Ab initio computational methods for electronic transport in nanoscaled systems are an invaluable tool for the design of quantum devices. We have developed a flexible and efficient algorithm for evaluating I-V characteristics of atomic junctions, which integrates the nonequilibrium Green's function method with density functional theory. This is currently implemented in the package SMEAGOL. The heart of SMEAGOL is our scheme for constructing the surface Green's functions describing the current-voltage probes. It consists of a direct summation of both open and closed scattering channels together with a regularization procedure of the Hamiltonian and provides great improvements over standard recursive methods. In particular it allows us to tackle material systems with complicated electronic structures, such as magnetic transition metals. Here we present a detailed description of SMEAGOL together with an extensive range of applications relevant for the two burgeoning fields of spin and molecular electronics.

We have developed an efficient simulation tool 'GOLLUM' for the computation of electrical, spin and thermal transport characteristics of complex nanostructures. The new multi-scale, multi-terminal tool addresses a number of new challenges and functionalities that have emerged in nanoscale-scale transport over the past few years. To illustrate the flexibility and functionality of GOL-LUM, we present a range of demonstrator calculations encompassing charge, spin and thermal transport, corrections to density functional theory such as local density approximation +U (LDA+U) and spectral adjustments, transport in the presence of non-collinear magnetism, the quantum Hall effect, Kondo and Coulomb blockade effects, finite-voltage transport, multi-terminal transport, quantum pumps, superconducting nanostructures, environmental effects, and pulling curves and conductance histograms for mechanically-controlled breakjunction experiments.New J. Phys. 16 (2014) 093029 J Ferrer et al that non-equilibrium transport codes are quite difficult to handle, in part because of their complex input data structures, which can create a steep learning curve, and also because they carry very heavy computational demands. As a consequence, we have devised the new code GOLLUM to be more user friendly, with simple and easy to understand input and output structures, and with no accuracy parameters to tune. We present now a short summary of the features and functionalities of the two programs to better appreciate their differences. SMEAGOL is a non-equilibrium Green's function (NEGF) program that computes the charge and spin transport properties of two-terminal junctions subject to a finite voltage bias. SMEAGOL cannot read a user-defined tight-binding Hamiltonian. Instead, it reads the meanfield Hamiltonian from the program SIESTA [27] and is tightly bound to the old versions of it. SMEAGOL can read from SIESTA Hamiltonians carrying non-collinear spin arrangements as well as the spin-orbit interaction. SIESTA and SMEAGOL have indeed been used successfully to simulate the magnetic anisotropies of atomic clusters [28][29][30] as well as the spin transport functionalities of several atomic chains and molecular junctions subjected to strong spin-orbit interaction [31,32]. However, SMEAGOL does not profit from other recent density functionals. Examples are the van der Waals family of functionals or those based on the local density approximation + U (LDA+U) approach.GOLLUM is a program that computes the charge, spin and electronic contribution to the thermal transport properties of multi-terminal junctions. In contrast to NEGF codes, GOLLUM is based on equilibrium transport theory, which means that it has a simpler structure, is faster, and consumes less memory. The program has been designed for user-friendliness and takes a considerable leap towards the realization of ab initio multi-scale simulations of conventional and more sophisticated transport functionalities.The simpler interface of GOLLUM allows it to read model tight-binding Hamiltonians. Fur...

Numerous clinical trials using folic acid for prevention of cardiovascular disease, stroke, cognitive decline, and neural tube defects have been completed or are underway. Yet, all functions of folate are performed by tetrahydrofolate and its one-carbon derivatives. Folic acid is a synthetic oxidized form not significantly found in fresh natural foods; to be used it must be converted to tetrahydrofolate by dihydrofolate reductase (DHFR). Increasing evidence suggests that this process may be slow in humans. Here we show, using a sensitive assay we developed, that the reduction of folic acid by DHFR per gram of human liver (n ‫؍‬ 6) obtained from organ donors or directly from surgery is, on average, less than 2% of that in rat liver at physiological pH. Moreover, in contrast to rats, there was almost a 5-fold variation of DHFR activity among the human samples. This limited ability to activate the synthetic vitamer raises issues about clinical trials using high levels of folic acid. The extremely low rate of conversion of folic acid suggests that the benefit of its use in high doses will be limited by saturation of DHFR, especially in individuals possessing lower than average activity. These results are also consistent with the reports of unmetabolized folic acid in plasma and urine.folate ͉ provitamin utilization ͉ unmetabolized folic acid ͉ vitamin supplements ͉ nutrition

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The high thermal conductivity of graphene and few-layer graphene undergoes severe degradations through contact with the substrate. Here we show experimentally that the thermal management of a micro heater is substantially improved by introducing alternative heat-escaping channels into a graphene-based film bonded to functionalized graphene oxide through amino-silane molecules. Using a resistance temperature probe for in situ monitoring we demonstrate that the hotspot temperature was lowered by ∼28 °C for a chip operating at 1,300 W cm−2. Thermal resistance probed by pulsed photothermal reflectance measurements demonstrated an improved thermal coupling due to functionalization on the graphene–graphene oxide interface. Three functionalization molecules manifest distinct interfacial thermal transport behaviour, corroborating our atomistic calculations in unveiling the role of molecular chain length and functional groups. Molecular dynamics simulations reveal that the functionalization constrains the cross-plane phonon scattering, which in turn enhances in-plane heat conduction of the bonded graphene film by recovering the long flexural phonon lifetime.

Using first principles simulations we perform a detailed study of the structural, electronic and transport properties of monoatomic platinum chains, sandwiched between platinum electrodes. First, we demonstrate that the most stable atomic configuration corresponds to a zigzag arrangement that gradually straightens as the chains are stretched. Secondly, we find that the averaged conductance shows slight parity oscillations with the number n of atoms in the chain. Additionally, the conductance of chains of fixed n oscillates as the end atoms are pulled apart, due to the gradual closing and opening of conductance channels as the chain straightens. 73.40.Jn,71.15.Ap The existence of single atom chains was demonstrated some time ago using the scanning tunneling microscope (STM) and mechanically-controllable break junctions (MCBJ) [1] where a quantized conductance close to G 0 = 2 e 2 /h for gold was measured, in agreement with previous theoretical predictions [2]. Since then, a number of experiments [3,4] and theoretical calculations [5] have proved that the 5d elements Au, Ir and Pt can be used to produce monoatomic chains. For gold chains [1], the average distance between conductance peaks was found to be 2.5Å with the conductance G of the last plateau being very close to G 0 . The ensemble-averaged conductance also shows small oscillations around G 0 as the length of the chain increases [4].For platinum, the average distance between the peaks in the length-histograms is about 1.9-2.3Å [3,4]. In contrast with gold, the conductance is no longer an integer multiple of G 0 , but instead decreases from 1.6 G 0 to 1.2 G 0 as the length of the chain increases [4]. In addition, significant conductance oscillations are superimposed on top of this decreasing trend, which have been attributed to a parity effect. [4,6]. The rich behavior of platinum compared with gold arises from the larger number of conduction channels at the Fermi energy (E F ) due to the presence of d bands [7].To understand the structural, electronic and transport properties of platinum chains, we have performed a complete series of first principles simulations of platinum chains attached to platinum fcc leads. We have employed our newly developed code SMEAGOL [8,9], which calculates the density matrix and the transmission coefficients of a two probe device using the non-equilibrium Green's Function formalism (NEGF) [10]. The scattering potential is calculated self-consistently using the SIESTA implementation of density functional theory [11,12,13]. We have approximated the exchange and correlation potential by the Local Density Approximation (LDA), since we have found that provides a slightly more accurate description of the structural and conducting properties of bulk and infinite platinum chains than GGA [14]. We have not included in our calculations spin polarization which is only relevant for very stretched chains [15]. Our main result is that the most stable arrangement of platinum chains corresponds

The cofactor product of the aromatic amino acid hydroxylases, 4a-hydroxy-6(R)-tetrahydrobiopterin, requires dehydration before tetrahydrobiopterin can be regenerated by dihydropteridine reductase. Carbinolamine dehydration occurs nonenzymatically, but the reaction is also catalyzed by 4a-hydroxytetrahydropterin dehydratase. This enzyme has the identical amino acid sequence to DCoH, the dimerization cofactor of the transcription regulator, HNF-1 alpha. The catalytic activity of rat liver dehydratase was characterized using a new assay employing chemically synthesized 4a-hydroxytetrahydropterins. The enzyme shows little sensitivity to the structure or configuration of the 6-substituent of its substrate, with Km's for 6(S)-methyl, 6(R)-methyl, 6(S)-propyl, and 6(R)-L-erythro-dihydroxypropyl all between 1.5 and 6 microM. Turnover numbers at 37 degrees C are 50-90 s-1 at pH 7.4 and 2.5-3-fold lower at pH 8.4. Both 4a(R)- and 4a(S)-hydroxytetrahydropterins are good substrates. The quinoid dihydropterin products are strong inhibitors of the dehydratase with KI's about one half of their respective Km's, but no inhibition was observed with 7,8-dihydropterins or tetrahydropterins. The enzyme contains no metals and no phosphorus. Reaction mechanisms which involve either acid and/or base catalysis are discussed. 4a-Hydroxy-6(R)-tetrahydrobiopterin was determined not to be a product inhibitor of phenylalanine hydroxylase. It is concluded that the dehydratase (which was found to be 6 microM in rat liver) is essential in vivo to prevent rearrangement of 4a-hydroxy-6(R)-tetrahydrobiopterin and to maintain the supply of tetrahydrobiopterin cofactor for the hydroxylases under conditions where the nonenzymatic rate would be inadequate.

Recent experiments by Venkatamaran et al. [Nature (London) 442, 904 (2006)] on a series of molecular wires with varying chemical compositions, revealed a linear dependence of the conductance on cos 2 θ, where θ is the angle of twist between neighboring aromatic rings. To investigate whether or not this dependence has a more general applicability, we present a first principles theoretical study of the transport properties of this family of molecules as a function of the chemical composition, conformation and the contact atom and geometry. If the Fermi energy EF lies within the HOMO-LUMO gap, then we reproduce the above experimental results. More generally, however, if EF is located within either the LUMO or HOMO states, the presence of resonances destroys the linear dependence of the conductance on cos 2 θ and gives rise to non-monotonic behaviour associated with the level structure of the different molecules. Our results suggest that the above experiments provide a novel method for extracting spectroscopic information about molecules contacted to electrodes.