability of BN shows a relatively weak dependence on the layer thickness.

10. Title: Nonconservative current-driven dynamics: beyond the nanoscale

Author(s): Cunningham B., Todorov T.N., Dundas D.

Beilstein Journal of Nanotechnology, 6, pp. 2140-2147 (13 November 2015)

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Long metallic nanowires combine crucial factors for nonconservative current-driven atomic motion. These systems have degenerate vibrational frequencies, clustered about a Kohn anomaly in the dispersion relation, that can couple under current to form nonequilibrium modes of motion growing exponentially in time. Such motion is made possible by nonconservative current-induced forces on atoms, and we refer to it generically as the waterwheel effect. Here the connection between the waterwheel effect and the stimulated directional emission of phonons propagating along the electron flow is discussed in an intuitive manner. Nonadiabatic molecular dynamics show that waterwheel modes self-regulate by reducing the current and by populating modes in nearby frequency, leading to a dynamical steady state in which nonconservative forces are counter-balanced by the electronic friction. The waterwheel effect can be described by an appropriate effective nonequilibrium dynamical response matrix. We show that the current-induced parts of this matrix in metallic systems are long-ranged, especially at low bias. This nonlocality is essential for the characterisation of nonconservative atomic dynamics under current beyond the nanoscale.

11. Title: Liquids with permanent porosity

Author(s): Giri N., Del Pópolo M.G., Melaugh G., Greenaway R.L., Rätzke K., Koschine T., Pison L., Costa Gomes M.F., Cooper A.I., James S.L.

Nature, 527, pp. 216-220 (12 November 2015)

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Porous solids such as zeolites and metal–organic frameworks are useful in molecular separation and in catalysis, but their solid nature can impose limitations. For example, liquid solvents, rather than porous solids, are the most mature technology for post-combustion capture of carbon dioxide because liquid circulation systems are more easily retrofitted to existing plants. Solid porous adsorbents offer major benefits, such as lower energy penalties in adsorption–desorption cycles, but they are difficult to implement in conventional flow processes. Materials that combine the properties of fluidity and permanent porosity could therefore offer technological advantages, but permanent porosity is not associated with conventional liquids. Here we report free-flowing liquids whose bulk properties are determined by their permanent porosity. To achieve this, we designed cage molecules that provide a well-defined pore space and that are highly soluble in solvents whose molecules are too large to enter the pores. The concentration of unoccupied cages can thus be around 500 times greater than in other molecular solutions that contain cavities, resulting in a marked change in bulk properties, such as an eightfold increase in the solubility of methane gas. Our results provide the basis for development of a new class of functional porous materials for chemical processes, and we present a one-step, multigram scale-up route for highly soluble ‘scrambled’ porous cages prepared from a mixture of commercially available reagents. The unifying design principle for these materials is the avoidance of functional groups that can penetrate into the molecular cage cavities.

12. Title: Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

Author(s): Ardevol A, Tribello G., Ceriotti M., Parrinello M.

Journal of Chemical Theory and Computation, 11, No. 3, pp. 1086-1093 (10 February 2015)

This work examines the conformational ensemble involved in β-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analyzed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild-type protein. Furthermore, certain mutations destabilize secondary-structure-containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations.

13. Title: Structural and Electrical Investigation of C60–Graphene Vertical Heterostructures

Author(s): Kim K., Lee T.H., Santos E.J.S., Jo P.S., Salleo A., Nishi Y., Bao Z.

ACS Nano (1 June 2015)

Graphene, with its unique electronic and structural qualities, has become an important playground for studying adsorption and assembly of various materials including organic molecules. Moreover, organic/graphene vertical structures assembled by van der Waals interaction have potential for multifunctional device applications. Here, we investigate structural and electrical properties of vertical heterostructures composed of C60 thin film on graphene. The assembled film structure of C60 on graphene is investigated using transmission electron microscopy, which reveals a uniform morphology of C60 film on graphene with a grain size as large as 500 nm. The strong epitaxial relations between C60 crystal and graphene lattice directions are found, and van der Waals ab initio calculations support the observed phenomena. Moreover, using C60–graphene heterostructures, we fabricate vertical graphene transistors incorporating n-type organic semiconducting materials with an on/off ratio above 3 × 103. Our work demonstrates that graphene can serve as an excellent substrate for assembly of molecules, and attained organic/graphene heterostructures have great potential for electronics applications.

14. Title: Length Matters: Keeping Atomic Wires in Check

Author(s): Cunningham B., Todorov T.N., Dundas D.

MRS Proceedings, 1753 (2015)

Dynamical effects of non-conservative forces in long, defect free atomic wires are investigated. Current flow through these wires is simulated and we find that during the initial transient, the kinetic energies of the ions are contained in a small number of phonon modes, closely clustered in frequency. These phonon modes correspond to the waterwheel modes determined from preliminary static calculations. The static calculations allow one to predict the appearance of non-conservative effects in advance of the more expensive real-time simulations. The ion kinetic energy redistributes across the band as non-conservative forces reach a steady state with electronic frictional forces. The typical ion kinetic energy is found to decrease with system length, increase with atomic mass, and its dependence on bias, mass and length is supported with a pen and paper model. This paper highlights the importance of non-conservative forces in current carrying devices and provides criteria for the design of stable atomic wires.

15. Title: A boron nitride - graphene - C60 heterostructure

Author(s): Ojeda-Aristizabal C., Santos E.J.G., Onishi S., Rasool H., Velasco J. Jr., Kahn S., Yan A., Zettl A.

APS March Meeting 2015, abstract #S16.004 (2015)

We have fabricated a new van-der-Waals heterostructure composed by BN/graphene/C60. We performed transport measurements on the preliminary BN/graphene device finding a sharp Dirac point at the neutrality point. After the deposition of a C60 thin film by thermal evaporation, we have observed a significant n-doping of the heterostructure. This suggests an unusual electron transfer from C60 into the BN/graphene structure. This BN/graphene/C60 heterostructure can be of interest in photovoltaic applications. It can be used to build devices like p-n junctions, where C60 can be easily deposited in defined regions of a graphene junction by the use of a shadow mask. Our results are contrasted with theoretical calculations.

16. Title: Abstract: M8.00007 : Graphene Template for Epitaxial Growth of Pentacene and C60 Thin Film

Author(s): Kwanpyo K., Santos E.J.G., Lee T.H., Nishi Y., Bao Z.

Bulletin of the American Physical Society, 60, No. 1 (2015)

Abstract

The study and reliable control of molecular packing structures at the graphene-molecule interface are of great importance for various applications. We utilize suspended graphene as an assembly template to investigate thin-film epitaxial growth of various organic molecules. Thin-film packing structures of pentacene and C60 on graphene are investigated using transmission electron microscopy. For pentacene thin-film, we observe an unusual polymorph growth on graphene, which shows significant strain along the c-axis of pentacene crystals. Moreover, the strained film exhibits a specific molecular orientation and a strong azimuthal correlation with underlying graphene lattice. For C60 crystals, we observe large grain sizes and somewhat strong azimuthal correlation with respect to underlying graphene lattice direction. Utilizing \textit{ab initio} electronic structure calculations with van der Waals interactions, we understand the observed molecular growth behavior mainly with graphene-molecule interaction.

17. Title: Abstract: W26.00010 : Screened Hybrid Exact Exchange Schemes to Adsorption Energies on Perovskite Oxides

Author(s): Santos E., Vojvodic A., Norskov J.K.

Bulletin of the American Physical Society, 60, No. 1 (2015)

Abstract

The bond formation between an oxide surface and oxygen, which is one of the important intermediates for oxygen evolution reaction, is investigated using hybrid functionals. We show that there exists a linear correlation between the adsorption energies of oxygen on LaMO3 (M=Sc-Cu) oxides at hybrid calculations to those computed using semilocal density functionals through the magnetic properties of the bulk phase. The energetics of the spin-polarized surfaces follow the same trend as corresponding bulk systems, which can be treated at a much lower computational cost. The difference in adsorption energy due to magnetism is linearly correlated to the magnetization energy of bulk, i.e., the energy difference between the spin-polarized and the non spin-polarized solutions. This suggests that one could estimate the correction to the semilocal density functional adsorption energies directly from the hybrid bulk magnetization energy.

18. Title: Cement As a Waste Form for Nuclear Fission Products: The Case of 90Sr and Its Daughters

Author(s): Dezerald L., Kohanoff J., Correa A., Caro A., Pellenq R., Ulm F., Saúl A.

Environmental Science & Technology (2015)

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One of the main challenges faced by the nuclear industry is the long-term confinement of nuclear waste. Because it is inexpensive and easy to manufacture, cement is the material of choice to store large volumes of radioactive materials, in particular the low-level medium-lived fission products. It is therefore of utmost importance to assess the chemical and structural stability of cement containing radioactive species. Here, we use ab initio calculations based on density functional theory (DFT) to study the effects of 90Sr insertion and decay in C–S–H (calcium-silicate-hydrate) in order to test the ability of cement to trap and hold this radioactive fission product and to investigate the consequences of its β-decay on the cement paste structure. We show that 90Sr is stable when it substitutes the Ca2+ ions in C–S–H, and so is its daughter nucleus 90Y after β-decay. Interestingly, 90Zr, daughter of 90Y and final product in the decay sequence, is found to be unstable compared to the bulk phase of the element at zero K but stable when compared to the solvated ion in water. Therefore, cement appears as a suitable waste form for ,90Sr storage.