On cycling risk and discomfort: urban safety mapping and bike route recommendations

Bike usage in Smart Cities is paramount for sustainable urban development: cycling promotes healthier lifestyles, lowers energy consumption, lowers carbon emissions, and reduces urban traffic. However, the expansion and increased use of bike infrastructure has been accompanied by a glut of bike accidents, a trend jeopardizing the urban bike movement. This paper leverages data from a diverse spectrum of sources to characterise geolocated bike accident severity and, ultimately, study cycling risk and discomfort. Kernel density estimation generates a continuous, empirical, spatial risk estimate which is mapped in a case study of Zürich city. The roles of weather, time, accident type, and severity are illustrated. A predominance of self-caused accidents motivates an open-source software artifact for personalized route recommendations. This software is used to collect open baseline route data that are compared with alternative routes minimizing risk and discomfort. These contributions have the potential to provide invaluable infrastructure improvement insights to urban planners, and may also improve the awareness of risk in the urban environment among experienced and novice cyclists alike

Conductance of Distorted Carbon Nanotubes

We have calculated the effects of structural distortions of armchair carbon nanotubes on their electrical transport properties. We found that the bending of the nanotubes decreases their transmission function in certain energy ranges and leads to an increased electrical resistance. Electronic structure calculations show that these energy ranges contain localized states with significant $\sigma$-$\pi$ hybridization resulting from the increased curvature produced by bending. Our calculations of the contact resistance show that the large contact resistances observed for SWNTs are likely due to the weak coupling of the NT to the metal in side bonded NT-metal configurations.Comment: 5 pages RevTeX including 4 figures, submitted to PR

System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields

The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein

DFT-based Conformational Analysis of a Phospholipid Molecule (DMPC)

The conformational space of the dimyristoyl phosphatidylcholine (DMPC) molecule has been studied using Density Functional Theory (DFT), augmented with a damped empirical dispersion energy term (DFT-D). Fourteen ground-state isomers have been found with total energies within less than 1 kcal/mol. Despite differences in combinations of their torsion angles, all these conformers share a common geometric profile, which includes a balance of attractive, repulsive and constraint forces between and within specific groups of atoms. The definition of this profile fits with most of the structural characteristics deduced from measured NMR properties of DMPC solutions. The calculated vibrational spectrum of the molecule is in good agreement with experimental data obtained for DMPC bilayers. These results support the idea that DMPC molecules preserve their individual molecular structures in the various assemblies.Comment: 31 pages, 6 Tables, 4 Figure

Exact exchange potential evaluated solely from occupied Kohn-Sham and Hartree-Fock solutions

The reported new algorithm determines the exact exchange potential v_x in a iterative way using energy and orbital shifts (ES, OS) obtained - with finite-difference formulas - from the solutions (occupied orbitals and their energies) of the Hartree-Fock-like equation and the Kohn-Sham-like equation, the former used for the initial approximation to v_x and the latter - for increments of ES and OS due to subsequent changes of v_x. Thus, solution of the differential equations for OS, used by Kummel and Perdew (KP) [Phys. Rev. Lett. 90, 043004 (2003)], is avoided. The iterated exchange potential, expressed in terms of ES and OS, is improved by modifying ES at odd iteration steps and OS at even steps. The modification formulas are related to the OEP equation (satisfied at convergence) written as the condition of vanishing density shift (DS) - they are obtained, respectively, by enforcing its satisfaction through corrections to approximate OS and by determining optimal ES that minimize the DS norm. The proposed method, successfully tested for several closed-(sub)shell atoms, from Be to Kr, within the DFT exchange-only approximation, proves highly efficient. The calculations using pseudospectral method for representing orbitals give iterative sequences of approximate exchange potentials (starting with the Krieger-Li-Iafrate approximation) that rapidly approach the exact v_x so that, for Ne, Ar and Zn, the corresponding DS norm becomes less than 10^{-6} after 13, 13 and 9 iteration steps for a given electron density. In self-consistent density calculations, orbital energies of 10^{-4} Hartree accuracy are obtained for these atoms after, respectively, 9, 12 and 12 density iteration steps, each involving just 2 steps of v_x iteration, while the accuracy limit of 10^{-6}--10^{-7} Hartree is reached after 20 density iterations.Comment: 21 pages, 5 figures, 3 table

First-principles study of TMNan (TM= Cr, Mn, Fe, Co, Ni; n = 4-7) clusters

Geometry, electronic structure, and magnetic properties of TMNan (TM=Cr-Ni; n = 4-7) clusters are studied within a gradient corrected density functional theory (DFT) framework. Two complementary approaches, the first adapted to all-electron calculations on free clusters, and the second been on plane wave projector augmented wave (PAW) method within a supercell approach are used. Except for NiNan, the clusters in this series are found to retain the atomic moments of the TM atoms, and the magnetic moment presented an odd-even oscillation with respect to the number of Na atoms. The origin of these odd-even oscillations is explained from the nature of chemical bonding in these clusters. Differences and similarities between the chemical bonding and the magnetic properties of these clusters and the TMNan (TM = Sc, V and Ti; n = 4-6) clusters on one hand, and TM-doped Au and Ag clusters on the other hand, are discussed

Characterization of optical properties and surface roughness profiles: The Casimir force between real materials

The Lifshitz theory provides a method to calculate the Casimir force between two flat plates if the frequency dependent dielectric function of the plates is known. In reality any plate is rough and its optical properties are known only to some degree. For high precision experiments the plates must be carefully characterized otherwise the experimental result cannot be compared with the theory or with other experiments. In this chapter we explain why optical properties of interacting materials are important for the Casimir force, how they can be measured, and how one can calculate the force using these properties. The surface roughness can be characterized, for example, with the atomic force microscope images. We introduce the main characteristics of a rough surface that can be extracted from these images, and explain how one can use them to calculate the roughness correction to the force. At small separations this correction becomes large as our experiments show. Finally we discuss the distance upon contact separating two rough surfaces, and explain the importance of this parameter for determination of the absolute separation between bodies.}Comment: 33 pages, 14 figures, to appear in Springer Lecture Notes in Physics, Volume on Casimir Physics, edited by Diego Dalvit, Peter Milonni, David Roberts, and Felipe da Ros