Excitonic effects in the optical properties of CdSe nanowires

Using a first-principle approach beyond density functional theory we calculate the electronic and optical properties of small diameter CdSe nanowires.Our results demonstrate how some approximations commonly used in bulk systems fail at this nano-scale level and how indispensable it is to include crystal local fields and excitonic effects to predict the unique optical properties of nanowires. From our results, we then construct a simple model that describes the optical gap as a function of the diameter of the wire, that turns out to be in excellent agreement with experiments for intermediate and large diameters.Comment: submitte

Construction of the B88 exchange-energy functional in two dimensions

We construct a generalized-gradient approximation for the exchange-energy density of finite two-dimensional systems. Guided by non-empirical principles, we include the proper small-gradient limit and the proper tail for the exchange-hole potential. The observed performance is superior to that of the two-dimensional local-density approximation, which underlines the usefulness of the approach in practical applications

Hygroscopy of Single-Stranded DNA Nano-Brushes: Atomic Workings of its Hydration-Induced Deformation

Hydration control of structure and mechanical properties is a process widely exploited in living organisms for key biological functions and, most recently, also in man-made smart materials. Here, the challenge of unveiling the underlying atomistic mechanisms of this phenomenon using all-atom Molecular Dynamics (MD) simulations to model the hygroscopic properties of polymer-brushes composed by single-stranded DNA (ssDNA) molecules is faced. The simulations identify three swelling regimes with a markedly different mechanical response. This evolution is produced by the competition between the formation of additional water–ssDNA and water–water hydrogen bonds, in a subtle interplay with the co-evolving structure of the ssDNA SAM. This cooperative interaction between conformational and hydration degrees of freedom should be applicable to other polymer brushes and related hydrogen-bonded systems. The results have direct implications for the use of ssDNA SAMs as sequencing devices, explaining the crucial role of the polymer-brush density in the SAM collective response to hydration, and for the alternative design of hygroscopic materials, that exploit the extreme hygroscopic power of biological polymers like ssDNA brusheThe authors thank the Spanish MINECO for financial support (project MAT2017-83273-R). J.G.V and R.P. acknowledge support from the Spanish Ministry of Science and Innovation, through project PID2020- 115864RB-I00 and the “María de Maeztu” Programme for Units of Excellence in R&D (CEX2018-000805-M). J.G.V. acknowledge support from the Spanish Ministry of Science and Innovation (PID2020- 113722RJ-I00) and Spanish CM “Talento Program” Project No. 2020-T1/ ND-2030

On the violation of a local form of the Lieb-Oxford bound

In the framework of density-functional theory, several popular density functionals for exchange and correlation have been constructed to satisfy a local form of the Lieb-Oxford bound. In its original global expression, the bound represents a rigorous lower limit for the indirect Coulomb interaction energy. Here we employ exact-exchange calculations for the G2 test set to show that the local form of the bound is violated in an extensive range of both the dimensionless gradient and the average electron density. Hence, the results demonstrate the severity in the usage of the local form of the bound in functional development. On the other hand, our results suggest alternative ways to construct accurate density functionals for the exchange energy.Comment: (Submitted on 27 April 2012

Dark matter effects in modified teleparallel gravity

This work investigates dark matter (DM) effects in compact objects in modified teleparallel gravity (MTG) in which a modification of Teleparallel Equivalent to General Relativity is used. We applied a tetrad to the modified field equations where a set of relations is found. The conservation equation allows us to rewrite our Tolman-Oppenheimer-Volkoff equations with an effective gravitational coupling constant. As input to these new equations, we use a relativistic mean-field (RMF) model with dark matter content included, obtained from a Lagrangian density with both, hadronic and dark particle degrees of freedom, as well as the Higgs boson, used as a mediator in both sectors of the theory. Through numerical calculations, we analyze the mass-radius diagrams obtained from different parametrizations of the RMF-DM model, generated by assuming different values of the dark particle Fermi momentum and running the free parameter coming from the MTG. Our results show that it is possible for the system simultaneously support more DM content, and be compatible with recent astrophysical data provided by LIGO and Virgo Collaboration, as well as by NASA's Neutron star Interior Composition Explorer (NICER).Comment: 8 pages, 2 figure

Mapping the sensitivity of split ring resonators using a localized analyte

Split ring resonator (SRR) based metamaterials have frequently been demonstrated for use as optical sensors of organic materials. This is made possible by matching the wavelength of the SRR plasmonic resonance with a molecular resonance of a specific analyte, which is usually placed on top of the metal structure. However, systematic studies of SRRs that identify the regions that exhibit a high electric field strength are commonly performed using simulations. In this paper we demonstrate that areas of high electric field strength, termed “hot-spots,” can be found by localizing a small quantity of organic analyte at various positions on or near the structure. Furthermore, the sensitivity of the SRR to the localized analyte can be quantified to determine, experimentally, suitable regions for optical sensing

Practical guide to single-protein AFM nanomechanical spectroscopy mapping: insights and pitfalls as unraveled by all-atom MD simulations on immunoglobulin G

Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive - a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime - where the mechanical response is linked to the presence of the water environment - followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potentialJ.G.V. acknowledges funding from a Marie Sklodowska-Curie Fellowship within the Horizon 2020 framework (Grant No. DLV-795286) and the Swiss National Science Foundation (Grant No. CRSK-2 190731/1). R.P. acknowledges support from the Spanish MINECO (Grant No. MAT2017-83273-R) and from the Ministerio de Ciencia e Innovación (MICINN) through the “María de Maeztu” Programme for Units of Excellence in R&D (Grant No. CEX2018-000805-M). R.G. acknowledges funding from the MICINN (Grant No. PID2019-106801GB-I00) and Comunidad de Madrid Grant No. S2018/NMT-4443 (Tec4Bio-CM). We thankfully acknowledge the computer resources, technical expertise, and assistance provided by the Red Española de Supercomputación (RES) at the Minotauro and CTE-Power9 supercomputers (BSC, Barcelona). We thank Dr. Alejandro Martín-González for fruitful discussion