Tuning the work function of graphite nanoparticles edge termination.

Graphite nanoparticles are important in energy materials applications such as lithium-ion batteries (LIBs), supercapacitors and as catalyst supports. Tuning the work function of the nanoparticles allows local control of lithiation behaviour in LIBs, and the potential of zero charge of electrocatalysts and supercapacitors. Using large scale density functional theory (DFT) calculations, we find that the surface termination of multilayer graphene nanoparticles can substantially modify the work function.

Nutritional responsiveness affects novel neutrophil parameters and reduces in-hospital mortality and costs in elective cancer oesophagectomy - a single centre, prospective, observational study.

Introduction: Malnutrition in surgical patients remains a common issue affecting the perioperative period. Oesophageal cancer is a disease associated with one of the highest malnutrition rates. Assessment of patient nutritional status remains a challenge due to limited validated tools.

Cost-Effectiveness Analysis of Innovative Therapies for Patients with Non-Alcoholic Fatty Liver Disease.

Objective: Currently there are no disease-specific approved therapies for non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH); however, several treatments are under development. This study aimed to estimate the cost-effectiveness of hypothetical innovative therapies compared with lifestyle intervention alone and combined with pioglitazone, and assess the health economic consequences of their future availability for patients.

Methods: A Markov cohort model was developed, considering fourteen disease health states and one absorbing state representing death.

HPV RNA and DNA testing in Polish women screened for cervical cancer - A single oncological center study.

Objectives: To evaluate the incidence of HPV infection, and the frequency of the various genotypes, using mRNA and DNA testing; to assess their relationship with the cervical lesions and women's age in the Polish patients.

Study Design: A group of 1840 women, most of whom had abnormal cytology, from the Franciszek Łukaszczyk Oncology Centre in Bydgoszcz, Poland were screened for presence of at least one of 13 high risk HPV. Following that, 545 HPV DNA positive women were tested for HPV infection using HPV mRNA with the Nucleic Acid Sequence-Based Amplification Assay (NASBA) method.

Massively parallel linear-scaling Hartree-Fock exchange and hybrid exchange-correlation functionals with plane wave basis set accuracy.

We extend our linear-scaling approach for the calculation of Hartree-Fock exchange energy using localized in situ optimized orbitals [Dziedzic et al., J. Chem.

Influence of surgical team activity on airborne bacterial distribution in the operating room with a mixing ventilation system: a case study at St. Olavs Hospital.

Background: Operating rooms (ORs) have strict requirements regarding cleanliness. While existing standards concerning the ventilation and staff guidelines are theoretically sufficient to subvert the threats posed by micro-organisms within the room, there exist potential sources of contamination due to human activity around the area. Studies exploring this influence of human activity on distribution of micro-organism contamination in ORs have relied on manual observations, or indirect methods such as number of door openings.

Electrochemistry from first-principles in the grand canonical ensemble.

Progress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by first-principles quantum mechanical simulations with Density Functional Theory (DFT). However, such simulations are typically performed on the electrode surface in the absence of its electrolyte environment and at constant charge.

Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces.

Density functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has non-zero charge, electrical neutrality has to be imposed, and this is often done via a uniform background charge of opposite sign ("jellium"). This artificial neutralization does not occur in reality, where a different mechanism is followed as in the example of a charged electrode in electrolyte solution, where the surrounding electrolyte screens the local charge at the interface.

A Novel Interaction of Translocator Protein 18 kDa (TSPO) with NADPH Oxidase in Microglia.

In the brain neuropil, translocator protein 18 kDa (TSPO) is a stress response protein that is upregulated in microglia and astrocytes in diverse central nervous system pathologies. TSPO is widely used as a biomarker of neuroinflammation in preclinical and clinical neuroimaging studies. However, there is a paucity of knowledge on the function(s) of TSPO in glial cells.

Preparation and Characterization of Novel Polymer-Based Gel Electrolyte for Dye-Sensitized Solar Cells Based on poly(vinylidene fluoride-co-hexafluoropropylene) and poly(acrylonitrile-co-butadiene) or poly(dimethylsiloxane) bis(3-aminopropyl) Copolymers.

Polymer gel electrolytes based on poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) and poly(acrylonitrile-co-butadiene) (PAB) or poly(dimethylsiloxane) bis(3-aminopropyl)-terminated (PDES-bAP) copolymers were prepared and investigated in dye-sensitized solar cells (DSSCs). Selected optical and electrochemical properties of all compositions with various ratio from 9:1 to 6:4 were investigated towards DSSC applications. The highest value of power conversion efficiency equal to 5.

The ONETEP linear-scaling density functional theory program.

We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints.

Designing Antennas for RFID Sensors in Monitoring Parameters of Photovoltaic Panels.

The importance of the radio-frequency identification (RFID) technology and photovoltaic (PV) systems has been growing systematically in the modern world full of intelligent products connected to the Internet. Monitoring parameters of green energy plants is a crucial issue for efficient conversion of solar radiation, and cheap RFID transponders/sensors can be involved in this process to provide better performance of module supervision in scattered installations. Since many components of PV panels disturb the radio-wave propagation, research in the antenna scope has to be carried out to reach the proposed fusion.

The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first-principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested.

Cervical Ectopic Pregnancy: A Rare Site of Implantation.

Background: Cervical ectopic pregnancies are rare, comprising < 1% of ectopic pregnancies, and life threatening if there is a delay in treatment or a misdiagnosis.

Case Report: This case report describes a presentation of cervical ectopic pregnancy. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: This case report reviews nonsurgical and surgical treatment options for patients with cervical ectopic pregnancies.

Mutually polarizable QM/MM model with in situ optimized localized basis functions.

We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem.

DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions.

Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory.

We present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The solvent-solute electrostatic interactions are computed by numerical solution of the nonhomogeneous Poisson equation and incorporated at the Hartree-Fock stage of the EOM-CCSD calculation by modification of the electrostatic potential.

Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis.

The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH, NH, CN) surrounded by increasing numbers of water molecules (up to 100).

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps.

Chemically Selective Alternatives to Photoferroelectrics for Polarization-Enhanced Photocatalysis: The Untapped Potential of Hybrid Inorganic Nanotubes.

elucidates the interplay between wall-polarization, bands separation, charge-transfer excitation, and tunable electrostatics inside and outside the NT-cavity. The results suggest that integration of polarization-enhanced selective photocatalysis and chemical separation into one overall dipole-free material should be possible. Strategies are proposed to increase the NT polarization for maximally enhanced electron-hole separation.

Sex and genetic differences in the effects of acute diesel exhaust exposure on inflammation and oxidative stress in mouse brain.

In addition to increased morbidity and mortality caused by respiratory and cardiovascular diseases, air pollution may also contribute to central nervous system (CNS) diseases. Traffic-related air pollution is a major contributor to global air pollution, and diesel exhaust (DE) is its most important component. DE contains more than 40 toxic air pollutants and is a major constituent of ambient particulate matter (PM), particularly of ultrafine-PM.

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field.

We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme.

Advanced Potential Energy Surfaces for Molecular Simulation.

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms.