Brief review related to the foundations of time-dependent density functional theory

The electron density n(\rb,t), which is the central tool of time-dependent density functional theory, is presently considered to be derivable from a one-body time-dependent potential V(\rb,t), via one-electron wave functions satisfying a time- dependent Schr\"{o}dinger equation. This is here related via a generalized equation of motion to a Dirac density matrix now involving $t$. Linear response theory is then surveyed, with a special emphasis on the question of causality with respect to the density dependence of the potential. Extraction of V(\rb,t) for solvable models is also proposed

Higher harmonics and ac transport from time dependent density functional theory

We report on dynamical quantum transport simulations for realistic molecular devices based on an approximate formulation of time-dependent Density Functional Theory with open boundary conditions. The method allows for the computation of various properties of junctions that are driven by alternating bias voltages. Besides the ac conductance for hexene connected to gold leads via thiol anchoring groups, we also investigate higher harmonics in the current for a benzenedithiol device. Comparison to a classical quasi-static model reveals that quantum effects may become important already for small ac bias and that the full dynamical simulations exhibit a much lower number of higher harmonics. Current rectification is also briefly discussed.Comment: submitted to J. Comp. Elec. (special issue

Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data

ELUCIDATING THE BIOCHEMICAL WIZARDRY OF TRITERPENE METABOLISM IN \u3ci\u3eBOTROYCOCCUS BRAUNII\u3c/i\u3e

B. braunii is a green alga that has attracted attention as a potential renewable fuel source due to its high oil content and the archeological record of its unique contribution to oil and coal shales. Three extant chemotypes of B. braunii have been described, namely race A, race B, and race L, which accumulate alkadienes and alkatrienes, botryococcene and squalene and their methylated derivatives, and lycopadiene, respectively. The methylated triterpenes, particularly botryococcenes, produced by race B can be efficiently converted to high quality combustible fuels and other petrochemicals; however, botryococcene biosynthesis has remained enigmatic. It has been suggested that botryococcene biosynthesis could resemble that of squalene, arising from an initial condensation of two molecules of farnesyl diphosphate (FPP) to form pre-squalene diphosphate (PSPP), which then undergoes a reductive rearrangement to form squalene, or in an alternative reductive rearrangement, botryococcene. Based on the proposed similarities, we predicted that a botryococcene synthase would resemble squalene synthase and hence, isolated squalene synthase-like genes from B. braunii race B. While B. braunii does harbor at least one typical squalene synthase, none of the other three squalene synthase-like (SSL) genes encode for botryococcene biosynthesis directly. SSL-1 catalyzes the biosynthesis of PSPP and SSL-2 the biosynthesis of bisfarnesyl ether and to a lesser extent squalene, while SSL-3 does not appear able to directly utilize FPP as a substrate. However, when SSL-1 is combined with either SSL-2 or SSL-3, in vivo and in vitro, robust squalene or botryococcene biosynthesis was observed, respectively. These findings were unexpected because squalene synthase, an ancient and likely progenitor to the other Botryococcus triterpene synthases, catalyzes a two-step reaction within a single enzyme unit without intermediate release, yet in B. braunii, these activities appear to have separated and evolved inter-dependently for specialized triterpene production. Expression of various configurations of the SSL genes in TN-7 yeast demonstrates that botryococcene can be efficiently produced in a heterologous host. Additionally, three triterpene methyltransferase (TMTs) were isolated which efficiently catalyze the transfer of a methyl group from S-adenosyl methionine (SAM) to either squalene (TMT-1 and TMT-2) or botryococcene (TMT-3) in vivo and in vitro. Co-expression of the various TMT genes with either squalene synthase or botryococcene synthase in TN-7 yeast resulted in the accumulation of C31 and C32 methyl derivatives of squalene or botryococcene, demonstrating their potential for heterologous production. The methylation sites were determined by NMR spectroscopy to be identical to C31 and C32 methyl-derivatives of squalene or botryococcene observed in B. braunii race B. Expression studies of various heterologous squalene synthase genes in S. cerevisiae corroborated an earlier but surprising observation reported in the literature. While the squalene synthase gene of S. cerevisiae was able to complement an erg9 (squalene synthase) knockout in yeast, squalene synthase genes from plants and animals were not. Chemical profiles revealed that squalene accumulated to significant levels in yeast expressing the squalene synthase of plant, animal, or S. cerevisiae. This suggested that it was not the ability of these heterologous synthase enzymes to produce squalene, but their inability to feed squalene into the native sterol biosynthetic pathway that prevented them from restoring normal ergosterol biosynthesis in S. cerevisiae. By examining the ability of chimera squalene synthase enzymes to complement the erg9 mutation, a discrete sequence of amino acids near the C-terminus of the enzyme was identified which is necessary and sufficient for allowing any squalene synthase to restore normal sterol metabolism

Effect of line defects on the electrical transport properties of monolayer MoS2_{2} sheet

We present a computational study on the impact of line defects on the electronic properties of monolayer MoS2. Four different kinds of line defects with Mo and S as the bridging atoms, consistent with recent theoretical and experimental observations are considered herein. We employ the density functional tight-binding (DFTB) method with a Slater-Koster type DFTB-CP2K basis set for evaluating the material properties of perfect and the various defective MoS2 sheets. The transmission spectra is computed with a DFTB-Non-Equilibrium Greens Function (NEGF) formalism. We also perform a detailed analysis of the carrier transmission pathways under a small bias and investigate the phase shifts in the transmission eigenstates of the defective MoS2 sheets. Our simulations show a 2-4 folds decrease in carrier conductance of MoS2 sheets in the presence of line defects as compared to that for the perfect sheet

Time-dependent versus static quantum transport simulations beyond linear response

To explore whether the density-functional theory non-equilibrium Green's function formalism (DFT-NEGF) provides a rigorous framework for quantum transport, we carried out time-dependent density functional theory (TDDFT) calculations of the transient current through two realistic molecular devices, a carbon chain and a benzenediol molecule inbetween two aluminum electrodes. The TDDFT simulations for the steady state current exactly reproduce the results of fully self-consistent DFT-NEGF calculations even beyond linear response. In contrast, sizable differences are found with respect to an equilibrium, non-self-consistent treatment which are related here to differences in the Kohn-Sham and fully interacting susceptibility of the device region. Moreover, earlier analytical conjectures on the equivalence of static and time-dependent approaches in the low bias regime are confirmed with high numerical precision.Comment: 4 pages, 4 figure

Towards a simplified description of thermoelectric materials: Accuracy of approximate density functional theory for phonon dispersions

We calculate the phonon-dispersion relations of several two-dimensional materials and diamond using the density-functional based tight-binding approach (DFTB). Our goal is to verify if this numerically efficient method provides sufficiently accurate phonon frequencies and group velocities to compute reliable thermoelectric properties. To this end, the results are compared to available DFT results and experimental data. To quantify the accuracy for a given band, a descriptor is introduced that summarizes contributions to the lattice conductivity that are available already in the harmonic approximation. We find that the DFTB predictions depend strongly on the employed repulsive pair-potentials, which are an important prerequisite of this method. For carbon-based materials, accurate pair-potentials are identified and lead to errors of the descriptor that are of the same order as differences between different local and semi-local DFT approaches

Optimal Detection for Diffusion-Based Molecular Timing Channels

This work studies optimal detection for communication over diffusion-based molecular timing (DBMT) channels. The transmitter simultaneously releases multiple information particles, where the information is encoded in the time of release. The receiver decodes the transmitted information based on the random time of arrival of the information particles, which is modeled as an additive noise channel. For a DBMT channel without flow, this noise follows the L\'evy distribution. Under this channel model, the maximum-likelihood (ML) detector is derived and shown to have high computational complexity. It is also shown that under ML detection, releasing multiple particles improves performance, while for any additive channel with $\alpha$-stable noise where $\alpha<1$ (such as the DBMT channel), under linear processing at the receiver, releasing multiple particles degrades performance relative to releasing a single particle. Hence, a new low-complexity detector, which is based on the first arrival (FA) among all the transmitted particles, is proposed. It is shown that for a small number of released particles, the performance of the FA detector is very close to that of the ML detector. On the other hand, error exponent analysis shows that the performance of the two detectors differ when the number of released particles is large.Comment: 16 pages, 9 figures. Submitted for publicatio

Liquid-solid slip on charged walls: dramatic impact of charge distribution

Nanofluidic systems show great promises for applications in energy conversion, where their performance can be enhanced by nanoscale liquid-solid slip. However, efficiency is also controlled by surface charge, which is known to reduce slip. Combining molecular dynamics simulations and analytical developments, we show the dramatic impact of surface charge distribution on the slip-charge coupling. Homogeneously charged graphene exhibits a very favorable slip-charge relation (rationalized with a new theoretical model correcting some weaknesses of the existing ones), leading to giant electrokinetic energy conversion. In contrast, slip is strongly affected on heterogeneously charged surfaces, due to the viscous drag induced by counter-ions trapped on the surface. In that case slip should depend on the detailed physical chemistry of the interface controlling the fraction of bound ions. Our numerical results and theoretical models provide new fundamental insight on the molecular mechanisms of liquid-solid slip, and practical guidelines for searching new functional interfaces with optimal energy conversion properties, e.g. for blue energy or waste heat harvesting.Comment: Main text: 7 pages, 3 figures; supplemental material: 22 pages, 5 figures; to be published in Physical Review Letter