Pedro Serena

CSIC (Consejo Superior de Investigaciones Científicas-Spanish National Research Council), ICMM, Faculty Member

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Papers by Pedro Serena

Assessing the Accuracy of Different Solvation Models To Describe Protein Adsorption

Journal of Chemical Theory and Computation, 2019

In protein adsorption, the surrounding solvent has an important role in mediating protein−surface... more In protein adsorption, the surrounding solvent has an important role in mediating protein−surface interactions. Therefore, it is of paramount importance that the solvent methods employed to model these kinds of processes are able to correctly capture the complex mechanisms occurring in the protein−water-surface interface. Here, we test the suitability of the two most popular implicit solvent methods based on the Generalized Born formalism to describe the adsorption process of the immunoglobulin G (IgG) on a hydrophobic graphene surface. Our results show that in both cases, IgG experiences an extreme and early (in less than 40 ns) unfolding as a result of the adsorption to the surface in contrast with previous experimental findings. A detailed energy decomposition analysis of explicit and implicit solvent simulations reveals that this discrepancy arises from the ill-characterization of two energy components in implicit solvent methods. These findings help to elucidate how implicit solvent models may be improved to accurately characterize the protein adsorption process.

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Nanowire condnctance experiments aboye amI helnw the reservoirs enrie temperature

The transpon properties nI' Ni nanowires me stuJied using J Scanning Tunneling ~'l¡crosC(... more The transpon properties nI' Ni nanowires me stuJied using J Scanning Tunneling ~'l¡crosC(lpe (STM) LIndel'c1eJn high vacuum condilions. A hasically lbl Il:lnowire conductance histogram is founJ independcntly 01' the magnetil: stalc 01' Ihe e1ectrodes. This agrees with our previous studies in air hui <..Iisagreeswlth recently puolishcd results. Thc possihle origin 01' these discrepancics, logether with additional experiments trying lo ¡Jisn.'rn the existellce 01' a spin-dcpcndent condllclancc in felTolllagnetic n:llI(lwirt's. :lre presellted.

Mechanism for diffusion of nanostructures and mesoscopic objects on surfaces

Surface Science, 1995

We have studied the diffusion of mesoscopic objects created on surfaces by applying time rescalin... more We have studied the diffusion of mesoscopic objects created on surfaces by applying time rescaling Monte Carlo algorithms. It is shown that under the effect of very small forces (0.01-0.03 eV/lattice constant), these nanostructures reach large velocities and long displacements are observable. The main mechanism involved in this displacement is the fast movement of the particles at the cluster perimeter, i.e. at an adequate temperature, for instance Au at room temperature, Au atoms move very fast along the cluster periphery and the application of a small driving force gives rise to the displacement of the object as a whole. Atomic metallic ion emission (AMIE) experiments are presented and explained in terms of our MC results.

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Formation of Stable Pentagonal Nanowires Under Stretching on FCC Metals

nanospainconf.org

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Molecular dynamics simulations of breaking metallic nanowires

International Journal of Nanotechnology, 2004

In the present work we have reviewed the importance of conductance histograms as an experimental ... more In the present work we have reviewed the importance of conductance histograms as an experimental tool able to address the statistical behaviour of the electronic transport through metallic nanowires. We have described how molecular dynamics techniques combined with embedded-atom method (EAM) are able to reproduce the general features noticed during metallic nanowire breaking experiments. We have studied the effect of temperature on the minimum cross-section histograms. Our results show that the breaking dynamics is strongly temperature dependent, giving rise to remarkable changes in the computed histograms. We found, for Gold, that conductance and configuration histograms are not correlated, thus indicating that experimental conductance peaks are due to actual quantized conductance effects. For Aluminum, the situation is different, since we found a strong correspondence between our minimum cross-section histograms and the experimental conductance histograms, indicating the relevant role of atomic configurations. We have addressed the study of the stretching of thick Au and Al nanocontacts, finding that there is evidence of the formation of preferred atomic configurations. The electronic origin of such stable atomic arrangements has been discarded, and a plausible explanation has been given in terms of the completion of ionic shells or subshells. Gold and Aluminum nanowires present at room temperature a similar character to that found for alkali wires at low temperatures.

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Conductance Quantization in Metallic Nanocontacts: Experimental Results and Novel Theoretical Aspects

Atomic and Molecular Wires, 1997

ABSTRACT In this paper we present results showing the main features of the conductance quantizati... more ABSTRACT In this paper we present results showing the main features of the conductance quantization in metallic contacts under uncontrolled and controlled conditions. We present histograms formed by thousands of single STM measurements, revealing the universality and reproducibility of this phenomenon. The analysis of such histograms reveals some interesting features, explained by tight-binding calculation in terms of the presence of disorder within the nanowire. We have determined the possible chaotic distribution of the electronic states within the nanocontact by studying the distribution of elapsed times in a given conductance level. We also present new results showing the existence of light emission from the nanocontact.

DISORDERED WAVE-GUIDES WITH ABSORPTION: Poster TRANSMITTANCES DISTRIBUTIONS AT THE DIFFUSIVE- LOCALIZED CROSSOVER

Propagation and localization of waves of various kinds in quasi-one dimensional disordered media ... more Propagation and localization of waves of various kinds in quasi-one dimensional disordered media have been studied intensively for several decades. Examples of particular interest are electron transport in disordered solid and electromagnetic wave propagation in random dielectric media. In contrast to electronic systems, where the total flux is conserved, in optical systems the transmittance may be affected as a result of absorption. The conductance (transmittance) distribution in electronic system P(T) is known to evolve from a Gaussian distribution P(T) (deep in the diffusive regime) to a lognormal distribution (deep in the localization regime) [1]. The analysis of the conductance distribution for disordered wires in the diffusive-localization crossover shows a non-obvious transition of the distribution between both regimes [2]. The properties of the transmittance of a multi-channel random wave-guide with absorption have been computed within the Random Matrix framework [3,4]. In t...

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Poster MECHANICAL PROPERTIES OF METALLIC PENTAGONAL NANOWIRES: TEMPERATURE DEPENDENCE

Nanotechnology covers a broad variety of basic and applied studies aiming at the control of diffe... more Nanotechnology covers a broad variety of basic and applied studies aiming at the control of different properties at the nanometer level for their use in promising applications. In particular, metallic nanowires are very interesting systems from a basic physics point of view as well as within the context of future nanoelectronics and sensors industry. However, suspended ultra-thin metallic nanowires are rather weak and hardly reproducible structures. Only monatomic chains have been obtained experimentally in a reproducible way, but they are only stable under extremely controlled conditions and at very low temperatures[1]. Nevertheless, recent theoretical and experimental studies have pointed towards the possibility of obtaining pentagonal (icosahedral) nanowires consistently from the breaking of metallic nanocontacts in certain conditions [2-5]. These icosahedral or pentagonal nanowires are formed by subsequent staggered parallel pentagonal rings (with a relative rotation of π/5) con...

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Quantum dynamical calculations on the magnetization reversal in clusters of spin-1/2 particles: Resonant coherent quantum tunneling

Physical Review B, 1996

In the present work the reversal of magnetization and the coherence of tunneling when an external... more In the present work the reversal of magnetization and the coherence of tunneling when an external magnetic field is rotated instantaneously are studied in systems of a few spin-1/2 particles described by an anisotropic Heisenberg Hamiltonian at Tϭ0. Our calculations demonstrate that this model for small magnetic particles exhibits collective tunneling of the magnetization only for some specific resonant values of the applied magnetic field. These resonant effects occur at fields much lower than the values corresponding to the vanishing of the barrier in the Stoner-Wohlfarth model. The former model is at variance with the exact calculations presented in this paper.

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Ni NANOCONTACTS: STUDY OF ATOMIC CONFIGURATIONS DURING FORMATION AND RUPTURE

Effect of condensed water on scanning near-field optical microscope measurement

Physica Scripta, 2013

ABSTRACT The relevance of the scanning near-field optical microscope (SNOM), for near-field chara... more ABSTRACT The relevance of the scanning near-field optical microscope (SNOM), for near-field characterization, is often shaded by the appearance of artifacts, especially when geometrical characterization is intended. Artifacts are related to many features such as the feedback system or the scanning mode. For non-vacuum environmental conditions, artifact sources may be related to tip geometry and the pollutants attached, either on the tip or on the studied surfaces, altering the optical image. As an environmental element, water vapor could be treated as a source for artifacts, but could also be used as a tool for chemical characterization of hydrophilic patches. Spontaneous meniscus formation between hydrophilic surfaces, such as the tip and the sample, may guide light from the tip to the sample, enhancing the transmitted signal. This study focuses on the effects that water condensation at the nanoscale has on the signals achieved by SNOM, combining two computational methods (Monte Carlo and finite difference time domain) in order to deal with light propagation through heterogeneous media and water condensation.

Evidence of shell structures in Au nanowires at room temperature

Nanotechnology, 2003

Statistical conductance properties of gold elongating nanowires at room temperature are studied e... more Statistical conductance properties of gold elongating nanowires at room temperature are studied experimentally. The measured conductance histogram, built with thousands of consecutive nanocontact breakage experiments, exhibits a rich structure of low-intensity peaks at high-conductance quanta values. Their position as a function of a peak index number suggests two markedly different regimes for electronic and atomic shell structures in these nanowires, as observed previously for alkali metal nanowires.

Ballistic resistivity in aluminum nanocontacts

Physical Review B, 2005

One of the major industrial challenges is to profit from some fascinating physical features prese... more One of the major industrial challenges is to profit from some fascinating physical features present at the nanoscale. The production of dissipationless nanoswitches (or nanocontacts) is one of such attractive applications. Nevertheless, the lack of knowledge of the real efficiency of electronic ballistic/non dissipative transport limits future innovations. For multi-valent metallic nanosystems -where several transport channels per atom are involvedthe only experimental technique available for statistical transport characterization is the conductance histogram. Unfortunately its interpretation is difficult because transport and mechanical properties are intrinsically interlaced. We perform a representative series of semiclassical molecular dynamics simulations of aluminum nanocontact breakages, coupled to full quantum conductance calculations, and put in evidence a linear relationship between the conductance and the contact minimum cross-section for the geometrically favored aluminum nanocontact configurations. Valid in a broad range of conductance values, such relation allows the definition of a transport parameter for nanomaterials, that represents the novel concept of ballistic resistivity.

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Atomic configurations of breaking nanocontacts of aluminium and nickel

A statistical study of favourable atomic configurations of aluminium and nickel nanocontacts duri... more A statistical study of favourable atomic configurations of aluminium and nickel nanocontacts during their fracture at 4 K and 300 K was performed. Nanowire breaking events are simulated by using molecular dynamics (MD), the atomic interactions being represented by the state-of-the-art embedded atom method (EAM) interatomic potentials, which are able to fit bulk and surface properties with a high degree of accuracy. A complete determination of atomic positions during the contact allows evaluation of the evolution of the minimum-cross section S m during stretching. By accumulating S m traces, obtained from many independent fractures of nanowires, minimum cross-section histograms H(S m ) were built. These simulated histograms reveal the presence of preferential geometrical arrangements during the breaking of the nanocontact and allow a direct comparison with experimental conductance histograms. In particular, aluminium histograms show a remarkable agreement between conductance and mini...

San Sebastian-Spain Ni NANOCONTACTS RUPTURES: DEPENDENCE ON STRETCHING DIRECTIONS

R. Paredes , P. García-Mochales , P.A. Serena , S. Peláez a a Instituto de Ciencia de Materiales ... more R. Paredes , P. García-Mochales , P.A. Serena , S. Peláez a a Instituto de Ciencia de Materiales de Madrid (ICMM), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, 28049 Madrid , Spain b Centro de Física, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas 1020A, Venezuela c Dpto Física de la Materia Condensada, Facultad de Ciencias C-III, Universidad Autónoma de Madrid (UAM), Cantoblanco, 28049 Madrid, Spain

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Magneto-optical Stern-Gerlach forces and nonreciprocal torques on small particles

Physical Review Research

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Studies of adsorption of alkali atoms Al(111) as a function of coverage

Surface Science Letters

ABSTRACT We have studied the adsorption of alkali atoms on Al(111) for different coverages θ. We ... more ABSTRACT We have studied the adsorption of alkali atoms on Al(111) for different coverages θ. We calculate the total energy of the system in which the ionic interaction potential is described by pseudopotentials averaged over the parallel directions to the surface. This method allows us to consider all regimes in θ. We find that adsorbed alkali atoms evolve from ionic to metallic and from low to large coverages. In particular, we calculate for the Cs/Al(111) system that the equilibrium distance increases 0.12 Å when coverage changes from 0.4 to 1 ML. Work functions are also presented. We note that in order to obtain well-defined values of the distance, it is necessary to keep the substrate at a low temperature, because the energy minima are very shallow as a function of the adatom-substrate separation.

THE 2-d HEISENBERG MODEL WITH VARIOUS TYPES OF INTERACTIONS: TEMPERATURE DEPENDENCE OF MAGNETIC PARAMETERS AND THE PHASE TRANSITION TEMPERATURE

International Journal of Modern Physics B

Using the low-temperature perturbation (spin wave) theory we calculate the temperature dependence... more Using the low-temperature perturbation (spin wave) theory we calculate the temperature dependence of anisotropy constant, spin-wave stiffness, spontaneous magnetization for a two-dimensional ferromagnetic Heisenberg model with various types of anisotropy and interactions. We found that the Polyakov renormalization procedure is inapplicable for ferromagnetic phase at any anisotropy. We did not find the reorientation phase transition due to dipole-dipole interaction predicted by Pescia and Pokrovsky. Taking into account the spin flips we obtained a phase transition temperature in good agreement with results of our Monte Carlo calculations. These results demonstrate also the effectiveness of the spin wave theory.

Trends in nanotechnology

2nd International Conference on Trends in Nanotechnology

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