Implementation of the harmonically mapped averaging (HMA) framework in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is presented for on-the-fly computations of the energy, pressure, and heat capacity of crystalline systems during canonical molecular dynamics simulations. HMA has a low central processing unit and storage requirements and is straightforward to use. As a case study, the properties of the Lennard-Jones and embedded-atom model (parameterized for nickel) crystals are computed. The results demonstrate the higher efficiency of the new class compared to the inbuilt LAMMPS classes for calculating these properties. However, HMA loses its effectiveness in systems where diffusion occurs in the crystal, and an example is presented to allow this behavior to be recognized. In addition to its improved precision, HMA is less affected by small errors introduced by having a larger time step in molecular dynamics simulations. We also present an analysis of the effect of potential truncation on anharmonic properties, and show that artifacts of truncation on the HMA averages can be eliminated simply by shifting the potential energy to zero at the truncation radius. Full properties can be obtained by adding easily computed values for the lattice and harmonic properties using the untruncated potential.
The objective of this study was to compare the risk factors and outcome of patients with preexisting resistant gram-negative bacilli (GNB) with those who develop sensitive GNB in the cardiac intensive care unit (ICU). Of the 3161 patients ( n=3,161) admitted to the ICU during the study period, 130 (4.11%) developed health care-associated infections (HAIs) with GNB and were included in the cohort study. Pseudomonas aeruginosa (37.8%) was the most common organism isolated followed by Klebsiella species (24.2%), E. coli (22.0%), Enterobacter species (6.1%), Stenotrophomonas maltophilia (5.7%), Acinetobacter species (1.3%), Serratia marcescens (0.8%), Weeksella virosa (0.4%) and Burkholderia cepacia (0.4%). Univariate analysis revealed that the following variables were significantly associated with the antibiotic-resistant GNB: females (P=0.018), re-exploration (P=0.004), valve surgery (P=0.003), duration of central venous catheter (P<0.001), duration of mechanical ventilation (P<0.001), duration of intra-aortic balloon counter-pulsation (P=0.018), duration of urinary catheter (P<0.001), total number of antibiotic exposures prior to the development of resistance (P=0.014), acute physiology and age chronic health evaluation score (APACHE II), receipt of anti-pseudomonal penicillins (piperacillin-tazobactam) (P=0.002) and carbapenems (P<0.001). On multivariate analysis, valve surgery (adjusted OR=2.033; 95% CI=1.052-3.928; P=0.035), duration of mechanical ventilation (adjusted OR=1.265; 95% CI=1.055-1.517; P=0.011) and total number of antibiotic exposure prior to the development of resistance (adjusted OR=1.381; 95% CI=1.030-1.853; P=0.031) were identified as independent risk factors for HAIs in resistant GNB. The mortality rate in patients with resistant GNB was significantly higher than those with sensitive GNB (13.9% vs. 1.8%; P=0.03). HAI with resistant GNB, in ICU following cardiac surgery, are independently associated with the following variables: valve surgeries, duration of mechanical ventilation and prior exposure to antibiotics. The mortality rate is significantly higher among patients with resistant GNB.
The kinetics of carbon condensation, or carbon clustering, in detonation of carbon-rich high explosives is modeled by solving a system of rate equations for concentrations of carbon particles. Unlike previous efforts, the rate equations account not only for the aggregation of particles but also for their fragmentation in a thermodynamically consistent manner. Numerical simulations are performed, yielding the distribution of particle concentrations as a function of time. In addition to that, analytical expressions are obtained for all the distinct steps and regimes of the condensation kinetics, which facilitates the analysis of the numerical results and allows one to study the sensitivity of the kinetic behavior to the variation of system parameters. The latter is important because the numerical values of many parameters are not reliably known at present. The theory of the kinetics of first-order phase transitions is found adequate to describe the general kinetic trends of carbon condensation, as described by the rate equations. Such physical phenomena and processes as the coagulation, nucleation, growth, and Ostwald ripening are observed, and their dependence on various system parameters is studied and reported. It is believed that the present work will become useful when analyzing the present and future results for the kinetics of carbon condensation, obtained from experiments or atomistic simulations.
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