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The quantum framework of the time-dependent density functional theory (TDDFT) for analyzing nanostructured devices is reviewed, and alternative methods for incorporating induced electromagnetic fields into the theory are discussed. To capture the retardation effects in larger electronic structures, the TDDFT equations can be formulated by applying the Lorenz gauge-fixing condition to the induced scalar and vector potentials (analogous to macroscopic formulations used in antenna theory). Evaluating the retarded potentials via radiation integrals, however, rapidly becomes the computational bottleneck within the TDDFT time-marching framework if done in a brute-force manner. This article demonstrates that 3D space or 4D space-time fast Fourier transform (FFT) schemes can be adopted to accelerate these computations and reduce the costs of evaluating the potentials below the typical computational bottleneck of TDDFT. Thus, FFT-accelerated Lorenz gauge retarded potentials become an attractive candidate for replacing the conventionally used electrostatic-induced scalar potential within TDDFT.

Electrodeposition of aluminum (Al) from an organic non-aqueous electrolyte of ethylbenzene containing aluminum bromide is demonstrated. It is offered as a simple method for the preparation of Al coatings. This work employs distinct electrochemical techniques and explores the effects of the experimental parameters on the kinetics of the process and the quality of the final coatings. The process presented here enables deposition of pure and crystalline Al at room temperature and facilitates the production of uniform Al coatings on various metallic substrates. Morphological studies establish that the growth of Al deposits follows an island mode, and thus, the most noteworthy effect of the substrate over the morphology of the deposits originates from its impact over the nucleation stage, and the density of islands. This study is complemented by theoretical modeling for the adsorption of Al atoms at the different surfaces. Corrosion evaluation determines the dissolution mechanisms of each of the studied substrates in the examined electrolyte. These findings further corroborate the claim that this electrolyte enables the reversible electrodeposition of Al.

In this work we performed fundamental investigations of the adsorption of O2 and Li2O2 molecules on seven transition-metal carbide (TMC) surfaces, which present 3d, 4d and 5d TM, where TM = Ti, V, ...

We outline a systematic experimental and theoretical study on the influence of ruthenium contamination on the oxygen reduction activity (ORR) of a Pt/C catalyst at potentials relevant to a polymer electrolyte fuel cell cathode. A commercial Pt/C catalyst was contaminated by different amounts of ruthenium, equivalent to 0.15-4 monolayers. The resulting ruthenium-contaminated Pt/C powders were characterized by Energy–Dispersive X–ray Spectroscopy (EDS), X–ray Photoelectron Spectroscopy (XPS) and Scanning Transmission Electron Microscopy (STEM) to verify ruthenium contamination. A rotating disk electrode (RDE) technique was used to study the influence of ruthenium on oxygen reduction kinetics. Density functional theory (DFT) calculations were performed to estimate the oxygen reduction activity of the platinum surface with increasing ruthenium coverage, simulating ruthenium-contaminated Pt/C. The binding energies of O and OH on the surfaces were used for activity estimations. It was found that the specific activity of the ORR at 0.85V vs RHE exhibited a pseudo-exponential decay with increased ruthenium contamination, decreasing by ~45% already at 0.15 monolayer-equivalent contamination. The results of the DFT calculations were qualitatively in line with experimental findings, verifying the effect of O and OH binding energies and the oxophilic nature of ruthenium on ORR and the ability of the chosen approach to predict the effect of ruthenium contamination on ORR on platinum.

This paper presents the utilization of hybrid carbon nano-tube (CNT) – manganese dioxide (MnO2) tissues as air electrodes in nonaqueous aluminum- and lithium-based battery systems. The CNT tissues are impregnated with α-manganese dioxide nanoparticles via a straightforward binder-free ultrasonic treatment, thereby enabling an improved oxygen reduction reaction (ORR) catalytic activity. Half-cell potentiodynamic measurements along with full-cell discharge evaluations of Li- and Al-based battery systems are reported. Higher discharge potentials and capacities were obtained from generic and advanced hybrid CNT–MnO2 air cathodes. The discharge products obtained on the air cathode surface were studied using high-resolution scanning electron microscopy. Their chemical compositions were evaluated using elemental mapping energy-dispersive X-ray spectroscopy. We complemented our analysis with density functional theory calculations of oxygen adsorption on MnO2 and graphene. The modifications obtained for the discharge products in both systems, along with their improved distribution within the cathode surface, supported longer discharge processes without clogging the O2 penetration pathways at the air cathode. The stability of the α-MnO2 catalyst was studied using X-ray photoelectron spectroscopy and electron paramagnetic resonance spectroscopy, thereby indicating the ongoing formation of an outer MnF2 shell layer, which affected the α-MnO2 functionality, as an efficient ORR catalyst.

The fundamental principles underlying the arrangement of elements into solid compounds with an enormous variety of crystal structures are still largely unknown. This study presents a general overview of the structure types appearing in an important subset of the solid compounds, i.e., binary and ternary compounds of the 6A column oxides, sulfides and selenides. It contains an analysis of these compounds, including the prevalence of various structure types, their symmetry properties, compositions, stoichiometries and unit cell sizes. It is found that these compound families include preferred stoichiometries and structure types that may reflect both their specific chemistry and research bias in the available empirical data. Identification of non-overlapping gaps and missing stoichiometries in these structure populations may be used as guidance in the search for new materials., 19 pages, 13 figures

We present the characterization by the rotating-disc-electrode (RDE) and cyclic-voltammetry (CV) methods of oxygen-reduction/oxygen-evolution (ORR/OER) processes in the Na-air battery containing fresh and aged polyethylene glycol dimethyl ether 500 (PEGDME500)-based electrolyte. It was found that the time of storage of this solvent affects the oxidation overpotentials of the reduction products. It is suggested that the reason for the PEGDME500 change originates from the synthesis process, in which the sodium alcoholate molecule can remain in the solvent. Insertion of metallic sodium prevents aging of PEGDME500. The results are compared with a tetraethylene glycol dimethyl ether (TEGDME)-based electrolyte. It was shown that the voltammogram of the TEGDME-based electrolyte is similar to that of the fresh PEGDME500, but with the opposite ratio of NaO2-to-Na2O2 oxidation currents. This indicates that Na2O2 is the main reduction product in TEGDME, and we suggest that in fresh PEGDME500, Na2O2 is formed by the chemical disproportionation of the dissolved NaO2 in the solution.

In this work we performed fundamental investigations of the adsorption of O2 and Li2O2 molecules on seven transition-metal carbide (TMC) surfaces, which present 3d, 4d, and 5d TM, where TM = Ti, V, Zr, Nb, Mo, Hf and Ta. We employed density functional theory (DFT) with the semilocal meta-GGA SCAN functional. The oxide layer behaves as a passivation layer on the TiC(111), ZrC(111) and MoC(001) systems upon Li2O2 adsorption, but promotes the formation of a Li1O3TM1 layer on the VC(111), NbC(111), MoC(111), and HfC(111) surfaces due to the change in stoichiometry which is caused by the first adsorbed Li2O2 molecule. We showed that with increasing the number of the Li2O2 molecules on the TMC surfaces, the contribution of the TMC surface states turns out less important to the adsorption energy of the molecules. After the first layer of Li2O2 it approaches the native crystal values, which occurs faster with the occupation of the TM $d$-bands. This work can make a contribution in fundamental understanding and development of new, TMC-based, catalysts for alkali-metal batteries.

The progress of nanotechnology has led to the development of nanometer scale devices such as nano-antennas, molecular junctions, and others. The calculation of such devices' electromagnetic response becomes a challenge as it requires the integration of the classical form of Maxwell's equations with the quantum equations governing the electronic structure. To that end, Time-Dependent Density Functional Theory (TDDFT) reliably predicts the optical and electronic properties of molecules in the presence of external fields. However, most TDDFT formalisms only account for the electrostatic scalar potential, ignoring the presence of induced magnetic fields, and the retardation effects which follow. Disregarding the vector potential leads to an incorrect characterization of electronic structures exceeding certain size-to-wavelength ratio, the wavelength being that of the external electromagnetic field. In this work, the inclusion of induced vector potentials in the time-dependent Kohn-Sham equation is explored in both the Coulomb and Lorentz gauges. Although the Coulomb gauge is the commonly adapted gauge-fixing condition in TDDFT, the Lorentz gauge is shown to be just as effective in characterizing the response of electronic structures, bypassing the need for a projection scheme of the current density, via Helmholtz decomposition. In both gauges, fully incorporating the scalar and vector potentials can be computationally costly due to the retardation effects. Specifically, direct evaluation of the retarded integrals with their intrinsic dependence on past densities creates a computational bottleneck. To overcome this difficulty, highly efficient FFT-based integral methods utilizing multilevel schemes are employed. Carbon systems reaching the nanometric regime are explored in both gauges and various properties, appearing as a consequence of the newly incorporated induced fields, are demonstrated.

Hybrid functionals have proven to be of immense practical value in density functional theory calculations. While they are often thought to be a heuristic construct, it has been established that this is in fact not the case. Here, we present a rigorous and formally exact analysis of generalized Kohn-Sham (GKS) density functional theory of hybrid functionals, in which exact remainder exchange-correlation potentials combine with a fraction of Fock exchange to produce the correct ground state density. First, we extend formal GKS theory by proving a generalized adiabatic connection theorem. We then use this extension to derive two different definitions for a rigorous distinction between multiplicative exchange and correlation components - one new and one previously postulated. We examine their density-scaling behavior and discuss their similarities and differences. We then present a new algorithm for obtaining exact GKS potentials by inversion of accurate reference electron densities and employ this algorithm to obtain exact potentials for simple atoms and ions. We establish that an equivalent description of the many-electron problem is indeed obtained with any arbitrary global fraction of Fock exchange and we rationalize the Fock-fraction dependence of the computed remainder exchange-correlation potentials in terms of the new formal theory. Finally, we use the exact theoretical framework and numerical results to shed light on the exchange-correlation potential used in approximate hybrid functional calculations and to assess the consequences of different choices of fractional exchange.

A fast evaluation of retarded electromagnetic potentials is presented for quantum calculations on a uniform Cartesian grid. The induced potentials are incorporated into the quantum Hamiltonian of the time-dependent density functional theory (TDDFT) in real space. Both Lorentz and Coulomb gauge-fixed Hamiltonians are implemented using a real-time propagation scheme. The efficiency of the resulting formalism and implementation enables the evaluation of retardation effects on long carbon chains.

In metal–air batteries, carbon dioxide (CO2) and nitrogen (N2) are, apart from oxygen (O2), also present as dissolved species in the liquid electrolyte. These dissolved gases can strongly influence the battery performance, as they affect the discharge mechanism and the stability of the lithium metal anode. Therefore, their solubility and diffusivity are important parameters, that are rarely considered in the development of electrolytes for metal–air batteries. In this work, the diffusion coefficients (D) and Henry’s law solubility constants (H cp ) of O2, N2 and CO2 in common ether-based (diglyme (2G), triglyme (3G) and tetraglyme (4G)) and DMSO-based electrolytes are measured by means of gas uptake measurements. Additionally, the diffusion coefficients are calculated through molecular dynamics simulations. The results agree well with the experimental data. Furthermore, the influence of solvent parameters, such as surface tension and viscosity, on the solubility and the diffusivity as well as the impact of the addition of LiTFSI as conducting salt are investigated. The reported data will help to assess the impact of dissolved gases on the cell chemistry of nonaqueous lithium–air batteries, especially on the solid electrolyte interphase (SEI) at the lithium anode, and to predict diffusivity and gas solubility in other electrolytes.

Due to their high theoretical energy density, Li–O2 and Li–air batteries are considered as a promising alternative to Li-ion batteries, especially for mobile applications. However, dissolved gases in the liquid electrolyte, in particular O2, can be involved in detrimental side reactions at the lithium anode. Moreover, CO2 that can form from side reactions with the electrolyte or the cathode material, and N2 from the ambient air might be dissolved in the electrolyte. In order to evaluate the impact of these dissolved gases on the stability of the anode and to know their concentrations in possible side reactions, the solubility and the diffusion coefficient for each gas in the electrolyte are crucial parameters to know. In this work, we utilize gas uptake measurements to systematically determine the diffusion coefficients and Henry’s law solubility constants of O2, N2 and CO2 in different ether- and DMSO-based electrolytes and pure solvents. Additionally, we calculate the diffusion coefficient with molecular dynamics simulations and show good qualitative agreement between simulations and experimental results. We discuss the influence of solvent parameters, such as surface tension and viscosity, on the solubility and the diffusivity as well as the impact of different conducting salts. All investigated conducting salts reduce the diffusivity of the gases; however, we observe the solubility can both decrease or increase, depending on the solvent, the gas and the molecular structure of the salt. Therefore, we emphasize that both components, solvent and conducting salt, have to be considered for optimizing the gas transport properties of the electrolyte for Li–O2 and Li–air batteries.

We describe an efficient projection-based real-space implementation of the nonlocal single-determinant exchange operator. Through a matrix representation of the projected operator, we show that this scheme works equally well for both occupied and virtual states. Our scheme reaches a speedup of 2 orders of magnitude and has no significant loss of accuracy compared to an implementation of the full nonlocal single-determinant exchange operator. We find excellent agreement upon comparing Hartree-Fock eigenvalues, dipoles, and polarizabilities of selected molecules calculated using our method to values in the literature. To illustrate the efficiency of this scheme we perform calculations on systems with up to 240 carbon atoms.

In this work, we present an all-atom molecular dynamics (MD) study of triglyme and perfluorinated carbons (PFCs) using classical atomistic force fields. Triglyme is a typical solvent used in nonaqueous Li-air battery cells. PFCs were recently reported to increase oxygen availability in such cells. We show that O2 diffusion in two specific PFC molecules (C6F14 and C8F18) is significantly faster than in triglyme. Furthermore, by starting with two very different initial configurations for our MD simulation, we demonstrate that C8F18 and triglyme do not mix. The mutual solubility of these molecules is evaluated both theoretically and experimentally, and a qualitative agreement is found. Finally, we show that the solubility of O2 in C8F18 is considerably higher than in triglyme. The significance of these results to Li-air batteries is discussed.

We employ Molecular Dynamics (MD) and Time-Dependent Density Functional Theory (TDDFT) to explore the fluorescence of Hydrogen-bonded dimer and trimer structures of Cyclic FF (Phe- Phe) molecules. We show that in some of these configurations a photon can induce either an \textit{intra}-molecular proton transfer, or an \textit{inter}-molecular proton transfer that can occur in the excited S1 and S2 states. This proton transfer, taking place within the Hydrogen bond, leads to a significant red-shift that can explain the experimentally observed visible fluorescence in biological and bioinspired peptide nanostructures with a $\beta$-sheet biomolecular arrangement. Finally, we also show that such proton transfer is highly sensitive to the geometrical bonding of the dimers and trimers, and that it occurs only in specific configurations allowed by the formation of Hydrogen bonds.

Strong field ionization of benzene, fluorobenzene, benzonitrile and 1-chloro-2-fluorobenzene, is studied within the framework of real-space and real-time time-dependent density functional theory. Analysis of the ionization rates as function of the molecule orientation, reveal significant multielectron contribution from inner Kohn-Sham orbitals that depends on the electronic structure and on the orbital symmetries of the molecule, as well as on the polarization and intensity of the external laser field. Calculated photoelectron angular distributions at different molecule orientations and in response to laser fields with different degree of ellipticity, further demonstrate the spatial dependency of the orbital ionization rates.

Hybrid functionals combine Density Functional Theory (DFT) with a fraction of Fock exchange. Screened hybrid functionals use a screened Fock exchange instead. In recent years, those methods became more popular as they yield results that are in better agreement with experiment for various physical properties. However, the calculation of Fock exchange can be computationally intensive for large systems. In this paper, we demonstrate the use of an efficient real-space approach that is based on projection schemes and an FFT based Poisson solver, for large atomistic systems. We apply this approach for silicon quantum dots and graphene nanoribbons and show the size dependence of physical properties such as the band gap and ionization potential. Finally, we show how those calculations can be further accelerated through the use of Graphical Processing Units (GPUs).

A direct and local deep learning (DL) model for atomic forces is presented. We demonstrate the model performance in bulk aluminum, sodium, and silicon; and show that its errors are comparable to those found in state-of-the-art machine learning and DL models. We then analyze the model's performance as a function of the number of neighbors included and show that one can ascertain physical attributes of the system from the analysis of the deep learning model's behavior. Finally, we test the size scaling performance of the model, and the transferability between different temperatures, and show that our model performs well in both scaling to larger systems and high-to-low temperature predictability.

A reconstructive phase transition has been found and studied in ultrashort di- and tripeptide nanostructures, self-assembled from biomolecules of different compositions and origin such as aromatic, aliphatic, linear, and cyclic (linear FF-diphenylalanine, linear LL-dileucine, FFF-triphenylalanine, and cyclic FF-diphenylalanine). The native linear aromatic FF, FFF and aliphatic LL peptide nanoensembles of various shapes (nanotubes and nanospheres) have asymmetric elementary structure and demonstrate nonlinear optical and piezoelectric effects. At elevated temperature, 140-180 °C, these native supramolecular structures (except for native Cyc-FF nanofibers) undergo an irreversible thermally induced transformation via reassembling into a completely new thermodynamically stable phase having nanowire morphology similar to those of amyloid fibrils. This reconstruction process is followed by deep and similar modification at all levels: macroscopic (morphology), molecular, peptide secondary, and electronic structures. However, original Cyc-FF nanofibers preserve their native physical properties. The self-fabricated supramolecular fibrillar ensembles exhibit the FTIR and CD signatures of new antiparallel β-sheet secondary folding with intermolecular hydrogen bonds and centrosymmetric structure. In this phase, the β-sheet nanofibers, irrespective of their native biomolecular origin, do not reveal nonlinear optical and piezoelectric effects, but do exhibit similar profound modification of optoelectronic properties followed by the appearance of visible (blue and green) photoluminescence (PL), which is not observed in the original peptides and their native nanostructures. The observed visible PL effect, ascribed to hydrogen bonds of thermally induced β-sheet secondary structures, has the same physical origin as that of the fluorescence found recently in amyloid fibrils and can be considered to be an optical signature of β-sheet structures in both biological and bioinspired materials. Such PL centers represent a new class of self-assembled dyes and can be used as intrinsic optical labels in biomedical microscopy as well as for a new generation of novel optoelectronic nanomaterials for emerging nanophotonic applications, such as biolasers, biocompatible markers, and integrated optics.

In this work we show the implementation of a linear scaling algorithm for the calculation of the Poisson integral. We use domain decomposition and non-uniform auxiliary grids (NGs) to calculate the electrostatic interaction. We demonstrate the approach within the PARSEC density functional theory code and perform calculations of long 1D carbon chains and other long molecules. Finally, we discuss possible applications to additional problems and geometries.

The calculation of Fock-exchange interaction is an important task in the computation of molecule and solid properties. In this work we describe how we implement the Fock exchange in the real-space formalism using the KLI approximation for the OEP equation for 3D periodic systems. The implementation is demonstrated within the PARSEC real-space pseudopotential code that uses a discrete uniform grid and norm conserving pseudopotentials for the ionic potentials.

We analyze with Density Functional Theory (DFT) calculations the adsorption of fluorine atoms on graphene. We show that the adsorbed atoms clustering is favored by energy considerations and show that there are long range patterns for the second atoms adsorption energy at different sites. Finally, we discuss the effect of the different adsorption patterns on the Fermi level shift and band structure distortion.

Thermally induced phase transformation in bioorganic nanotubes, which self-assembled from two ultrashort dipeptides of different origin, aromatic diphenylalanine (FF) and aliphatic dileucine (LL), is studied. In both FF and LL nanotubes, irreversible phase transformation found at 120-180 °C is governed by linear-to-cyclic dipeptide molecular modification followed by formation of extended β-sheet structure. As a result of this process, native open-end FF and LL nanotubes are transformed into ultrathin nanofibrils. Found deep reconstructions at all levels from macroscopic (morphology) and structural space symmetry to molecular give rise to new optical properties in both aromatic FF and aliphatic LL nanofibrils and generation of blue photoluminescence (PL) emission. It is shown that observed blue PL peak is similar in these supramolecular nanofibrillar structures and is excited by the network of non-covalent hydrogen bonds that link newly thermally induced neighboring cyclic dipeptide strands to final extended β-sheet structure of amyloid-like nanofibrils. The observed blue PL peak in short dipeptide nanofibrils is similar to the blue PL peak that was recently found in amyloid fibrils and can be considered as the optical signature of β-sheet structures. Nanotubular structures were characterized by environmental scanning electron microscope, ToF-secondary ion mass spectroscopy, CD and fluorescence spectroscopy.

We use an efficient projection scheme for the Fock operator to analyze the size dependence of silicon quantum dots (QDs) electronic properties. We compare the behavior of hybrid, screened hybrid and local density functionals as a function of the dot size up to $\sim$800 silicon atoms and volume of up to $\sim$20nm$^3$. This allows comparing the calculations of hybrid and screened hybrid functionals to experimental results over a wide range of QD sizes. We demonstrate the size dependent behavior of the band gap, density of states, ionization potential and HOMO level shift after ionization. Those results are compared to experiment and to other theoretical approaches, such as tight-binding, empirical pseudopotentials, TDDFT and GW.

© 2016 Author(s). Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

We examine the current response of molecularly controlled semiconductor devices to the presence of weakly interacting analytes. We evaluate the response of two types of devices, a silicon oxide coated silicon device and a GaAs/AlGaAs device, both coated with aliphatic chains and exposed to the same set of analytes. By comparing the device electrical response with contact potential difference and surface photovoltage measurements, we show that there are two mechanisms that may affect the underlying substrate, namely, formation of layers with a net dipolar moment and molecular interaction with surface states. We find that whereas the Si device response is mostly correlated to the analyte dipole, the GaAs device response is mostly correlated to interactions with surface states. Existence of a silicon oxide layer, whether native on the Si or deliberately grown on the GaAs, eliminates analyte interaction with the surface states.

A real-space high order finite difference method is used to analyze the effect of spherical domain size on the Hartree-Fock (and density functional theory) virtual eigenstates. We show the domain size dependence of both positive and negative virtual eigenvalues of the Hartree-Fock equations for small molecules. We demonstrate that positive states behave like a particle in spherical well and show how they approach zero. For the negative eigenstates, we show that large domains are needed to get the correct eigenvalues. We compare our results to those of Gaussian basis sets and draw some conclusions for real-space, basis-sets, and plane-waves calculations. (C) 2016 AIP Publishing LLC.

Molecules in (or as) electronic devices are attractive because the variety and flexibility inherent in organic chemistry can be harnessed towards a systematic design of electrical properties. Specifically, monolayers of polar molecules introduce a net dipole, which controls surface and interface barriers and enables chemical sensing via dipole modification. Due to the long range of electrostatic phenomena, polar monolayer properties are determined not only by the type of molecules and/or bonding configuration to the substrate, but also by size, (dis-)order, and adsorption patterns within the monolayer. Thus, a comprehensive understanding of polar monolayer characteristics and their influence on electronic devices requires an approach that transcends typical chemical designs, i.e., one that incorporates long-range effects, in addition to short-range effects due to local chemistry. We review and explain the main uses of polar organic monolayers in shaping electronic device properties, with an emphasis on long-range cooperative effects and on the differences between electrical properties of uniform and non-uniform monolayers.

Whole cell biosensors, which have been genetically engineered to respond to environmental stress, trigger a sequence of processes, which leads to generation of electrical current. This work presents a mathematical model describing the kinetic properties of the bacterial enzymatic reactions in response to toxic chemicals, and the resulting electro-active molecule diffusion to the electrode in a miniaturized electrochemical cell. The model characterizes the generated electrical current as a function of bacteria and toxicant concentrations, electrochemical cell dimensions and electrode dimensions. A model was framed for a 100 nL spherical electrochemical cell. Its performance was simulated and compared to experimental data. This simulation results agreed well with the measured data and therefore it should be useful in predicting current variations in similar systems with different geometries, materials and biological components.

Concept of edge polarizability produced by support of the edge quantum states is demonstrated by the example of graphene nanoribbon with zigzag edge configuration. This concept allows to formulate physically correct edge conditions for electromagnetic field in nanostructures instead of ordinary Meixner conditions in classical electrodynamics.

The Automatic-Flow ( AFLOW ) standard for the high-throughput construction of materials science electronic structure databases is described. Electronic structure calculations of solid state materials depend on a large number of parameters which must be understood by researchers, and must be reported by originators to ensure reproducibility and enable collaborative database expansion. We therefore describe standard parameter values for k-point grid density, basis set plane wave kinetic energy cut-off, exchange-correlation functionals, pseudopotentials, DFT+U parameters, and convergence criteria used in AFLOW calculations., 19 pages, 5 tables

We discuss methodological aspects of first principles calculations of surface dipoles and potentials in general, and surface-adsorbed self-assembled monolayers in particular, using density functional theory with a slab/super-cell approach. We show that calculations involving asymmetric slabs may yield highly erroneous results for the surface dipole and demonstrated the efficacy of a simple dipole correction scheme. We explain the importance of the electrostatic dipole distribution, show how to compute it, and establish conditions for the equivalence of calculations for the dipole distribution and the electrostatic potential distribution.

The solution of the Poisson equation is an essential stage in the calculation of quantum properties of materials as it appears both in the electrostatic Hartree term and in the Fock exchange operator. We discuss here an integral method for the calculation of Poisson potential and demonstrate its integration with a Density Functional Theory (DFT) code. We show some results on elongated carbon chains.

The calculation of Fock-Exchange integral is becoming an important computational challenge in solving the quantum properties of systems with many electrons. In this work we show how techniques that are used in electromagnetic simulations for the similar Poisson equation can help in accelerating the calculation of such exchange integrals. The approach we present can be especially efficient for quasi-planar systems such as Graphene nano-ribbons (GNRs) or elongated systems such as carbon nano-tubes (CNTS) and the 1D Carbyne.

Thermally induced phase transformation in bioorganic nanotubes, which self-assembled from two ultrashort dipeptides of different origin, aromatic diphenylalanine (FF) and aliphatic dileucine (LL), is studied. In both FF and LL nanotubes, irreversible phase transformation found at 120-180 °C is governed by linear-to-cyclic dipeptide molecular modification followed by formation of extended β-sheet structure. As a result of this process, native open-end FF and LL nanotubes are transformed into ultrathin nanofibrils. Found deep reconstructions at all levels from macroscopic (morphology) and structural space symmetry to molecular give rise to new optical properties in both aromatic FF and aliphatic LL nanofibrils and generation of blue photoluminescence (PL) emission. It is shown that observed blue PL peak is similar in these supramolecular nanofibrillar structures and is excited by the network of non-covalent hydrogen bonds that link newly thermally induced neighboring cyclic dipeptide strands to final extended β-sheet structure of amyloid-like nanofibrils. The observed blue PL peak in short dipeptide nanofibrils is similar to the blue PL peak that was recently found in amyloid fibrils and can be considered as the optical signature of β-sheet structures. Nanotubular structures were characterized by environmental scanning electron microscope, ToF-secondary ion mass spectroscopy, CD and fluorescence spectroscopy.

Chemical modification of graphene is a common approach to control its electronic properties and hence fabricate electronic devices with new or improved functionalities. In this work we analyze, with density functional based calculations, the effect of chemical adsorption of fluorine atoms at different coverage levels on the electronic structure of graphene. We suggest a simple and general model for the shift of the Fermi level with coverage level and show the trends of the band gap and the Fermi level shift with coverage. We then show that the same model can be applied to explain the Fermi level shift in a different system of nitrogen substitution in graphene. Finally, we analyze the resulting charge transfer patterns and show that they are consistent with the model for the Fermi level shift.