Importance of electronic self-consistency in the TDDFT based treatment of nonadiabatic molecular dynamics

A mixed quantum-classical approach to simulate the coupled dynamics of electrons and nuclei in nanoscale molecular systems is presented. The method relies on a second order expansion of the Lagrangian in time-dependent density functional theory (TDDFT) around a suitable reference density. We show that the inclusion of the second order term renders the method a self-consistent scheme and improves the calculated optical spectra of molecules by a proper treatment of the coupled response. In the application to ion-fullerene collisions, the inclusion of self-consistency is found to be crucial for a correct description of the charge transfer between projectile and target. For a model of the photoreceptor in retinal proteins, nonadiabatic molecular dynamics simulations are performed and reveal problems of TDDFT in the prediction of intra-molecular charge transfer excitations.Comment: 9 pages, 8 figures. Minor changes in content wrt older versio

Polyyne electronic and vibrational properties under environmental interactions

Recently the novel system of linear carbon chains inside double-walled carbon nanotubes has extended the length of sp1 hybridized carbon chains from 44 to thousands of atoms [Shi, Nat. Mater. 15, 634 (2016)1476-112210.1038/nmat4617]. The optoelectronic properties of these ultralong chains are poorly described by current theoretical models, which are based on short chain experimental data and assume a constant environment. As such, a physical understanding of the system in terms of charge transfer and van der Waals interactions is widely missing. We provide a reference for the intrinsic Raman frequency of polyynes in vacuo and explicitly describe the interactions between polyynes and carbon nanotubes. We find that van der Waals interactions strongly shift this frequency, which has been neither expected nor described for other intramolecular C-C stretching vibrations. As a consequence of charge transfer from the tube to the chain, the Raman response of long chains is qualitatively different from the known phonon dispersion of polymers close to the Γ point. Based on these findings we show how to correctly interpret the Raman data, considering the nanotube's properties. This is essential for its use as an analytical tool to optimize the growth process for future applications. © 2016 American Physical Society

Confined linear carbon chains as a route to bulk carbyne

Strong chemical activity and extreme instability in ambient conditions characterize carbyne, an infinite sp1 hybridized carbon chain. As a result, much less has been explored about carbyne as compared to other carbon allotropes such as fullerenes, nanotubes and graphene. Although end-capping groups can be used to stabilize carbon chains, length limitations are still a barrier for production, and even more so for application. We report a method for the bulk production of long acetylenic linear carbon chains protected by thin double-walled carbon nanotubes. The synthesis of very long arrangements is confirmed by a combination of transmission electron microscopy, X-ray diffraction and (near-field) resonance Raman spectroscopy. Our results establish a route for the bulk production of exceptionally long and stable chains composed of more than 6,000 carbon atoms, representing an elegant forerunner towards the final goal of carbyne's bulk production. © 2016 Macmillan Publishers Limited

The Three-Dimensional Distribution of αA-Crystalline in Rat Lenses and Its Possible Relation to Transparency

Lens transparency depends on the accumulation of massive quantities (600–800 mg/ml) of twelve primary crystallines and two truncated crystallines in highly elongated “fiber” cells. Despite numerous studies, major unanswered questions are how this heterogeneous group of proteins becomes organized to bestow the lens with its unique optical properties and how it changes during cataract formation. Using novel methods based on conical tomography and labeling with antibody/gold conjugates, we have profiled the 3D-distribution of the αA-crystalline in rat lenses at ∼2 nm resolutions and three-dimensions. Analysis of tomograms calculated from lenses labeled with anti-αA-crystalline and gold particles (∼3 nm and ∼7 nm diameter) revealed geometric patterns shaped as lines, isosceles triangles and polyhedrons. A Gaussian distribution centered at ∼7.5 nm fitted the distances between the ∼3 nm diameter gold conjugates. A Gaussian distribution centered at ∼14 nm fitted the Euclidian distances between the smaller and the larger gold particles and another Gaussian at 21–24 nm the distances between the larger particles. Independent of their diameters, tethers of 14–17 nm in length connected files of gold particles to thin filaments or clusters to ∼15 nm diameter “beads.” We used the information gathered from tomograms of labeled lenses to determine the distribution of the αA-crystalline in unlabeled lenses. We found that αA-crystalline monomers spaced ∼7 nm or αA-crystalline dimers spaced ∼15 nm center-to-center apart decorated thin filaments of the lens cytoskeleton. It thus seems likely that lost or gain of long-range order determines the 3D-structure of the fiber cell and possible also cataract formation

Clingo goes linear constraints over reals and integers

The recent series 5 of the ASP system clingo provides generic means to enhance basic Answer Set Programming (ASP) with theory reasoning capabilities. We instantiate this framework with different forms of linear constraints and elaborate upon its formal properties. Given this, we discuss the respective implementations, and present techniques for using these constraints in a reactive context. More precisely, we introduce extensions to clingo with difference and linear constraints over integers and reals, respectively, and realize them in complementary ways. Finally, we empirically evaluate the resulting clingo derivatives clingo[dl] and clingo[lp] on common language fragments and contrast them to related ASP systems.Peer reviewe