QuantumATK: An integrated platform of electronic and atomic-scale modelling tools

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.Comment: Submitted to Journal of Physics: Condensed Matte

Binary data corruption due to a Brownian agent

We introduce a model of binary data corruption induced by a Brownian agent (active random walker) on a d-dimensional lattice. A continuum formulation allows the exact calculation of several quantities related to the density of corrupted bits \rho; for example the mean of \rho, and the density-density correlation function. Excellent agreement is found with the results from numerical simulations. We also calculate the probability distribution of \rho in d=1, which is found to be log-normal, indicating that the system is governed by extreme fluctuations.Comment: 39 pages, 10 figures, RevTe

2D photonic-crystal optomechanical nanoresonator

We present the optical optimization of an optomechanical device based on a suspended InP membrane patterned with a 2D near-wavelength grating (NWG) based on a 2D photonic-crystal geometry. We first identify by numerical simulation a set of geometrical parameters providing a reflectivity higher than 99.8 % over a 50-nm span. We then study the limitations induced by the finite value of the optical waist and lateral size of the NWG pattern using different numerical approaches. The NWG grating, pierced in a suspended InP 265 nm-thick membrane, is used to form a compact microcavity involving the suspended nano-membrane as end mirror. The resulting cavity has a waist size smaller than 10 $\mu$m and a finesse in the 200 range. It is used to probe the Brownian motion of the mechanical modes of the nanomembrane

Linear and nonlinear capacitive coupling of electro-opto-mechanical photonic crystal cavities

We fabricate and characterize a microscale silicon electro-opto-mechanical system whose mechanical motion is coupled capacitively to an electrical circuit and optically via radiation pressure to a photonic crystal cavity. To achieve large electromechanical interaction strength, we implement an inverse shadow mask fabrication scheme which obtains capacitor gaps as small as 30 nm while maintaining a silicon surface quality necessary for minimizing optical loss. Using the sensitive optical read-out of the photonic crystal cavity, we characterize the linear and nonlinear capacitive coupling to the fundamental 63 MHz in-plane flexural motion of the structure, showing that the large electromechanical coupling in such devices may be suitable for realizing efficient microwave-to-optical signal conversion.Comment: 8 papers, 4 figure

Organic electronic ratchet devices : exploring the electronic ratchet and investigating a solar ratchet

This presentation reports on the investigation of two related topics, the (in)-organic electronic ratchet and the organic solar ratchet. These are two implementations of the electronic ratchet device that will first be introduced. The electronic ratchet generates electrical current and voltage by rectifying an external perturbation, in the present case an oscillating voltage. The oscillation is rectified by a periodic, asymmetric potential in which electronic charges are placed. The external perturbation drives the system away from equilibrium, causing detailed balance to be broken; consequently the periodic asymmetry of the potential leads to a net motion of the charges, comparable to the net motion of marbles on a shaking washboard. Note that under equilibrium conditions no (spontaneous) current will flow in any potential. In this presentation we show that the generated current as a function of the frequency of the driving signal can be scaled onto a universal profile, covering many orders of magnitude in frequency. Simulations show that this profile is predominantly dependent on drift (as opposed to diffusion) currents in the ratchet. Experimentally this is verified by combining measurements on three different disordered semiconducting materials. IGZO (Indium Gallium Zinc Oxide) as an inorganic amorphous electron semiconductor and Pentacene and P3HT/PCBM as organic hole semiconductors. The combined scaled current profile shows a consistent behavior for the three materials over at least seven orders of magnitude of (scaled) frequency. The solar ratchet is a lateral solar cell which can in lowest order be seen as multiple solar cells in series, which is comparable to a multi-junction tandem solar cell. The goal is to create a large open circuit voltage with the intention to create a more efficient solar cell. Simulation of this device turned out to be troublesome due to numerical problems related to the calculation of diffusion currents and of bimolecular recombination. However the first version of the simulation tool, in which drift and diffusion currents are calculated sequentially, shows the possible behavior of the solar ratchet. The second version, in which the drift and diffusion currents are simultaneously calculated using the Boltzmann transport equation, predicts the solar ratchet to be non-functional due to zero recombination. However, the depletion length of the recombination zones can be calculated. On basis of this an analogy can be made with the recombination zone in the pn-junction in a conventional tandem solar cell. As the tandem solar cell is known to work the solar ratchet is predicted to work as well. Experimental proofs of principle of the ratchet solar cell were tried to be made but unfortunately no suitable solar ratchet was produced due to various problems that will be discussed. This presentation reports on the investigation of two related topics, the (in)-organic electronic ratchet and the organic solar ratchet. These are two implementations of the electronic ratchet device that will first be introduced. The electronic ratchet generates electrical current and voltage by rectifying an external perturbation, in the present case an oscillating voltage. The oscillation is rectified by a periodic, asymmetric potential in which electronic charges are placed. The external perturbation drives the system away from equilibrium, causing detailed balance to be broken; consequently the periodic asymmetry of the potential leads to a net motion of the charges, comparable to the net motion of marbles on a shaking washboard. Note that under equilibrium conditions no (spontaneous) current will flow in any potential. In this presentation we show that the generated current as a function of the frequency of the driving signal can be scaled onto a universal profile, covering many orders of magnitude in frequency. Simulations show that this profile is predominantly dependent on drift (as opposed to diffusion) currents in the ratchet. Experimentally this is verified by combining measurements on three different disordered semiconducting materials. IGZO (Indium Gallium Zinc Oxide) as an inorganic amorphous electron semiconductor and Pentacene and P3HT/PCBM as organic hole semiconductors. The combined scaled current profile shows a consistent behavior for the three materials over at least seven orders of magnitude of (scaled) frequency. The solar ratchet is a lateral solar cell which can in lowest order be seen as multiple solar cells in series, which is comparable to a multi-junction tandem solar cell. The goal is to create a large open circuit voltage with the intention to create a more efficient solar cell. Simulation of this device turned out to be troublesome due to numerical problems related to the calculation of diffusion currents and of bimolecular recombination. However the first version of the simulation tool, in which drift and diffusion currents are calculated sequentially, shows the possible behavior of the solar ratchet. The second version, in which the drift and diffusion currents are simultaneously calculated using the Boltzmann transport equation, predicts the solar ratchet to be non-functional due to zero recombination. However, the depletion length of the recombination zones can be calculated. On basis of this an analogy can be made with the recombination zone in the pn-junction in a conventional tandem solar cell. As the tandem solar cell is known to work the solar ratchet is predicted to work as well. Experimental proofs of principle of the ratchet solar cell were tried to be made but unfortunately no suitable solar ratchet was produced due to various problems that will be discussed

Interacting Ions in Biophysics: Real is not Ideal

Ions in water are important in biology, from molecules to organs. Classically, ions in water are treated as ideal noninteracting particles in a perfect gas. Excess free energy of ion was zero. Mathematics was not available to deal consistently with flows, or interactions with ions or boundaries. Non-classical approaches are needed because ions in biological conditions flow and interact. The concentration gradient of one ion can drive the flow of another, even in a bulk solution. A variational multiscale approach is needed to deal with interactions and flow. The recently developed energetic variational approach to dissipative systems allows mathematically consistent treatment of bio-ions Na, K, Ca and Cl as they interact and flow. Interactions produce large excess free energy that dominate the properties of the high concentration of ions in and near protein active sites, channels, and nucleic acids: the number density of ions is often more than 10 M. Ions in such crowded quarters interact strongly with each other as well as with the surrounding protein. Non-ideal behavior has classically been ascribed to allosteric interactions mediated by protein conformation changes. Ion-ion interactions present in crowded solutions--independent of conformation changes of proteins--are likely to change interpretations of allosteric phenomena. Computation of all atoms is a popular alternative to the multiscale approach. Such computations involve formidable challenges. Biological systems exist on very different scales from atomic motion. Biological systems exist in ionic mixtures (extracellular/intracellular solutions), and usually involve flow and trace concentrations of messenger ions (e.g., 10-7 M Ca2+). Energetic variational methods can deal with these characteristic properties of biological systems while we await the maturation and calibration of all atom simulations of ionic mixtures and divalents

A Study of Hole Transport in Crystalline Monoclinic Selenium Using Bulk Monte Carlo Techniques

abstract: Amorphous materials can be uniformly deposited over a large area at lower cost compared to crystalline semiconductors (Silicon or Germanium). This property along with its high resistivity and wide band-gap found many applications in devices like rectifiers, xerography, xero-radiography, ultrahigh sensitivity optical cameras, digital radiography, and mammography (2D and 3D tomosynthesis). Amorphous selenium is the only amorphous material that undergoes impact ionization where only holes avalanche at high electric fields. This leads to a small excess noise factor which is a very important performance comparison matrix for avalanche photodetectors. Thus, there is a need to model high field avalanche process in amorphous selenium. At high fields, the transport in amorphous selenium changes from low values of activated trap-limited drift mobility to higher values of band transport mobility, via extended states. When the transport shifts from activated mobility with a high degree of localization to extended state band transport, the wavefunction of the amorphous material resembles that of its crystalline counterpart. To that effect, crystalline monoclinic selenium which has the closest resemblance to vapor deposited amorphous selenium has been studied. Modelling a crystalline semiconductor makes calculations simpler. The transport phenomena in crystalline monoclinic selenium is studied by using a bulk Monte Carlo technique to solve the semi-classical Boltzman Transport equation and thus calculate vital electrical parameters like mobility, critical field and mobility variations against temperatures. The band structure and the density of states function for monoclinic selenium was obtained by using an atomistic simulation tool, the Atomistic Toolkit in the Virtual Nano Lab, Quantum Wise, Copenhagen, Denmark. Moreover, the velocity and energy against time characteristics have been simulated for a wide range of electric fields (1-1000 $\frac{kV}{cm}$), which is further used to find the hole drift mobility. The low field mobility is obtained from the slope of the velocity vs. electric field plot. The low field hole mobility was calculated to be 5.51 $\frac{cm^{2}}{Vs}$ at room temperature. The experimental value for low field hole mobility is 7.29 $\frac{cm^{2}}{Vs}$. The energy versus electric field simulation at high fields is used to match the experimental onset of avalanche (754 $\frac{kV}{cm}$) for an ionization threshold energy of 2.1 eV. The Arrhenius plot for mobility against temperature is simulated and compared with published experimental data. The experimental and simulation results show a close match, thus validating the study.Dissertation/ThesisMasters Thesis Electrical Engineering 201