First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bio-inorganic system

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metallorganic systems. Our results show that accurate Density-Functional Theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.Comment: 29 pages, 4 Postscript figures, revtex

DC Conductance of Molecular Wires

Inspired by the work of Kamenev and Kohn, we present a general discussion of the two-terminal dc conductance of molecular devices within the framework of Time Dependent Current-Density Functional Theory. We derive a formally exact expression for the adiabatic conductance and we discuss the dynamical corrections. For junctions made of long molecular chains that can be either metallic or insulating, we derive the exact asymptotic behavior of the adiabatic conductance as a function of the chain's length. Our results follow from the analytic structure of the bands of a periodic molecular chain and a compact expression for the Green's functions. In the case of an insulating chain, not only do we obtain the exponentially decaying factors, but also the corresponding amplitudes, which depend very sensitively on the electronic properties of the contacts. We illustrate the theory by a numerical study of a simple insulating structure connected to two metallic jellium leads.Comment: 15 pgs and 9 figure

Using information to deliver safer care: a mixed-methods study exploring general practitioners’ information needs in North West London primary care

The National Health Service in England has given increasing priority to improving inter-professional communication, enabling better management of patients with chronic conditions and reducing medical errors through effective use of information. Despite considerable efforts to reduce patient harm through better information usage, medical errors continue to occur, posing a serious threat to patient safety.This study explores the range, quality and sophistication of existing information systems in primary care with the aim to capture what information practitioners need to provide a safe service and identify barriers to its effective use in care pathways.Data were collected through semi-structured interviews with general practitioners from surgeries in North West London and a survey evaluating their experience with information systems in care pathways.Important information is still missing, specifically discharge summaries detailing medication changes and changes in the diagnosis and management of patients, blood results ordered by hospital specialists and findings from clinical investigations. Participants identified numerous barriers, including the communication gap between primary and secondary care, the variable quality and consistency of clinical correspondence and the inadequate technological integration.Despite attempts to improve integration and information flow in care pathways, existing systems provide practitioners with only partial access to information, hindering their ability to take informed decisions. This study offers a framework for understanding what tools should be in place to enable effective use of information in primary care

First principles study of adsorbed Cu_n (n=1-4) microclusters on MgO(100): structural and electronic properties

We present a density functional study of the structural and electronic properties of small Cu_n (n=1,4) aggregates on defect-free MgO(100). The calculations employ a slab geometry with periodic boundary conditions, supercells with up to 76 atoms, and include full relaxation of the surface layer and of all adsorbed atoms. The preferred adsorption site for a single Cu adatom is on top of an oxygen atom. The adsorption energy and Cu-O distance are E_S-A = 0.99 eV and d_S-A = 2.04 Angstroems using the Perdew-Wang gradient corrected exchange correlation functional. The saddle point for surface diffusion is at the "hollow" site, with a diffusion barrier of around 0.45 eV. For the adsorbed copper dimer, two geometries, one parallel and one perpendicular to the surface, are very close in energy. For the adsorbed Cu_3, a linear configuration is preferred to the triangular geometry. As for the tetramer, the most stable adsorbed geometry for Cu_4 is a rhombus. The adsorption energy per Cu atom decreases with increasing the size of the cluster, while the Cu-Cu cohesive energy increases, rapidly becoming more important than the adsorption energy.Comment: Major revision, Latex(2e) document, 23 pages, 11 figures, accepted for publication in J. of Chem. Phys., paper available at http://irrmawww.epfl.ch/vm/vm_wor

Tunneling and delocalization in hydrogen bonded systems: a study in position and momentum space

Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.Comment: 14 pages, 13 figure

Hybrid Superconductor-Quantum Point Contact Devices using InSb Nanowires

Proposals for studying topological superconductivity and Majorana bound states in nanowires proximity coupled to superconductors require that transport in the nanowire is ballistic. Previous work on hybrid nanowire-superconductor systems has shown evidence for Majorana bound states, but these experiments were also marked by disorder, which disrupts ballistic transport. In this letter, we demonstrate ballistic transport in InSb nanowires interfaced directly with superconducting Al by observing quantized conductance at zero-magnetic field. Additionally, we demonstrate that the nanowire is proximity coupled to the superconducting contacts by observing Andreev reflection. These results are important steps for robustly establishing topological superconductivity in InSb nanowires

Digital health sensing for personalized dermatology

The rapid evolution of technology, sensors and personal digital devices offers an opportunity to acquire health related data seamlessly, unobtrusively and in real time. In this opinion piece, we discuss the relevance and opportunities for using digital sensing in dermatology, taking eczema as an exemplar

Novel highly-soluble peptide-chitosan polymers: Chemical synthesis and spectral characterization

Novel water-soluble polymers, N-(gamma-propanoyl-valin)-chitosan and N-(gamma-propanoyi-aspartic acid)-chitosan, were synthesized by reaction of low molecular weight chitosan with N-alpha-(3-bromopropanoyl)-valine and N-alpha-(3-bromopropanoyl)-aspartic acid, respectively, under mild conditions. Prior to reaction with chitosan, the peptide substituents have been prepared by standard peptide chemistry methods from 3-bromopropanoic acid and the relevant a-amino acid tert-butyl esters. The chemical structure and physical properties of the novel chitosan derivatives were characterized by H-1 NMR and IR spectroscopy. The polymers are highly soluble in a wide pH range, which opens new perspectives for the applications of chitosan-based materials

How well do Car-Parrinello simulations reproduce the Born-Oppenheimer surface ? Theory and Examples

We derive an analytic expression for the average difference between the forces on the ions in a Car-Parrinello simulation and the forces obtained at the same ionic positions when the electrons are at their ground state. We show that for common values of the fictitious electron mass, a systematic bias may affect the Car-Parrinello forces in systems where the electron-ion coupling is large. We show that in the limit where the electronic orbitals are rigidly dragged by the ions the difference between the two dynamics amounts to a rescaling of the ionic masses, thereby leaving the thermodynamics intact. We study the examples of crystalline magnesium oxide and crystalline and molten silicon. We find that for crystalline silicon the errors are very small. For crystalline MgO the errors are very large but the dynamics can be quite well corrected within the rigid-ion model. We conclude that it is important to control the effect of the electron mass parameter on the quantities extracted from Car-Parrinello simulations.Comment: Submitted to the Journal of Chemical Physic

Acceleration Schemes for Ab-Initio Molecular Dynamics and Electronic Structure Calculations

We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest descent algorithms while retaining their numerical cost per time step. Our damped dynamics has efficiency comparable to that of conjugate gradient methods in typical electronic minimization problems. Then, we analyse the factors that limit the size of the integration time step in approaches based on plane-wave expansions. The maximum allowed time step is dictated by the highest frequency components of the fictitious electronic dynamics. These can result either from the large wavevector components of the kinetic energy or from the small wavevector components of the Coulomb potential giving rise to the so called {\it charge sloshing} problem. We show how to eliminate large wavevector instabilities by adopting a preconditioning scheme that is implemented here for the first-time in the context of Car-Parrinello ab-initio molecular dynamics simulations of the ionic motion. We also show how to solve the charge-sloshing problem when this is present. We substantiate our theoretical analysis with numerical tests on a number of different silicon and carbon systems having both insulating and metallic character.Comment: RevTex, 9 figures available upon request, to appear in Phys. Rev.