Molecular recognition in olfaction

The mechanism by which the chemical identity of odourants is established by olfactory receptors is a matter of intense debate. Here we present an overview of recent ideas and data with a view to summarising what is known, and what has yet to be determined. We outline the competing theories, and summarise experimental results employing isotopes obtained for mammals, insects, and individual receptors that enable us to judge the relative correctness of the theories

Efficient electron open boundaries for simulating electrochemical cells

Nonequilibrium electrochemistry raises new challenges for atomistic simulation: we need to perform molecular dynamics for the nuclear degrees of freedom with an explicit description of the electrons, which in turn must be free to enter and leave the computational cell. Here we present a limiting form for electron open boundaries that we expect to apply when the magnitude of the electric current is determined by the drift and diffusion of ions in a solution and which is sufficiently computationally efficient to be used with molecular dynamics. We present tight-binding simulations of a parallel-plate capacitor with nothing, a dimer, or an atomic wire situated in the space between the plates. These simulations demonstrate that this scheme can be used to perform molecular dynamics simulations when there is an applied bias between two metal plates with, at most, weak electronic coupling between them. This simple system captures some of the essential features of an electrochemical cell, suggesting this approach might be suitable for simulations of electrochemical cells out of equilibrium

Efficient simulations with electronic open boundaries

We present a reformulation of the Hairy Probe method for introducing electronic open boundaries that is appropriate for steady state calculations involving non-orthogonal atomic basis sets. As a check on the correctness of the method we investigate a perfect atomic wire of Cu atoms, and a perfect non-orthogonal chain of H atoms. For both atom chains we find that the conductance has a value of exactly one quantum unit, and that this is rather insensitive to the strength of coupling of the probes to the system, provided values of the coupling are of the same order as the mean inter-level spacing of the system without probes. For the Cu atom chain we find in addition that away from the regions with probes attached, the potential in the wire is uniform, while within them it follows a predicted exponential variation with position. We then apply the method to an initial investigation of the suitability of graphene as a contact material for molecular electronics. We perform calculations on a carbon nanoribbon to determine the correct coupling strength of the probes to the graphene, and obtain a conductance of about two quantum units corresponding to two bands crossing the Fermi surface. We then compute the current through a benzene molecule attached to two graphene contacts and find only a very weak current because of the disruption of the π-conjugation by the covalent bond between the benzene and the graphene. In all cases we find that very strong or weak probe couplings suppress the current

Which wets TiB2 inoculant particles: Al or Al3Ti?

TiB2 particles are proven effective nucleants of commercial purity aluminium, resulting in smaller grains and hence greater desired mechanical properties; however, there is uncertainty as to the mechanism by which it operates. Here we clarify what happens in the initial stages by computing the total Gibbs energy change associated with four possible nucleation mechanisms, each characterised by the termination of the TiB2(0001) substrate (Ti or B) and the solid that forms on it (Al or Al3Ti). The appropriate solid//solid interfacial energies are derived from Density Functional Theory (DFT) calculations, while the bulk energies are derived from thermodynamic data, supplemented with strain energies calculated from DFT. Solid//liquid interfacial energies are estimated using simple models with parameters based on the literature and DFT calculations. The results suggest that the Ti termination of TiB2 is more stable than the B termination in the melt, and that the direct formation of Al off a Ti-terminated TiB2 substrate is the most favourable mechanism for the nucleation of Al rather than the previously proposed formation of a Al3Ti interlayer. On the B termination of TiB2, Al formation is more stable for thick solid layers, but this is much more uncertain for thin solid layers where it is possible that Al3Ti formation is more stable

Classical and quantum calculations of the temperature dependence of the free energy of argon

The free energy is central to statistical mechanics and thermodynamics, and its accurate calculation via. computational modelling is important for a large number of applications, especially when its experimental value is hard to obtain. Several established and general methods for calculating the Helmholtz free energy across different length scales, including continuum, atomistic and quantum mechanical, are compared and analyzed. A computational approach is then proposed to calculate the temperature dependences of internal energy and absolute Helmholtz free energy for solid and liquid phases with the coupling of thermodynamic integration (TI) and harmonic approximation calculations from both classical molecular dynamics (MD) and density functional theory (DFT). We use the Lennard-Jones system as an example (i.e. argon) for the demonstration of the approach. It is observed that the free energy transits smoothly from being describable by the harmonic approximation to including anharmonic effects at a transition temperature around 0.56 Tm; below this temperature, the quantum behavior of atoms is important. At higher temperatures (T > 0.56 Tm), the TI and harmonic approximation results for the Helmholtz free energy functions become increasingly divergent with the increase of temperature. This work demonstrates that a multiscale approach employing TI, MD, and DFT can provide accurate calculations of the temperature dependence of absolute Helmholtz free energy for both solid and liquid phases

Implicit and explicit host effects on excitons in pentacene derivatives

An ab initio study of the effects of implicit and explicit hosts on the excited state properties of pentacene and its nitrogen-based derivatives has been performed using ground state density func- tional theory (DFT), time-dependent DFT and ∆SCF. We observe a significant solvatochromic redshift in the excitation energy of the lowest singlet state (S 1 ) of pentacene from inclusion in a p -terphenyl host compared to vacuum; for an explicit host consisting of six nearest neighbour p -terphenyls, we obtain a redshift of 65 meV while a conductor-like polarisable continuum model (CPCM) yields a 78 meV redshift. Comparison is made between the excitonic properties of pen- tacene and four of its nitrogen-based analogues, 1,8-, 2,9-, 5,12-, and 6,13-diazapentacene with the latter found to be the most distinct due to local distortions in the ground state electronic struc- ture. We observe that a CPCM is insufficient to fully understand the impact of the host due to the presence of a mild charge-transfer (CT) coupling between the chromophore and neighbouring p -terphenyls, a phenomenon which can only be captured using an explicit model. The strength of this CT interaction increases as the nitrogens are brought closer to the central acene ring of pentacene

Systematic development of ab initio tight-binding models for hexagonal metals

A systematic method for building an extensible tight-binding model from ab initio calculations has been developed and tested on two hexagonal metals: Zr and Mg. The errors introduced at each level of approximation are discussed and quantified. For bulk materials, using a limited basis set of s p d orbitals is shown to be sufficient to reproduce with high accuracy bulk energy versus volume curves for fcc, bcc, and hcp lattice structures, as well as the electronic density of states. However, the two-center approximation introduces errors of several tenths of eV in the pair potential, crystal-field terms, and hopping integrals. Environmentally dependent corrections to the former two have been implemented, significantly improving the accuracy. Two-center hopping integrals were corrected by taking many-center hopping integrals for a set of structures of interest, rotating them into the bond reference frame, and then fitting a smooth function through these values. Finally, a pair potential was fitted to correct remaining errors. However, this procedure is not sufficient to ensure transferability of the model, especially when point defects are introduced. In particular, it is shown to be problematic when interstitial elements are added to the model, as demonstrated in the case of octahedral self-interstitial atoms

The bonding of H in Zr under strain

Accurate computer simulation is important for understanding the role of irradiation-induced defects in zirconium alloys found in nuclear reactors. Of particular interest is the distribution and trapping of hydrogen, and the formation of zirconium hydride. These simulations require an accurate representation of Zr-H bonding in order to predict the behaviour of H around atomic-scale defects, dislocation lines, and dislocation loops. Here we explore the bonding of H in Zr under strain, how well it is represented by state-of-the-art Embedded Atom Method (EAM) potentials, and what physics is needed for an accurate representation in a Linear Combination of Atomic Orbitals (LCAO) Density Functional Theory (DFT) framework. For H in dilute solution under hydrostatic strain in the range -10% to +10%, solution energies and Zr-H bond lengths computed using EAM potentials are found to be in poor agreement with plane-wave DFT results. We note that the bond lengths are in a poor agreement even in equilibrium. LCAO basis sets are used to explore the importance of electron distribution around H atoms, and the transfer of electrons between H and Zr. The electron distribution around H atoms is found to be important to the explanation of the difference between octahedral and tetrahedral interstitial sites for H, with H in a tetrahedral site having very similar bonding to H in zirconium hydrides. The interatomic electron transfer has a smaller impact but is needed for maximum accuracy

Sizing Up Allometric Scaling Theory

Metabolic rate, heart rate, lifespan, and many other physiological properties vary with body mass in systematic and interrelated ways. Present empirical data suggest that these scaling relationships take the form of power laws with exponents that are simple multiples of one quarter. A compelling explanation of this observation was put forward a decade ago by West, Brown, and Enquist (WBE). Their framework elucidates the link between metabolic rate and body mass by focusing on the dynamics and structure of resource distribution networks—the cardiovascular system in the case of mammals. Within this framework the WBE model is based on eight assumptions from which it derives the well-known observed scaling exponent of 3/4. In this paper we clarify that this result only holds in the limit of infinite network size (body mass) and that the actual exponent predicted by the model depends on the sizes of the organisms being studied. Failure to clarify and to explore the nature of this approximation has led to debates about the WBE model that were at cross purposes. We compute analytical expressions for the finite-size corrections to the 3/4 exponent, resulting in a spectrum of scaling exponents as a function of absolute network size. When accounting for these corrections over a size range spanning the eight orders of magnitude observed in mammals, the WBE model predicts a scaling exponent of 0.81, seemingly at odds with data. We then proceed to study the sensitivity of the scaling exponent with respect to variations in several assumptions that underlie the WBE model, always in the context of finite-size corrections. Here too, the trends we derive from the model seem at odds with trends detectable in empirical data. Our work illustrates the utility of the WBE framework in reasoning about allometric scaling, while at the same time suggesting that the current canonical model may need amendments to bring its predictions fully in line with available datasets