arXiv subjects

Ruben Perez

Publications and source records attributed to Ruben Perez.

9 recordsLinked to original sources

arXiv2026

Reconstruction-Dependent Imaging, Reactivity and Local Reduction of the CeO$_2$(100) surface

The possibility of mapping the local reactivity and reduction state to the atomic structure of chemically active oxide surfaces opens new avenues for further understanding of catalysis. Here, we combine scanning tunnelling (STM) and atomic force microscopy (AFM) with first-principles modelling to explore this possibility on the CeO2(100) surface. While STM reveals the periodicity of cerium-terminated and oxygen-terminated CeO$_2$(100) reconstructions coexisting on the same surface, AFM imaging and force spectroscopy provide direct identification of the exposed atomic species and their reactivity as the chemical interaction with the probe. Density functional theory based STM and AFM simulations reproduce the main experimental observations and show that STM contrast cannot be in general assigned to the atomic positions of certain chemical species, as traditionally assumed from previous studies. Simulated STM contrast of the two reconstructions across different reduction states associated with the removal of oxygen atoms in deeper layers, evidence that STM alone does not offer a robust fingerprint of the local reduction state for the cerium-terminated reconstruction, but it is sensitive to the reduced state in the case of the oxygen-terminated one, being able to provide information on a mixed distribution of Ce$^{3+}$ and Ce$^{4+}$ ions on the first sub-surface Ce layer.

cond-mat.mtrl-sci↗

arXiv2025

Bond-resolved STM with density-based methods

Bond-resolved STM (BRSTM) is a recent technique that combines the advantages of scanning tunneling microscopy (STM) with the outstanding intramolecular resolution provided by non-contact atomic force microscopy (ncAFM) using a CO-functionalized tips, offering unique insights into molecular interactions at surfaces. In this work, we present a novel and easily implementable approach for simulating BRSTM images, which we have applied to reproduce new experimental BRSTM data of Perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) on Ag(111), obtained with unprecedented control of tip-sample separation ($\sim$10~pm). Our method integrates the Full-Density-Based Model (FDBM) developed for High-Resolution Atomic Force Microscopy (HRAFM) with Chen's derivative approximation for tunneling channels, effectively capturing the contributions of both $\sigma$ and $\pi$ channels, while accounting for the CO-tip deflection induced by probe-sample interactions. This approach accurately reproduces the experimental results for both PTCDA/Ag(111) and 1,5,9-trioxo-13-azatriangulene (TOAT)/Cu(111) systems, including intricate tip-sample distance-dependent features. Furthermore, we also demonstrate the important role of substrate-induced effects, which can modify molecular orbital occupation and the relaxation of the CO probe, resulting in distinct BRSTM image characteristics.

cond-mat.mtrl-sci↗

arXiv2024

Transforming Design Spaces Using Pareto-Laplace Filters

Optimization is a critical tool for addressing a broad range of human and technical problems. However, the paradox of advanced optimization techniques is that they have maximum utility for problems in which the relationship between the structure of the problem and the ultimate solution is the most obscure. The existence of solution with limited insight contrasts with techniques that have been developed for a broad range of engineering problems where integral transform techniques yield solutions and insight in tandem. Here, we present a ``Pareto-Laplace'' integral transform framework that can be applied to problems typically studied via optimization. We show that the framework admits related geometric, statistical, and physical representations that provide new forms of insight into relationships between objectives and outcomes. We argue that some known approaches are special cases of this framework, and point to a broad range of problems for further application.

cs.CE↗

arXiv2018

Conformation And Mechanical Response of Spray Deposited Single Strand DNA on Gold

Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far, single base detection might be possible in more drastic cleanliness conditions such as ultra high vacuum. Here, we report on high resolution imaging and pulling attempts at low temperature (5K) of a single strand DNA (ssDNA) molecules composed of 20 cytosine bases adsorbed on Au(111) by scanning probe microscopy and numerical calculations. Using electrospray deposition technique, the ssDNA were successfully transferred from solution onto a surface kept in ultra high vacuum. Real space characterizations reveal that the ssDNA have an amorphous structure on gold in agreement with numerical calculations. Subsequent substrate annealing promotes the desorption of solvent molecules, DNA as individual molecules as well as the formation of DNA self assemblies. Furthermore, pulling experiments by force spectroscopy have been conducted to measure the mechanical response of the ssDNA while detaching. A periodic pattern of 0.2 to 0.3nm is observed in the force curve which arises from the stick slip of single nucleotide bases over the gold. Although an intra molecular response is obtained in the force curve, a clear distinction of each nucleotide detachment is not possible due the complex structure of ssDNA adsorbed on gold.

cond-mat.soft↗

arXiv2010

An upper bound for the magnetic force gradient in graphite

Cervenka et al. have recently reported ferromagnetism along graphite steps. We present Magnetic Force microscopy (MFM) data showing that the signal along the steps is independent of an external magnetic field. Moreover, by combining Kelvin Probe Force Microscopy (KPFM) and MFM, we are able to separate the electrostatic and magnetic interactions along the steps obtaining an upper bound for the magnetic force gradient of about16 microN/m, a figure six times lower than the lowest theoretical bound reported by Cervenka et al. Our experiments suggest absence of MFM signal in graphite at room temperature.

cond-mat.mtrl-sci↗

arXiv2005

H$_2$ dissociation over Au-nanowires and the fractional conductance quantum

The dissociation of H$_2$ molecules on stretched Au nanowires and its effect on the nanowire conductance are analyzed using a combination of Density Functional (DFT) total energy calculations and non-equilibrium Keldish-Green function methods. Our DFT simulations reproduce the characteristic formation of Au monoatomic chains with a conductance close to % the conductance quantum $G_0 = 2e^2/h$. These stretched Au nanowires are shown to be better catalysts for H$_2$ dissociation than Au surfaces. This is confirmed by the nanowire conductance evidence: while not affected practically by molecular hydrogen, atomic hydrogen induces the appearance of fractional conductances ($G \sim 0.5 G_0$) as observed experimentally.

cond-mat.mes-hall↗

arXiv2001

Electron correlation effects and ferromagnetism in Iron

Electron correlation effects in Fe are analyzed using a first principles LCAO-scheme. In our approach, we first use a local orbital DFT-LDA solution to introduce a Hubbard Hamiltonian without fitting parameters. In a second step, we introduce a many-body solution to this Hamiltonian using a DMF approximation. Our analysis shows that magnetism in Fe is an effect associated with the first atomic Hund's rule. Moreover, we also find important correlation effects in the Fe-spin polarized DOS. The photoemision spectra is explained using a value of U_eff as large as 4 eV, provided the satellite peaks appearing around 3-5 eV below the Fermi energy are interpreted appropriately.

cond-mat.str-el↗

arXiv2001

Ge-substitutional defects and the r3xr3 <--> 3x3 transition in alpha--SnGe(111)

The structure and energetics of Ge substitutional defects on the alpha-Sn/Ge(111) surface are analyzed using Density Functional Theory (DFT) molecular dynamics (MD) simulations. An isolated Ge defect induces a very local distortion of the 3x3 reconstruction, confined to a significant downwards displacement (-0.31 A) at the defect site and a modest upward displacement (0.05 A) of the three Sn nearest neighbours with partially occupied dangling bonds. Dynamical fluctuations between the two degenerate ground states yield the six-fold symmetry observed around a defect in the experiments at room temperature. Defect-defect interactions are controlled by the energetics of the deformation of the 3x3 structure: They are negligible for defects on the honeycomb lattice and quite large for a third defect on the hexagonal lattice, explaining the low temperature defect ordering.

cond-mat.mtrl-sci↗

arXiv2001

Surface soft phonon and the root3 x root3 <--> 3 x 3 phase transition in Sn/Ge(111) and Sn/Si(111)

Density Functional Theory (DFT) calculations show that the reversible Sn/Ge(111) $\sqrt{3}\times\sqrt{3} \leftrightarrow 3\times3$ phase transition can be described in terms of a surface soft phonon. The isovalent Sn/Si(111) case does not display this transition since the $\sqrt{3}\times\sqrt{3}$ phase is the stable structure at low temperature, although it presents a partial softening of the $3\times3$ surface phonon. The rather flat energy surfaces for the atomic motion associated with this phonon mode in both cases explain the experimental similarities found at room temperature between these systems. The driving force underlying the $\sqrt{3}\times\sqrt{3} \leftrightarrow 3\times3$ phase transition is shown to be associated with the electronic energy gain due to the Sn dangling bond rehybridization.

cond-mat.mtrl-sci↗