Publications by authors named "Jose M Soler"

23 Publications

  • Page 1 of 1

Critical analysis of the response function in low dimensional materials.

J Phys Condens Matter 2021 Feb 26. Epub 2021 Feb 26.

Departamento de Fisica de la Materia Condensada, Universidad Autonoma de Madrid, Cantoblanco, Madrid, 28049, SPAIN.

The presence of sharp peaks in the real part of the static dielectric response function are usually accepted as indication of charge or spin instabilities in a material. However, there are misconceptions that Fermi surface (FS) nesting guarantees a peak in the response function like in one-dimensional systems, and, in addition, response function matrix elements between empty and occupied states are usually considered of secondary importance and typically set to unity like in the free electron gas case. In this work, we explicitly show, through model systems and real materials, within the framework of density functional theory, that predictions about the peaks in the response function, using FS nesting and constant matrix elements yields erroneous conclusions. We find that the inclusion of the matrix elements completely alters the structure of the response function. In all the cases studied other than the one-dimensional case we find that the inclusion of matrix elements washes out the structure found with constant matrix elements. Our conclusion is that it is imperative to calculate the full response function, with matrix elements, when making predictions about instabilities in novel materials.
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http://dx.doi.org/10.1088/1361-648X/abea41DOI Listing
February 2021

The CECAM electronic structure library and the modular software development paradigm.

J Chem Phys 2020 Jul;153(2):024117

Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.
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http://dx.doi.org/10.1063/5.0012901DOI Listing
July 2020

Siesta: Recent developments and applications.

J Chem Phys 2020 May;152(20):204108

Departamento de Ciencias de la Tierra y Física de la Materia Condensada, Universidad de Cantabria, Cantabria Campus Internacional, Avenida de los Castros s/n, 39005 Santander, Spain.

A review of the present status, recent enhancements, and applicability of the Siesta program is presented. Since its debut in the mid-1990s, Siesta's flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of Siesta combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as wannier90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering Siesta runs, and various post-processing utilities. Siesta has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments.
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http://dx.doi.org/10.1063/5.0005077DOI Listing
May 2020

Band unfolding made simple.

J Phys Condens Matter 2020 May;32(20):205902

Departamento e Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.

We present a simple view on band unfolding of the energy bands obtained from supercell calculations. It relies on the relationship between the local density of states in reciprocal space and the fully unfolded band structure. This provides an intuitive and valid approach not only for periodic, but also for systems with no translational symmetry. By refolding into the primitive Brillouin zone of the pristine crystal we recover the conventional unfolded bands. We implement our algorithm in the Siesta package. As an application, we study a set of benchmark examples, ranging from simple defects on crystals to systems with increasing complexity and of current interest, as the effect of external pressure on rotated graphene bilayers.
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http://dx.doi.org/10.1088/1361-648X/ab6e8eDOI Listing
May 2020

High Electrical Conductivity of Single Metal-Organic Chains.

Adv Mater 2018 May 16;30(21):e1705645. Epub 2018 Apr 16.

Departamento de Química Inorgánica and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, E-28049, Spain.

Molecular wires are essential components for future nanoscale electronics. However, the preparation of individual long conductive molecules is still a challenge. MMX metal-organic polymers are quasi-1D sequences of single halide atoms (X) bridging subunits with two metal ions (MM) connected by organic ligands. They are excellent electrical conductors as bulk macroscopic crystals and as nanoribbons. However, according to theoretical calculations, the electrical conductance found in the experiments should be even higher. Here, a novel and simple drop-casting procedure to isolate bundles of few to single MMX chains is demonstrated. Furthermore, an exponential dependence of the electrical resistance of one or two MMX chains as a function of their length that does not agree with predictions based on their theoretical band structure is reported. This dependence is attributed to strong Anderson localization originated by structural defects. Theoretical modeling confirms that the current is limited by structural defects, mainly vacancies of iodine atoms, through which the current is constrained to flow. Nevertheless, measurable electrical transport along distances beyond 250 nm surpasses that of all other molecular wires reported so far. This work places in perspective the role of defects in 1D wires and their importance for molecular electronics.
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http://dx.doi.org/10.1002/adma.201705645DOI Listing
May 2018

Optimization of an exchange-correlation density functional for water.

J Chem Phys 2016 Jun;144(22):224101

Departamento e Instituto de Física de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.

We describe a method, that we call data projection onto parameter space (DPPS), to optimize an energy functional of the electron density, so that it reproduces a dataset of experimental magnitudes. Our scheme, based on Bayes theorem, constrains the optimized functional not to depart unphysically from existing ab initio functionals. The resulting functional maximizes the probability of being the "correct" parameterization of a given functional form, in the sense of Bayes theory. The application of DPPS to water sheds new light on why density functional theory has performed rather poorly for liquid water, on what improvements are needed, and on the intrinsic limitations of the generalized gradient approximation to electron exchange and correlation. Finally, we present tests of our water-optimized functional, that we call vdW-DF-w, showing that it performs very well for a variety of condensed water systems.
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http://dx.doi.org/10.1063/1.4953081DOI Listing
June 2016

Room temperature compressibility and diffusivity of liquid water from first principles.

J Chem Phys 2013 Nov;139(19):194502

CIC nanoGUNE, 20018 Donostia-San Sebastián, Spain.

The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density functionals. While both functionals predict compressibilities within ~30% of experiment, only one of them accurately reproduces, within the uncertainty of the simulation, the density dependence of the self-diffusion coefficient in the anomalous region. The discrepancies between the two functionals are explained in terms of the low- and high-density structures of the liquid.
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http://dx.doi.org/10.1063/1.4832141DOI Listing
November 2013

Optimal finite-range atomic basis sets for liquid water and ice.

J Phys Condens Matter 2013 Oct 9;25(43):435504. Epub 2013 Oct 9.

CIC nanoGUNE, E-20018 Donostia-San Sebastián, Spain.

Finite-range numerical atomic orbitals are the basis functions of choice for several first principles methods, due to their flexibility and scalability. Generating and testing such basis sets, however, remains a significant challenge for the end user. We discuss these issues and present a new scheme for generating improved polarization orbitals of finite range. We then develop a series of high-accuracy basis sets for the water molecule, and report on their performance in describing the monomer and dimer, two phases of ice, and liquid water at ambient and high density. The tests are performed by comparison with plane-wave calculations, and show the atomic orbital basis sets to exhibit an excellent level of transferability and consistency. The highest-order bases (quadruple-ζ) are shown to give accuracies comparable to a plane-wave kinetic energy cutoff of at least ~1000 eV for quantities such as energy differences and ionic forces, as well as achieving significantly greater accuracies for total energies and absolute pressures.
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http://dx.doi.org/10.1088/0953-8984/25/43/435504DOI Listing
October 2013

Coordination chemistry of 6-thioguanine derivatives with cobalt: toward formation of electrical conductive one-dimensional coordination polymers.

Inorg Chem 2013 May 18;52(9):5290-9. Epub 2013 Apr 18.

Departamento de Química Inorgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain.

In this work we have synthetized and characterized by X-ray diffraction five cobalt complexes with 6-thioguanine (6-ThioGH), 6-thioguanosine (6-ThioGuoH), or 2'-deoxy-6-thioguanosine (2'-d-6-ThioGuoH) ligands. In all cases, these ligands coordinate to cobalt via N7 and S6 forming a chelate ring. However, independently of reagents ratio, 6-ThioGH provided monodimensional cobalt(II) coordination polymers, in which the 6-ThioG(-) acts as bridging ligand. However, for 2'-d-6-ThioGuoH and 6-ThioGuoH, the structure directing effect of the sugar residue gives rise to mononuclear cobalt complexes which form extensive H-bond interactions to generate 3D supramolecular networks. Furthermore, with 2'-d-6-ThioGuoH the cobalt ion remains in the divalent state, whereas with 6-ThioGuoH oxidation occurs and Co(III) is found. The electrical and magnetic properties of the coordination polymers isolated have been studied and the results discussed with the aid of DFT calculations, in the context of molecular wires.
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http://dx.doi.org/10.1021/ic400237hDOI Listing
May 2013

Intrinsic electrical conductivity of nanostructured metal-organic polymer chains.

Nat Commun 2013 ;4:1709

Departamento de Química Inorgánica, Universidad Autónoma de Madrid, Madrid 28049, Spain.

One-dimensional conductive polymers are attractive materials because of their potential in flexible and transparent electronics. Despite years of research, on the macro- and nano-scale, structural disorder represents the major hurdle in achieving high conductivities. Here we report measurements of highly ordered metal-organic nanoribbons, whose intrinsic (defect-free) conductivity is found to be 10(4) S m(-1), three orders of magnitude higher than that of our macroscopic crystals. This magnitude is preserved for distances as large as 300 nm. Above this length, the presence of structural defects (~ 0.5%) gives rise to an inter-fibre-mediated charge transport similar to that of macroscopic crystals. We provide the first direct experimental evidence of the gapless electronic structure predicted for these compounds. Our results postulate metal-organic molecular wires as good metallic interconnectors in nanodevices.
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http://dx.doi.org/10.1038/ncomms2696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644075PMC
October 2013

Dispersion interactions in room-temperature ionic liquids: results from a non-empirical density functional.

J Chem Phys 2011 Oct;135(15):154505

Atomistic Simulation Centre, Queen's University Belfast, Belfast BT7 1NN, Northern IrelandSchool of Chemistry, University of Bristol, Bristol BS2 1TS, United Kingdom.

The role of dispersion or van de Waals (VDW) interactions in imidazolium-based room-temperature ionic liquids is studied within the framework of density functional theory, using a recently developed non-empirical functional [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)], as efficiently implemented in the SIESTA code [G. Román-Pérez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009)]. We present results for the equilibrium structure and lattice parameters of several crystalline phases, finding a general improvement with respect to both the local density (LDA) and the generalized gradient approximations (GGA). Similar to other systems characterized by VDW bonding, such as rare gas and benzene dimers as well as solid argon, equilibrium distances and volumes are consistently overestimated by ≈7%, compared to -11% within LDA and 11% within GGA. The intramolecular geometries are retained, while the intermolecular distances and orientations are significantly improved relative to LDA and GGA. The quality is superior to that achieved with tailor-made empirical VDW corrections ad hoc [M. G. Del Pópolo, C. Pinilla, and P. Ballone, J. Chem. Phys. 126, 144705 (2007)]. We also analyse the performance of an optimized version of this non-empirical functional, where the screening properties of the exchange have been tuned to reproduce high-level quantum chemical calculations [J. Klimes, D. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 074203 (2010)]. The results for solids are even better with volumes and geometries reproduced within 2% of experimental data. We provide some insight into the issue of polymorphism of [bmim][Cl] crystals, and we present results for the geometry and energetics of [bmim][Tf] and [mmim][Cl] neutral and charged clusters, which validate the use of empirical force fields.
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http://dx.doi.org/10.1063/1.3652897DOI Listing
October 2011

Density, structure, and dynamics of water: the effect of van der Waals interactions.

J Chem Phys 2011 Jan;134(2):024516

Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA.

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.
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http://dx.doi.org/10.1063/1.3521268DOI Listing
January 2011

Stability, adsorption, and diffusion of CH₄, CO₂, and H₂ in clathrate hydrates.

Phys Rev Lett 2010 Oct 28;105(14):145901. Epub 2010 Sep 28.

Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.

We present a study of the adsorption and diffusion of CH₄, CO₂, and H₂ molecules in clathrate hydrates using ab initio van der Waals density functional formalism [M. Dion, Phys. Rev. Lett. 92, 246401 (2004)10.1103/PhysRevLett.92.246401]. We find that the adsorption energy is dominated by van der Waals interactions and that, without them, gas hydrates would not be stable. We calculate the maximum adsorption capacity as well as the maximum hydrocarbon size that can be adsorbed. The relaxation of the host lattice is essential for a good description of the diffusion activation energies, which are estimated to be of the order of 0.2, 0.4, and 1.0 eV for H₂, CO₂, and CH₄, respectively.
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http://dx.doi.org/10.1103/PhysRevLett.105.145901DOI Listing
October 2010

Azafullerene-like nanosized clusters.

ACS Nano 2009 Nov;3(11):3352-7

Departamento de Química Inorgánica, Universidad Autónoma de Madrid, Madrid, Spain.

Carbon nitride materials have extraordinary potential in various applications, including catalysts, filled-particles, and superhard materials. Carbon nitride nanoclusters have been prepared under mild solvothermal conditions by a reaction between 1,3,5-trichlotriazine and sodium azide in toluene. The bulk material formed has a C(3)N(4) composition and consists of spheres with diameters ranging from approximately 1 nm to 4 mum. Nanometer-sized clusters of C(3)N(4) stoichiometry have been isolated on surfaces by sublimation or simple physicochemical methods. The clusters have then been characterized by atomic force microscopy and X-ray photoelectron spectroscopy. The laser desorption ionization mass spectra show peaks assignable to the C(12)N(16), C(21)N(28), and C(33)N(44) molecules which could correspond to cage structures with 4, 7, and 11 units of the C(3)N(4) subunit, respectively. The structure and stability of these new nitrogen-rich carbon nitride nanocages has been investigated using density functional theory calculations.
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http://dx.doi.org/10.1021/nn900496eDOI Listing
November 2009

Energetics and dynamics of H(2) adsorbed in a nanoporous material at low temperature.

Phys Rev Lett 2009 Aug 27;103(9):096103. Epub 2009 Aug 27.

Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854-8019, USA.

Molecular hydrogen adsorption in a nanoporous metal-organic framework structure (MOF-74) is studied via van der Waals density-functional calculations. The primary and secondary binding sites for H(2) are confirmed. The low-lying rotational and translational energy levels are calculated, based on the orientation and position dependent potential energy surface at the two binding sites. A consistent picture is obtained between the calculated rotational-translational transitions for different H(2) loadings and those measured by inelastic neutron scattering exciting the singlet to triplet (para to ortho) transition in H(2). The H(2) binding energy after zero-point energy correction due to the rotational and translational motions is predicted to be approximately 100 meV in good agreement with the experimental value of approximately 90 meV.
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http://dx.doi.org/10.1103/PhysRevLett.103.096103DOI Listing
August 2009

Efficient implementation of a van der Waals density functional: application to double-wall carbon nanotubes.

Phys Rev Lett 2009 Aug 27;103(9):096102. Epub 2009 Aug 27.

Departamento de Física de la Materia Condensada, C-III, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.

We present an efficient implementation of the van der Waals density functional of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)], which expresses the nonlocal correlation energy as a double spatial integral. We factorize the integration kernel and use fast Fourier transforms to evaluate the self-consistent potential, total energy, and atomic forces, in O(NlogN) operations. The resulting overhead, for medium and large systems, is a small fraction of the total computational cost, representing a dramatic speedup over the O(N(2)) evaluation of the double integral. This opens the realm of first-principles simulations to the large systems of interest in soft matter and biomolecular problems. We apply the method to calculate the binding energies and the barriers for relative translation and rotation in double-wall carbon nanotubes.
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http://dx.doi.org/10.1103/PhysRevLett.103.096102DOI Listing
August 2009

Formation of gold nanowires with impurities: a first-principles molecular dynamics simulation.

Phys Rev Lett 2007 Mar 27;98(9):096102. Epub 2007 Feb 27.

Departamento de Física de la Materia Condensada, C-III, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.

We present first-principles molecular dynamics simulations of the formation of monatomic gold nanowires with different impurities (H, C, O, S). Special care was taken not to bias the probability that the impurity atoms participate in the monatomic wire, which is the main focus of this work. Hydrogen always evaporated before the formation of the monatomic chains. Carbon and oxygen were found in the final chains with low probability ( approximately 10%), while sulfur almost always participated in it (probabability approximately 90%). The mean distances between gold atoms bridged by carbon, oxygen, and sulfur were 3.3, 4.4, and 5.0 A, respectively, in good agreement with experimental observations. The contributions of carbon, oxygen, and sulfur to the density of electronic states at the Fermi level are neglegible, moderate, and large, respectively.
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http://dx.doi.org/10.1103/PhysRevLett.98.096102DOI Listing
March 2007

Strain-dependence of the electronic properties in periodic quadruple helical G4-wires.

J Phys Chem B 2005 Dec;109(47):22301-7

National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, c/o Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy.

The electronic structure of periodic quadruple helix guanine wires, which mimic G4-DNA molecules, was studied as a function of the stacking distance between consecutive planes, by means of first principles density functional theory calculations. We show that, whereas for the native DNA interplane separation of 3.4 A the HOMO- and LUMO-derived bands are poorly dispersive, the bandwidths can be significantly increased when compressive strain is applied along the helical axis. Our findings indicate that efficient band conduction for both holes and electrons can be supported by such wires for stacking distances below 2.6 A, which imply a huge axial deformation with respect to double and quadruple helices in solutions and in crystals.
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http://dx.doi.org/10.1021/jp054274qDOI Listing
December 2005

Comment on "Magnetism in atomic-size palladium contacts and nanowires".

Phys Rev Lett 2006 Feb 22;96(7):079701; author reply 079702. Epub 2006 Feb 22.

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http://dx.doi.org/10.1103/PhysRevLett.96.079701DOI Listing
February 2006

Tip and surface determination from experiments and simulations of scanning tunneling microscopy and spectroscopy.

Phys Rev Lett 2005 Feb 11;94(5):056103. Epub 2005 Feb 11.

Departamento de Física de la Materia Condensada, C-III, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.

We present a very efficient and accurate method to simulate scanning tunneling microscopy images and spectra from first-principles density functional calculations. The wave functions of the tip and sample are calculated separately on the same footing and propagated far from the surface using the vacuum Green function. This allows us to express the Bardeen matrix elements in terms of convolutions and to obtain the tunneling current at all tip positions and bias voltages in a single calculation. The efficiency of the method opens the door to real time determination of both tip and surface composition and structure, by comparing experiments to simulated images for a variety of precomputed tips. Comparison with the experimental topography and spectra of the Si111-(7 x 7) surface shows a much better agreement with Si than with W tips, implying that the metallic tip is terminated by silicon.
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http://dx.doi.org/10.1103/PhysRevLett.94.056103DOI Listing
February 2005

Efficient mixed-force first-principles molecular dynamics.

Phys Rev E Stat Nonlin Soft Matter Phys 2003 Nov 18;68(5 Pt 2):055701. Epub 2003 Nov 18.

Departamento de Física de la Materia Condensada, C-III, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.

We present an efficient method to mix well converged ab initio forces with simpler and faster ones in molecular dynamics. While the cheap forces are evaluated every time step, the converged ones correct the trajectory only every n time steps. For convenience, both types of forces are calculated with the same basic scheme, using density functional theory, norm-conserving pseudopotentials, and a basis set of numerical atomic orbitals. The cheap forces are evaluated with a short-range minimal basis set and the non-self-consistent Harris functional. Since these evaluations are hundreds of times faster than those of the converged forces, they add a negligible cost, and the boost in computational efficiency is approximately a factor n. Our results indicate that one can use values of n of up to 10, without affecting significantly the calculated structural and dynamical magnitudes.
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http://dx.doi.org/10.1103/PhysRevE.68.055701DOI Listing
November 2003

Small polarons in dry DNA.

Phys Rev Lett 2003 Sep 5;91(10):108105. Epub 2003 Sep 5.

Departamento de Física, ICEx, Universidade Federal de Minas Gerais, C.P. 702, 30123-970 Belo Horizonte, MG, Brazil.

We report ab initio calculations for positively charged fragments of dry poly(dC)-poly(dG) DNA, with up to 4 C-G pairs. We find a strong hole-lattice coupling and clear evidence for the formation of small polarons. The largest geometry distortions occur in only one or two base pairs. They involve the stretching of weak bonds within each base pair, increasing the distance of positive hydrogens, and decreasing that of negative oxygens, to the region in which the hole localizes. We obtain an energy of approximately 0.30 eV for the polaron formation, nearly independent of the chain size. From it, we can estimate an activation energy for polaron hopping of approximately 0.15 eV, consistent with the available experimental value.
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http://dx.doi.org/10.1103/PhysRevLett.91.108105DOI Listing
September 2003