Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations

A coarse-grained model for simulating structural properties of double-stranded RNA is developed with parameters obtained from quantum-mechanical calculations. This model follows previous parametrization for double-stranded DNA, which is based on mapping the all-atom picture to a coarse-grained four-bead scheme. Chemical and structural differences between RNA and DNA have been taken into account for the model development. The parametrization is based on simulations using density functional theory (DFT) on separate units of the RNA molecule without implementing experimental data. The total energy is decomposed into four terms of physical significance: hydrogen bonding interaction, stacking interactions, backbone interactions, and electrostatic interactions. The first three interactions are treated within DFT, whereas the last one is included within a mean field approximation. Our double-stranded RNA coarse-grained model predicts stable helical structures for RNA. Other characteristics, such as structural or mechanical properties are reproduced with a very good accuracy. The development of the coarse-grained model for RNA allows extending the spatial and temporal length scales accessed by computer simulations and being able to model RNA-related biophysical processes, as well as novel RNA nanostructures

Relationship between singlet-triplet excitation energies and the Kohn-Sham orbitals obtained with potentials that exhibit a wrong asymptotic behavior

A linear relationship was found between the singlet-triplet excitation energy and the energy difference presented by the Kohn-Sham frontier molecular orbitals, independently of the used exchange-correlation functional and of the basis set functions quality. The relationship was explored in three different situations: (a) when the number of carbons is increased in an all-trans acetylene family; (b) rotation of the trans-butadiene around the single bond; (c) dissociation process of the molecules H-2 and FH. Additionally, it was found a strong relationship between the vertical singlet-triplet excitation energy obtained with the B3LYP and the multiconfiguration-self consistent methods

Achieving performance portability in Gaussian basis set density functional theory on accelerator based architectures in NWChemEx

The numerical integration of the exchange–correlation (XC) potential is one of the primary computational bottlenecks in Gaussian basis set Kohn–Sham density functional theory (KS-DFT). To achieve optimal performance and accuracy, care must be taken in this numerical integration to preserve local sparsity as to allow for near linear weak scaling with system size. This leads to an integration scheme with several performance critical kernels which must be hand optimized for each architecture of interest. As the set of available accelerator hardware goes more diverse, a key challenge for developers of KS-DFT software is to maintain performance portability across a wide range of computational architectures. In this work, we examine a modular software design pattern which decouples the implementation details of performance critical kernels from the expression of high-level algorithmic workflows in a device-agnostic language such as C++; thus allowing for developers to target existing and emerging accelerator hardware within a single code base. We consider the efficacy of such a design pattern in the numerical integration of the XC potential by demonstrating its ability to achieve performance portability across a set of accelerator architectures which are representative of those on current and future U.S. Department of Energy Leadership Computing Facilities

Precipitación y recarga en la cuenca de La Paz, BCS, México

Durante los últimos años, el acuífero de La Paz, BCS se ha visto seriamente afectado por la sobreexplotación debida a un mayor abastecimiento requerido por el crecimiento de la población, lo que ha provocado su contaminación por intrusión de agua de mar, de lo que se deduce que el manejo del recurso es inadecuado ya que se ha extraído más agua que la que proporciona la recarga natural por lluvias. Con el objetivo de estimar los volúmenes que manejan algunas de las componentes principales del sistema hidrológico de la cuenca de La Paz, se utilizó la ecuación general de balance hidrológico aplicada en un sistema de información geográfica (SIG) con lo que se generaron modelos digitales de precipitación, temperatura, evapotranspiración, escurrimiento y recarga, a partir de datos climatológicos de 25 años (1980 a 2004). Se estimó una precipitación de 410 Mm3 año-1, evapotranspiración de 330 Mm3 año-1, escurrimiento superficial de 15 Mm3 año-1, y una recarga potencial por lluvias de 65 Mm3 año-1. La recarga por lluvias ocurre principalmente en las elevaciones montañosas ubicadas al este y sureste de la cuenca (sierra Las Cruces y El Novillo) y es equivalente al 15.9% de la precipitación. La subcuenca de El Novillo es la que cubre una mayor superficie y capta más del 50% del total de las lluvias

Molecular dynamics and charge transport in organic semiconductors: a classical approach to modeling electron transfer

Organic photovoltaics (OPVs) are a promising carbon-neutral energy conversion technology, with recent improvements pushing power conversion efficiencies over 10%. A major factor limiting OPV performance is inefficiency of charge transport in organic semiconducting materials (OSCs). Due to strong coupling with lattice degrees of freedom, the charges form polarons, localized quasi-particles comprised of charges dressed with phonons. These polarons can be conceptualized as pseudo-atoms with a greater effective mass than a bare charge. We propose that due to this increased mass, polarons can be modeled with Langevin molecular dynamics (LMD), a classical approach with a computational cost much lower than most quantum mechanical methods. Here we present LMD simulations of charge transfer between a pair of fullerene molecules, which commonly serve as electron acceptors in OSCs. We find transfer rates consistent with experimental measurements of charge mobility, suggesting that this method may provide quantitative predictions of efficiency when used to simulate materials on the device scale. Our approach also offers information that is not captured in the overall transfer rate or mobility: in the simulation data, we observe exactly when and why intermolecular transfer events occur. In addition, we demonstrate that these simulations can shed light on the properties of polarons in OSCs. Much remains to be learned about these quasi-particles, and there are no widely accepted methods for calculating properties such as effective mass and friction. Our model offers a promising approach to exploring mass and friction as well as providing insight into the details of polaron transport in OSCs.National Science Foundation (U.S.) (Grant CHE-146480