yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible I/O procedures and is interfaced to several publicly available density functional ground-state codes. 71.45.Gm, 71.15.Qe

We present a reciprocal space analytical method to cut off the long range interactions in supercell calculations for systems that are infinite and periodic in one or two dimensions, generalizing previous work to treat finite systems. The proposed cutoffs are functions in Fourier space, that are used as a multiplicative factor to screen the bare Coulomb interaction. The functions are analytic everywhere except in a subdomain of the Fourier space that depends on the periodic dimensionality. We show that the divergences that lead to the nonanalytical behavior can be exactly canceled when both the ionic and the Hartree potential are properly screened. This technique is exact, fast, and very easy to implement in already existing supercell codes. To illustrate the performance of the scheme, we apply it to the case of the Coulomb interaction in systems with reduced periodicity ͑as one-dimensional chains and layers͒. For these test cases, we address the impact of the cutoff on different relevant quantities for ground and excited state properties, namely: the convergence of the ground state properties, the static polarizability of the system, the quasiparticle corrections in the GW scheme, and the binding energy of the excitonic states in the Bethe-Salpeter equation. The results are very promising and easy to implement in all available first-principles codes.

yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as Quantum ESPRESSO and Abinit. yambo's capabilities include the calculation of linear response quantities (both independentparticle and including electron-hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron-phonon interactions to the implementation of a real-time propagation scheme for simulating linear and nonlinear optical properties. Improvements to numerical algorithms and the user interface are outlined. Particular emphasis is given to the new and efficient parallel structure that makes it possible to exploit modern high performance computing architectures. Finally, we demonstrate the possibility to automate workflows by interfacing with the yambopy and AiiDA software tools. CONTENTS

We performed first-principles calculations of the optical response of the green fluorescent protein (GFP) within a combined quantum-mechanical molecular-mechanics and time-dependent density-functional theory approach. The computed spectra are in excellent agreement with experiments assuming the presence of two, protonated and deprotonated, forms of the photoreceptor in a approximately 4:1 ratio, which supports the conformation model of photodynamics in GFP. Furthermore, we discuss charge transfer, isomerization, and environment effects. The present approach allows for systematic studies of excited-state electron-ion dynamics in biological systems.

We investigate from first principles the optoelectronic properties of nanometer-sized armchair graphene nanoribbons (GNRs). We show that many-body effects are essential to correctly describe both energy gaps and optical response. As a signature of the confined geometry, we observe strongly bound excitons dominating the optical spectra, with a clear family dependent binding energy. Our results demonstrate that GNRs constitute 1D nanostructures whose absorption and luminescence performance can be controlled by changing both family and edge termination. Graphite-related nanoscale materials, such as fullerenes and nanotubes, have long been the subject of an intense research for their remarkable properties [1]. The recent discovery of stable, single-layer graphene [2,3,4] has prompted the attention on a different graphitic quasi-1D nanostructure, i.e. graphene nanoribbons (GNRs). These systems have been theoretically studied in the past decade [5,6,7,8,9] as simplified models of defective nanotubes and graphite nano-fragments. However, only very recently isolated nanometer-sized GNRs have been actually synthetized by etching larger graphene samples, or by CVD growth on suitably patterned surfaces [10,11,12]. The production techniques advanced in these pioneering works are expected to become highly controllable, opening up new avenues for both fundamental nanoscience and nanotechnology applications.One of the most striking features of GNRs is the high sensitivity of their properties to the details of the atomic structure [5,6,7,13,14,15,16]. In particular, the edge shape dictates their classification in armchair (A), zigzag (Z) or chiral (C) ones, thus determining their energy band gaps. In addition to an overall decrease of energy gaps with increasing ribbon width, also observed experimentally [11], theoretical studies predict a superimposed oscillation feature [13,14,15], which is maximized for A-GNRs. According to this behaviour, A-GNRs are further classified in three distinct families, i. e. N = 3p − 1, N = 3p, N = 3p + 1, with p integer, where N indicates the number of dimer lines across the ribbon width. This fine sensitivity to the atomic configuration raise the opportunity to tailor the optoelectronic properties of AGNRs by appropriately selecting both ribbon family and width.In spite of this interest, previous theoretical studies of the electronic (see e.g. Refs. 6, 15, 16) and optical properties [14] of GNRs were only based on the independentparticle approximation or on semi-empirical calculations. However, many body effects are expected to play a key role in low dimensional systems [17,18,19,20,21] due to enhanced electron-electron correlation. Motivated by this theoretical issue and by recent experimental progress [10,11,12] pursuing the potential of GNRs for nanotechnolgy applications, we have carried out ab initio calculations to study the effects of many-body interactions on the optical spectra of 1-nm-wide A-GNRs belonging to different families.In this Letter, we show that a sound and accurate descript...

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We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchangecorrelation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and π-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.

Hole transfer processes between base pairs in natural DNA and size-expanded DNA (xDNA) are studied and compared, by means of an accurate first principles evaluation of the effective electronic couplings (also known as transfer integrals), in order to assess the effect of the base augmentation on the efficiency of charge transport through double-stranded DNA. According to our results, the size expansion increases the average electronic coupling, and thus the CT rate, with potential implications in molecular biology and in the implementation of molecular nanoelectronics. Our analysis shows that the effect of the nucleobase expansion on the charge-transfer (CT) rate is sensitive to the sequence of base pairs. Furthermore, we find that conformational variability is an important factor for the modulation of the CT rate. From a theoretical point of view, this work offers a contribution to the CT chemistry in π-stacked arrays. Indeed, we compare our methodology against other standard computational frameworks that have been adopted to tackle the problem of CT in DNA, and unravel basic principles that should be accounted for in selecting an appropriate theoretical level.