Inelastic scattering and local heating in atomic gold wires

Local Strain Effects on Lattice Defect Dynamics and Interstitial Dislocation Loop Formation in Irradiated Tungsten-Molybdenum Alloys: A Molecular Dynamics Study

In this study, molecular dynamics (MD) simulations were used to investigate how alloying tungsten (W) with molybdenum (Mo) and local strain affect the primary defect formation and interstitial dislocation loops (IDLs) in W-Mo alloys. While the number of Frenkel pairs (FPs) in the W-Mo alloy is similar to pure W, it is half that of pure Mo. The W-20% Mo alloy, chosen for further analysis, showed minimal FP variance after collision cascades induced by primary knock-on atoms (PKAs) at 10 to 80 keV. The research examined hydrostatic strains from -1.4% to 1.6%, finding that higher strains correlated with increased FP counts and cluster formation, including IDLs. The following two types of IDLs were identified: majority ½ <111> loops as well as <100> IDLs that formed within the initial picoseconds of the simulations under higher tensile strain (1.6%) and larger PKA energies (80 keV). The strain effects also correlated with changes in threshold displacement energy (TDE), with higher FP formation under tensile strain. This study highlights the impact of strain and alloying on radiation damage, particularly in low-temperature, high-energy environments.

Theoretical study on the structure, spectroscopic, and current-voltage behavior of 11-Cis and Trans retinal isomers in rhodopsin

In this study, the electronic transport properties of 11-Cis and Trans retinal, components of rhodopsin, were investigated as optical molecular switches using the nonequilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT). These isomers, which can be reversibly converted into each other, were examined in detail. The structural and spectroscopic properties, including infrared (IR), Raman, nuclear magnetic resonance (NMR), and ultraviolet (UV) spectra, were analyzed using the hybrid B3LYP/6-311 +  + G** level of theory. Complete vibrational assignments were performed for both forms utilizing the scaled quantum mechanical force field (SQMFF) methodology. To evaluate the conductivity of these molecules, we utilized current-voltage (I-V) characteristics, transmission spectra, molecular projected self-consistent Hamiltonian (MPSH), HOMO-LUMO gap, and second-order interaction energies (E2). The trendline extrapolation of the current-voltage plots confirmed our findings. We investigated the effect of different electrodes (Ag, Au, Pt) and various connection sites (hollow, top, bridge) on conductivity. The Ag electrode with the hollow site exhibited the highest efficiency. Our results indicate that the Cis form has higher conductivity than the Trans form.

Phonon and Magnon Jets above the Critical Current in Nanowires with Planar Domain Walls

We show through nonequilibrium nonadiabatic electron-spin-lattice simulations that above a critical current in magnetic atomic wires with a narrow domain wall (DW), a couple of atomic spaces in width, the electron flow triggers violent stimulated emission of phonons and magnons with an almost complete conversion of the incident electron momentum flux into a phonon and magnon flux. Just below the critical levels of the current flow, the DW achieves maximal velocity of about 3×10^{4}  m/s, entering a strongly nonadiabatic regime of DW propagation, followed by a breakdown at higher biases. Above this threshold, a further increase of the current with the applied bias is impossible-the electronic current suffers a heavy suppression and the DW stops. This poses a fundamental limit to the current densities attainable in atomic wires. At the same time it opens up an exciting way of generating the alternative quasiparticle currents, described above, once the requisite electronic-structure properties are met.

First principles study of thermoelectric performance in pristine and binary alloyed monolayers of noble metals

In search of novel thermoelectric materials, we have investigated the thermoelectric performance of freestanding pristine and binary alloyed monolayers of noble metals (viz. Au, Ag, Cu, Pt) in honeycomb morphology using first principles methods based on density functional theory (DFT) and the non-equilibrium Green's function (NEGF) approach. The requisite electron transmission function is calculated using the TranSIESTA code - a module of the SIESTA package, while its phonon counterpart is obtained using the Phonons module of the python package along with the NEGF utility - PHtrans. Transport is explored along both the armchair (ac) and zigzag (zz) directions. Due to greater transverse length of the unit cell, electron and phonon transport is found to be more in the zz-direction. Among the pristine monolayers, Pt is found to exhibit ferromagnetism as well as the highest thermoelectric efficiency ZT ∼ 8 with an external bias of μ = 0.795 eV. However, alloying brings in a characteristic energy gap in the phononic transmission function, which diminishes the (room-temperature) relative phononic conductance to less than 5% in Pt-containing alloys. Also, monolayers of AuAg and AuCu turn semiconducting, with the former yielding a high Seebeck coefficient of 1264.96 μV K^-1 at μ ∼ -0.055 eV. Moreover, they exhibit an enhanced ZT near the edges of the band gap, with ZT_max as high as 3.74 and 3.05, respectively. Interestingly, the Pt-containing alloyed monolayers also show a ferromagnetic character and hence, a spin-dependent Seebeck effect. In the CuPt monolayer, the bias μ can be tuned to attain an appreciable charge figure of merit Z_cT = 4.80 at μ = 0.58 eV, while a decent spin figure of merit Z_sT = 1.43 at μ = 0.56 eV. Instead, the pristine Pt monolayer shows a much better Z_sT = 5.45 for a bias of μ = 0.785 eV. Nevertheless, the predicted ZT remains smaller than the corresponding alloyed atomic chains in double zigzag topology.

A simple approximation to the electron-phonon interaction in population dynamics

The modeling of coupled electron-ion dynamics including a quantum description of the nuclear degrees of freedom has remained a costly and technically difficult practice. The kinetic model for electron-phonon interaction provides an efficient approach to this problem, for systems evolving with low amplitude fluctuations, in a quasi-stationary state. In this work, we propose an extension of the kinetic model to include the effect of coherences, which are absent in the original approach. The new scheme, referred to as Liouville-von Neumann + Kinetic Equation (or LvN + KE), is implemented here in the context of a tight-binding Hamiltonian and employed to model the broadening, caused by the nuclear vibrations, of the electronic absorption bands of an atomic wire. The results, which show close agreement with the predictions given by Fermi's golden rule (FGR), serve as a validation of the methodology. Thereafter, the method is applied to the electron-phonon interaction in transport simulations, adopting to this end the driven Liouville-von Neumann equation to model open quantum boundaries. In this case, the LvN + KE model qualitatively captures the Joule heating effect and Ohm's law. It, however, exhibits numerical discrepancies with respect to the results based on FGR, attributable to the fact that the quasi-stationary state is defined taking into consideration the eigenstates of the closed system rather than those of the open boundary system. The simplicity and numerical efficiency of this approach and its ability to capture the essential physics of the electron-phonon coupling make it an attractive route to first-principles electron-ion dynamics.

Electro-thermal transport in disordered nanostructures: a modeling perspective

Following the emergence of novel classes of atomic systems with amorphous active regions, device simulations had to rapidly evolve to devise strategies to account for the influence of disordered phases, defects, and interfaces into its core physical models. We review here how molecular dynamics and quantum transport can be combined to shed light on the performance of, for example, conductive bridging random access memories (CBRAM), a type of non-volatile memory. In particular, we show that electro-thermal effects play a critical role in such devices and therefore present a method based on density functional theory and the non-equilibrium Green's function formalism to accurately describe them. Three CBRAM configurations are investigated to illustrate the functionality of the proposed modeling approach.

On the Fano Line Shape of Single Molecule Electroluminescence Induced by a Scanning Tunneling Microscope

The coupling between molecular exciton and gap plasmons plays a key role in single molecular electroluminescence induced by a scanning tunneling microscope (STM). But it has been difficult to clarify the complex experimental phenomena. By employing the nonequilibrium Green's function method, we propose a general theoretical model to understand the light emission spectrum of single molecule and gap plasmons from an energy transport point of view. The coherent interaction between gap plasmons and molecular exciton leads to a prominent Fano resonance in the emission spectrum. We analyze the dependence of the Fano line shape on the system parameters, based on which we provide a unified account of several recent experimental observations. Moreover, we highlight the effect of the tip-molecule electronic coupling on the spectrum.

Origin of Vibrational Instabilities in Molecular Wires with Separated Electronic States

Current-induced heating in molecular junctions stems from the interaction between tunneling electrons and localized molecular vibrations. If the electronic excitation of a given vibrational mode exceeds heat dissipation, a situation known as vibrational instability is established, which can seriously compromise the integrity of the junction. Using out of equilibrium first-principles calculations, we demonstrate that vibrational instabilities can take place in the general case of molecular wires with separated unoccupied electronic states. From the ab initio results, we derive a model to characterize unstable vibrational modes and construct a diagram that maps mode stability. These results generalize previous theoretical work and predict vibrational instabilities in a new regime.

Controlling the Conductance of a Graphene-Molecule Nanojunction by Proton Transfer

The possibility of using single molecule junctions as components of nanoelectronic devices has motivated intensive experimental and theoretical research on the underlying transport mechanism in these systems. In this Letter, we investigate from a theoretical perspective intramolecular proton transfer reactions as a mechanism for controlling the conductance state of graphene-based molecular junctions. Employing a methodology that combines first-principles electronic structure methods with transport approaches, we show that the proton transfer reaction proceeds via a stepwise mechanism, giving rise to several tautomers with different conductance states. The analysis reveals that the relative stability of the tautomers as well as the energy barrier for their interconversion can be controlled by means of an external electrostatic field, which provides a mechanism for switching the nanojunction.

Band-Engineered Local Cooling in Nanoscale Junctions

The stability and performance of nanoscale junctions are closely related to the local effective temperature. The local effective temperature is mainly caused by the competition between heating and cooling processes in inelastic electron-phonon scat- tering. Local cooling occurs when the rate of energy in cooling exceeds that in heating. Previous research has been done using either specific potential configuration or an adatom to achieve local cooling. We propose an engineer-able local-cooling mechanism in asymmetric two-terminal tunneling junctions, in which one electrode is made of metal, whereas the other is made of a selectable bad-metal, such as heavily-doped polysilicon. The width of energy window of the selectable material, defined as the width covering all possible energy states counting from the conduction band minimum, can be engineered through doping. Interestingly, we have shown that substantial local cooling can be achieved at room temperature when the width of energy window of the low-density electrode is comparable to the energy of the phonon. The unusual local cooling is caused by the narrowed width of energy window, which obstructs the inelastic scattering for heating.

Evolution of shot noise in suspended lithographic gold break junctions with bias and temperature

Shot noise is a powerful tool to probe correlations and microscopic transport details that conductance measurements alone cannot reveal. Even in atomic-scale Au devices that are well described by Landauer-Büttiker physics, complications remain such as local heating and electron-phonon interactions. We report systematic rf measurements of shot noise in individual atomic-scale gold break junctions at multiple temperatures, with most bias voltages well above the energy of the Au optical phonon mode. Motivated by the previous experimental evidence that electron-phonon interactions can modify Fano factors and result in kinked features in bias dependence of shot noise, we find that the temperature dependence of shot noise from 4.2 to 100 K is minimal. Enhanced Fano factors near [Formula: see text] and features beyond simply linear bias dependence of shot noise near the [Formula: see text] plateau are observed. Both are believed to have non-interacting origins and the latter likely results from slightly bias-dependent transmittance of the dominant quantum channel.

Revisiting the inelastic electron tunneling spectroscopy of single hydrogen atom adsorbed on the Cu(100) surface

Inelastic electron tunneling spectroscopy (IETS) of a single hydrogen atom on the Cu(100) surface in a scanning tunneling microscopy (STM) configuration has been investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. The electron-vibration interaction is treated at the level of lowest order expansion. Our calculations show that the single peak observed in the previous STM-IETS experiments is dominated by the perpendicular mode of the adsorbed H atom, while the parallel one only makes a negligible contribution even when the STM tip is laterally displaced from the top position of the H atom. This propensity of the IETS is deeply rooted in the symmetry of the vibrational modes and the characteristics of the conduction channel of the Cu-H-Cu tunneling junction, which is mainly composed of the 4s and 4pz atomic orbitals of the Cu apex atom and the 1s orbital of the adsorbed H atom. These findings are helpful for deepening our understanding of the propensity rules for IETS and promoting IETS as a more popular spectroscopic tool for molecular devices.

Vibration-mediated Kondo transport in molecular junctions: conductance evolution during mechanical stretching

The vibration-mediated Kondo effect attracted considerable theoretical interest during the last decade. However, due to lack of extensive experimental demonstrations, the fine details of the phenomenon were not addressed. Here, we analyze the evolution of vibration-mediated Kondo effect in molecular junctions during mechanical stretching. The described analysis reveals the different contributions of Kondo and inelastic transport.

Insights into Solid-State Electron Transport through Proteins from Inelastic Tunneling Spectroscopy: The Case of Azurin

Surprisingly efficient solid-state electron transport has recently been demonstrated through "dry" proteins (with only structural, tightly bound H2O left), suggesting proteins as promising candidates for molecular (bio)electronics. Using inelastic electron tunneling spectroscopy (IETS), we explored electron-phonon interaction in metal/protein/metal junctions, to help understand solid-state electronic transport across the redox protein azurin. To that end an oriented azurin monolayer on Au is contacted by soft Au electrodes. Characteristic vibrational modes of amide and amino acid side groups as well as of the azurin-electrode contact were observed, revealing the azurin native conformation in the junction and the critical role of side groups in the charge transport. The lack of abrupt changes in the conductance and the line shape of IETS point to far off-resonance tunneling as the dominant transport mechanism across azurin, in line with previously reported (and herein confirmed) azurin junctions. The inelastic current and hence electron-phonon interaction appear to be rather weak and comparable in magnitude with the inelastic fraction of tunneling current via alkyl chains, which may reflect the known structural rigidity of azurin.

A variational approach for dissipative quantum transport in a wide parameter space

Recent development of theoretical method for dissipative quantum transport has achieved notable progresses in the weak or strong electron-phonon coupling regime. However, a generalized theory for dissipative quantum transport in a wide parameter space had not been established. In this work, a variational polaron theory for dissipative quantum transport in a wide range of electron-phonon coupling is developed. The optimal polaron transformation is determined by the optimization of the Feynman-Bogoliubov upper bound of free energy. The free energy minimization ends up with an optimal mean-field Hamiltonian and a minimal interaction Hamiltonian. Hence, second-order perturbation can be applied to the transformed system, resulting in an accurate and efficient method for the treatment of dissipative quantum transport with different electron-phonon coupling strength. Numerical benchmark calculation on a single site model coupled to one phonon mode is presented.

Large-voltage behavior of charge transport characteristics in nanosystems with weak electron-vibration coupling

We study analytically the Full Counting Statistics of the charge transport through a nanosystem consisting of a few electronic levels weakly coupled to a discrete vibrational mode. In the limit of large transport voltage bias the cumulant generating function can be evaluated explicitly based solely on the intuitive physical arguments and classical master equation description of the vibration mode. We find that for the undamped vibrational modes mutual dynamical interplay between electronic and vibronic degrees of freedom leads to strongly nonlinear (in voltage) transport characteristics of the nanosystem. In particular, we find that for large voltages the k-th cumulant of the current grows as V (2k) to be contrasted with the linear dependence in case of more strongly externally damped and thus thermalized vibrational modes.

Current-induced forces and hot spots in biased nanojunctions

We investigate theoretically the interplay of current-induced forces (CIFs), Joule heating, and heat transport inside a current-carrying nanoconductor. We find that the CIFs, due to the electron-phonon coherence, can control the spatial heat dissipation in the conductor. This yields a significant asymmetric concentration of excess heating (hot spot) even for a symmetric conductor. When coupled to the electrode phonons, CIFs drive different phonon heat flux into the two electrodes. First-principles calculations on realistic biased nanojunctions illustrate the importance of the effect.

Thermoelectric effect in Aharonov-Bohm structures

The thermoelectric effects of a single Aharonov-Bohm (SAB) ring and coupled double Aharonov-Bohm (DAB) rings have been investigated on a theoretical basis, taking into account the contributions of both electrons and phonons to the transport process by using the nonequilibrium Green's function technique. The thermoelectric figure of merit of the coupled DAB rings cannot be predicted directly by combining the values of two SAB ring systems due to the contribution of electron-phonon interaction to coupling between the two sites connecting the rings. We find that thermoelectric efficiency can be optimized by modulating the phases of the magnetic flux threading the two rings.

Detection of vibration-mode scattering in electronic shot noise

We present shot noise measurements on Au nanowires showing very pronounced vibration-mode features. In accordance to recent theoretical predictions the sign of the inelastic signal, i.e., the signal due to vibration excitations, depends on the transmission probability becoming negative below a certain transmission value. We argue that the negative contribution to noise arises from coherent two-electron processes mediated by electron-phonon scattering and the Pauli exclusion principle. These signals can provide unique information on the local phonon population and lattice temperature of the nanoscale system.

Critical comparison of electrode models in density functional theory based quantum transport calculations

We study the performance of two different electrode models in quantum transport calculations based on density functional theory: parametrized Bethe lattices and quasi-one-dimensional wires or nanowires. A detailed account of implementation details in both the cases is given. From the systematic study of nanocontacts made of representative metallic elements, we can conclude that the parametrized electrode models represent an excellent compromise between computational cost and electronic structure definition as long as the aim is to compare with experiments where the precise atomic structure of the electrodes is not relevant or defined with precision. The results obtained using parametrized Bethe lattices are essentially similar to the ones obtained with quasi-one-dimensional electrodes for large enough cross-sections of these, adding a natural smearing to the transmission curves that mimics the true nature of polycrystalline electrodes. The latter are more demanding from the computational point of view, but present the advantage of expanding the range of applicability of transport calculations to situations where the electrodes have a well-defined atomic structure, as is the case for carbon nanotubes, graphene nanoribbons, or semiconducting nanowires. All the analysis is done with the help of codes developed by the authors which can be found in the quantum transport toolbox ALACANT and are publicly available.

Transient electron dynamics in a vibrating quantum dot in the Kondo regime

We employ the time-dependent non-crossing approximation to investigate the joint effect of strong electron-electron and electron-phonon interaction on the instantaneous conductance of a single-molecule transistor which is abruptly moved into the Kondo regime by means of a gate voltage. We find that the instantaneous conductance exhibits decaying sinusoidal oscillations on the long timescale for infinitesimal bias. The ambient temperature and electron-phonon coupling strength influence the amplitude of these oscillations. The frequency of the oscillations is found to be equal to the phonon frequency. We argue that the origin of these oscillations can be attributed to the interference between the emerging Kondo resonance and its phonon sidebands. We discuss the effect of finite bias on these oscillations.

Unified description of charge transfer mechanisms and vibronic dynamics in nanoscale junctions

We propose a general framework that unifies the description of counting statistics of transmitted (fermionic) charges as it is commonly used in the quantum transport community with the description of counting statistics of phonons (bosons). As a particular example, we study on the same footing the counting statistics of electrons transferred through a molecular junction and the corresponding population dynamics of the associated molecular vibrational mode. In the tunnel limit, non-perturbative results in the electron-phonon interaction are derived that unify complementary approaches based on rate equations or on the use of non-equilibrium Green functions.

Inelastic electron tunneling spectroscopy of single-molecule junctions using a mechanically controllable break junction

We report the use of electrical measurements to identify simultaneously the number and type of organic molecules within metal-molecule-metal junctions. Our strategy combines analyses of single-molecule conductance and inelastic electron tunneling spectra, exploiting a nanofabricated mechanically controllable break junction. We found that the peak linewidth of the inelastic electron tunneling spectrum decreased as the modulation voltage and temperature decreased, and that the selection rule for inelastic electron tunneling spectroscopy agrees with that for Raman spectroscopy. Furthermore, the differential conductance curve of the single-molecule junction suggests that it has asymmetrical electrode-molecule coupling.

Phonon-assisted current noise in molecular junctions

We investigate the effects of phonon scattering on the electronic current noise through nanojunctions using the nonequilibrium Green's functions formalism extended to include the counting field. In the case of weak electron-phonon coupling and a single broad electronic level, we derive an analytic expression for the current noise at arbitrary temperature and identify physically distinct contributions based on their voltage dependence. We apply our theory to the experimentally relevant case of a D_{2} molecule placed in a break junction and predict a significant inelastic contribution to the current noise.

Phonon generation and phonon energy current fluctuation in quantum dot molecules

We study the phonon dynamics in a biased molecular junction with the interplay of electron-phonon coupling and Coulomb interaction. These interactions are taken into account within the self-consistent Born approximation and mean-field methods. It is found that the Coulomb interaction can enhance the nonequilibrium phonon generation. A general formula for the zero-frequency power spectral density of the phonon energy current fluctuation is presented in terms of the nonequilibrium phonon Green's functions.

Coupled electron-phonon transport from molecular dynamics with quantum baths

Based on generalized quantum Langevin equations for the tight-binding wavefunction amplitudes and lattice displacements, electron and phonon quantum transport are obtained exactly using molecular dynamics (MD) in the ballistic regime. The electron-phonon interactions can be handled with a quasi-classical approximation. Both charge and energy transport and their interplay can be studied. We compare the MD results with those of a fully quantum mechanical nonequilibrium Green's function (NEGF) approach for the electron currents. We find a ballistic to diffusive transition of the electron conduction in one-dimensional chains as the chain length increases.

The SIESTA method; developments and applicability

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

Systematic study on quantum confinement and waveguide effects for elastic and inelastic currents in atomic gold wire: importance of the phase factor for modeling electrodes

Quantum confinement of the electrodes is an important issue for electron transport through molecular or atomic wire junctions. To assess the importance of waveguide effects by quantum confinement of the electrodes, we have calculated elastic and inelastic conductance and inelastic electron tunneling spectra of atomic gold wire with gold electrodes for several models. The results show the quite important role of the phase factors between the modeled electrodes and the contact region.

Electron transport via local polarons at interface atoms

Electronic transport is profoundly modified in the presence of strong electron-vibration coupling. We show that in certain situations, the electron flow takes place only when vibrations are excited. By controlling the segregation of boron in semiconducting Si(111)-square root 3 x square root 3 R 30 degrees surfaces, we create a type of adatom with a dangling-bond state that is electronically decoupled from any other electronic state. However, probing this state with scanning tunnelling microscopy at 5 K yields high currents. These findings are rationalized by ab-initio calculations that show the formation of a local polaron in the transport process.

Classical nuclear motion in quantum transport

An ab initio quantum-classical mixed scheme for the time evolution of electrode-device-electrode systems is introduced to study nuclear dynamics in quantum transport. Two model systems are discussed to illustrate the method. Our results provide the first example of current-induced molecular desorption as obtained from a full time-dependent approach and suggest the use of ac biases as a way to tailor electromigration. They also show the importance of nonadiabatic effects for ultrafast phenomena in nanodevices.

Inelastic transport through molecules: comparing first-principles calculations to experiments

We present calculations of the elastic and inelastic conductance through three different hydrocarbon molecules connected to gold electrodes. Our method is based on a combination of the nonequilibrium Green's function method with density functional theory. Vibrational effects in these molecular junctions were previously investigated experimentally by Kushmerick et al. (Nano Lett. 2004, 4, 639). Our results are in good agreement with the measurements and provide insights into (i) which vibrational modes are responsible for inelastic scattering, (ii) the width of the inelastic electron tunneling signals, and (iii) the mechanisms of heating and cooling of the vibrational modes induced by the coupling to the charge carriers.

Effect of electron-phonon scattering on shot noise in nanoscale junctions

We investigate the effect of electron-phonon inelastic scattering on shot noise in nanoscale junctions in the regime of quasiballistic transport. We predict that when the local thermal energy of the junction is larger than its lowest vibrational mode energy eV(c), the inelastic contribution to shot noise (conductance) increases (decreases) with bias as V (sqrt[V]). The corresponding Fano factor thus increases as sqrt[V]. We also show that the inelastic contribution to the Fano factor saturates with increasing thermal current exchanged between the junction and the bulk electrodes to a value which, for V >> V(c), is independent of bias. These predictions can be readily tested experimentally.

Ab initio analysis of electron-phonon coupling in molecular devices

We report a first principles analysis of electron-phonon coupling in molecular devices under external bias voltage and during current flow. Our theory and computational framework are based on carrying out density functional theory within the Keldysh nonequilibrium Green's function formalism. Using a molecular tunnel junction of a 1,4-benzenedithiolate molecule contacted by two aluminum leads as an example, we analyze which molecular vibrational modes are most relevant to charge transport under nonequilibrium conditions. We find that the low-lying modes are most important. As a function of bias voltage, the electron-phonon coupling strength can change drastically while the vibrational spectrum changes at a few percent level.