Molecular dynamics simulations of the adsorption and diffusion behavior of pure and mixed alkanes in silicalite

The adsorption and diffusion of mixed hydrocarbon components in silicalite have been studied using molecular dynamic simulation methods. We have investigated the effect of molecular loadings and temperature on the diffusional behavior of both pure and mixed alkane components. For binary mixtures with components of similar sizes, molecular diffusional behavior in the channels was noticed to be reversed as loading is increased. This behavior was noticeably absent for components of different sizes in the mixture. Methane molecules in the methane/propane mixture have the highest diffusion coefficients across the entire loading range. Binary mixtures containing ethane molecules prove more difficult to separate compared to other binary components. In the ternary mixture, however, ethane molecules diffuse much faster at 400 K in the channel with a tendency to separate out quickly from other components. © 2005 Elsevier Inc. All rights reserved.

Monte Carlo and molecular dynamics simulations of methane in potassium montmorillonite clay hydrates at elevated pressures and temperatures

The structure and dynamics of methane in hydrated potassium montmorillonite clay have been studied under conditions encountered in sedimentary basin and compared to those of hydrated sodium montmorillonite clay using computer simulation techniques. The simulated systems contain two molecular layers of water and followed gradients of 150 barkm-1 and 30 Kkm-1 up to a maximum burial depth of 6 km. Methane particle is coordinated to about 19 oxygen atoms, with 6 of these coming from the clay surface oxygen. Potassium ions tend to move away from the center towards the clay surface, in contrast to the behavior observed with the hydrated sodium form. The clay surface affinity for methane was found to be higher in the hydrated K-form. Methane diffusion in the two-layer hydrated K-montmorillonite increases from 0.39×10-9 m2s-1 at 280 K to 3.27×10-9 m2s-1 at 460 K compared to 0.36×10-9 m2s-1 at 280 K to 4.26×10-9 m2s-1 at 460 K in Na-montmorillonite hydrate. The distributions of the potassium ions were found to vary in the hydrates when compared to those of sodium form. Water molecules were also found to be very mobile in the potassium clay hydrates compared to sodium clay hydrates. © 2004 Elsevier Inc. All All rights reserved.

Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide:can the α3 and β2m domains be neglected?

Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histo-compatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVY-DGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histocompatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVYDGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available for this study allow us to compare directly differences in the behavior of very large molecular models; in this case, the entire extracellular portion of the peptide–MHC complex vs. the isolated peptide binding domain. Comparison of the results from the partial and the whole system simulations indicates that the peptide is less tightly bound in the partial system than in the whole system. From a detailed study of conformations, solvent-accessible surface area, the nature of the water network structure, and the binding energies, we conclude that, when considering the conformation of the α1–α2 domain, the α3 and β2m domains cannot be neglected. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1803–1813, 2004

Using SPICE for power system simulations

Power system simulation software is a useful tool for teaching the fundamentals of power system design and operation. However, existing commercial packages are not ideal for teaching work-based students because of high-cost, complexity of the software and licensing restrictions. This paper describes a set of power systems libraries that have been developed for use with the free, student-edition of a Micro-Cap Spice that overcomes these problems. In addition, these libraries are easily adapted to include power electronic converter based components into the simulation, such as HVDC, FACTS and smart-grid devices, as well as advanced system control functions. These types of technology are set to become more widespread throughout existing power networks, and their inclusion into a power engineering degree course is therefore becoming increasingly important.

Monte Carlo Random Walk Simulations Based on Distributed Order Differential Equations with Applications to Cell Biology

Mathematics Subject Classification: 65C05, 60G50, 39A10, 92C37

Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

CO adsorption over Pd nanoparticles:a general framework for IR simulations on nanoparticles

CO vibrational spectra over catalytic nanoparticles under high coverages/pressures are discussed from a DFT perspective. Hybrid B3LYP and PBE DFT calculations of CO chemisorbed over Pd4 and Pd13 nanoclusters, and a 1.1 nm Pd38 nanoparticle, have been performed in order to simulate the corresponding coverage dependent infrared (IR) absorption spectra, and hence provide a quantitative foundation for the interpretation of experimental IR spectra of CO over Pd nanocatalysts. B3LYP simulated IR intensities are used to quantify site occupation numbers through comparison with experimental DRIFTS spectra, allowing an atomistic model of CO surface coverage to be created. DFT adsorption energetics for low CO coverage (θ → 0) suggest the CO binding strength follows the order hollow > bridge > linear, even for dispersion-corrected functionals for sub-nanometre Pd nanoclusters. For a Pd38 nanoparticle, hollow and bridge-bound are energetically similar (hollow ≈ bridge > atop). It is well known that this ordering has not been found at the high coverages used experimentally, wherein atop CO has a much higher population than observed over Pd(111), confirmed by our DRIFTS spectra for Pd nanoparticles supported on a KIT-6 silica, and hence site populations were calculated through a comparison of DFT and spectroscopic data. At high CO coverage (θ = 1), all three adsorbed CO species co-exist on Pd38, and their interdiffusion is thermally feasible at STP. Under such high surface coverages, DFT predicts that bridge-bound CO chains are thermodynamically stable and isoenergetic to an entirely hollow bound Pd/CO system. The Pd38 nanoparticle undergoes a linear (3.5%), isotropic expansion with increasing CO coverage, accompanied by 63 and 30 cm− 1 blue-shifts of hollow and linear bound CO respectively.

Queue Length Simulations in a Finite Single-line Queueing System with Repeated Calls

2000 Mathematics Subject Classification: 60K25.

Szimulációk és érzékenységvizsgálatok a magyar gazdaság egy középméretű makromodelljével = Simulations and sensitivity analyses with a medium-sized macro model of the Hungarian economy

A tanulmányban a Pénzügyminisztérium gazdaságpolitikai főosztálya és az MTA Közgazdaságtudományi Intézete által kifejlesztett középméretű negyedéves makrogazdasági modell segítségével elemezzük a magyar gazdaság legfontosabb mechanizmusait. A modellezés során követett alapelvek és a modell blokkjainak bemutatása után egy forgatókönyv-elemzés keretében vizsgáljuk a makrogazdasági és költségvetési folyamatokat befolyásoló főbb faktorok hatásait. A - tágan értelmezett - "bizonytalansági tényezőket" három csoportba soroljuk: megkülönböztetjük a külső környezet (például árfolyam) változását, a gazdasági szereplők viselkedésében rejlő bizonytalanságokat (például a bérigazodás sebességének vagy a fogyasztássimítás mértékének bizonytalanságát), valamint a gazdaságpolitikai lépéseket (például állami bérek emelését). Megmutatjuk, hogy e kockázatok makrokövetkezményei nem függetlenek egymástól, például egy árfolyamváltozás hatását befolyásolja a bérigazodás sebessége. ______ This paper analyses the most important mechanisms of the Hungarian economy using a medium-sized quarterly macroeconomic model developed jointly by the Economic Policy Department of the Ministry of Finance and the Institute of Economics of the Hungarian Academy of Sciences. After introducing the fundamental principles of modelling and the building blocks of the model investigated, within a scenario analysis, the authors present the effects of the main factors behind the macroeconomic and budgetary processes. The sources of uncertainty - defined in a broad sense - are categorized in three groups: change in the external environment (e.g. the exchange rate), uncertainties in the behav-iour of economic agents (e.g. in speed of wage adjustment or extent of consumption smoothing), and economic policy decisions (e.g. the increase in public sector wages). The macroeconomic consequences of these uncertainties are shown not to be independent of each other. For instance, the effects of an exchange rate shock are influenced by the speed of wage adjustment.

Simulations of Theoretical Ecosystem Growth Model (TEGM) during various climate conditions

Climate change has a great impact on the build and the work of natural ecosystems. Disappearance of some population or growth of the number in some species can be already caused by little change in temperature. A Theoretical Ecosystem Growth Model was investigated in order to examine the effects of various climate patterns on the ecological equilibrium. The answers of the ecosystems which are given to the climate change could be described by means of global climate modelling and dynamic vegetation models. The examination of the operation of the ecosystems is only possible in huge centres on supercomputers because of the number and the complexity of the calculation. The number of the calculation could be decreased to the level of a PC by considering the temperature and the reproduction during the modelling of a theoretical ecosystem and several important theoretical questions could be answered.

Achievement of generic baccalaureate student nurses using computer -assisted instruction simulations during a nursing review course

The use of computer assisted instruction (CAI) simulations as an instructional strategy provides nursing students with a critical thinking approach for evaluating risks and benefits and choosing correct alternatives in "safe" patient care situations. It was hypothesized that using CAI simulations during an upper level nursing review course would have a positive effect on the students' posttest scores. Subjects (n = 36) were senior nursing students enrolled in a nursing review course in an undergraduate baccalaureate program. A limitation of the study was the small sample size. The study employed a modified group experimental design using the t test for independent samples. The group who received the CAI simulations during the physiological system review demonstrated a significant increase (p $<$.01) in the posttest score mean when compared to the lecture-discussion group score mean. There was no significant difference between high and low clinical grade point average (GPA) students in the CAI and lecture-discussion groups and their score means on the posttest. However, score mean differences of the low clinical GPA students showed a greater increase for the CAI group than the lecture-discussion group. There was no significant difference between the groups in their system content subscore means on the exit examination completed three weeks later. It was concluded that CAI simulations are as effective as lecture-discussion in assisting upper level students to process information for clinical decision making. CAI simulations can be considered as an instructional strategy to supplement or replace lecture content during a review course, allowing more efficient use of faculty time. It is recommended that the study be repeated using a larger sample size. Further investigations are recommended in comparing the effectiveness of computer software formats and various instructional strategies for other learning situations and student populations. ^

Mechanisms governing the eyewall replacement cycle in numerical simulations of tropical cyclones

Eyewall replacement cycle (ERC) is frequently observed during the evolution of intensifying Tropical Cyclones (TCs). Although intensely studied in recent years, the underlying mechanisms of ERC are still poorly understood, and the forecast of ERC remains a great challenge. To advance our understanding of ERC and provide insights in improvement of numerical forecast of ERC, a series of numerical simulations is performed to investigate ERCs in TC-like vortices on a f-plane. The simulated ERCs possess key features similar to those observed in real TCs including the formation of a secondary tangential wind maximum associated with the outer eyewall. The Sawyer-Eliassen equation and tangential momentum budget analyses are performed to diagnose the mechanisms underlying the secondary eyewall formation (SEF) and ERC. Our diagnoses reveal crucial roles of outer rainband heating in governing the formation and development of the secondary tangential wind maximum and demonstrate that the outer rainband convection must reach a critical strength relative to the eyewall before SEF and the subsequent ERC can occur. A positive feedback among low-level convection, acceleration of tangential winds in the boundary layer, and surface evaporation that leads to the development of ERC and a mechanism for the demise of inner eyewall that involves interaction between the transverse circulations induced by eyewall and outer rainband convection are proposed. The tangential momentum budget indicates that the net tendency of tangential wind is a small residual resultant from a large cancellation between tendencies induced by the resolved and sub-grid scale (SGS) processes. The large SGS contribution to the tangential wind budget explains different characteristics of ERC shown in previous numerical studies and poses a great challenge for a timely correct forecast of ERC. The sensitivity experiments show that ERCs are strongly subjected to model physics, vortex radial structure and background wind. The impact of model physics on ERC can be well understood with the interaction among eyewall/outer rainband heating, radilal inflow in the boundary layer, surface layer turbulent processes, and shallow convection in the moat. However, further investigations are needed to fully understand the exhibited sensitivities of ERC to vortex radial structure and background wind.

Theoretical model simulations for variations in thermal reaction norms

Thermal reaction norms for growth rates of six Emiliania huxleyi isolates originating from the central Atlantic (Azores, Portugal) and five isolates from the coastal North Atlantic (Bergen, Norway) were assessed. We used the template mode of variation model to decompose variations in growth rates into modes of biological interest: vertical shift, horizontal shift, and generalist-specialist variation. In line with the actual habitat conditions, isolates from Bergen (Bergen population) grew well at lower temperatures, and isolates from the Azores (Azores population) performed better at higher temperatures. The optimum growth temperature of the Azores population was significantly higher than that of the Bergen population. Neutral genetic differentiation was found between populations by microsatellite analysis. These findings indicate that E. huxleyi populations are adapted to local temperature regimes. Next to between-population variation, we also found variation within populations. Genotype-by-environment interactions resulted in the most pronounced phenotypic differences when isolates were exposed to temperatures outside the range they naturally encounter. Variation in thermal reaction norms between and within populations emphasizes the importance of using more than one isolate when studying the consequences of global change on marine phytoplankton. Phenotypic plasticity and standing genetic variation will be important in determining the potential of natural E. huxleyi populations to cope with global climate change.

Evaluating the urban heat island for cities of Emilia-Romagna region through numerical simulations

Lo scopo di questo studio è la comprensione della dinamica dello strato limite urbano per città dell’Emilia Romagna tramite simulazioni numeriche. In particolare, l’attenzione è posta sull’ effetto isola di calore, ovvero sulla differenza di temperatura dell’aria in prossimità del suolo fra zone rurali e urbane dovuta all’urbanizzazione. Le simulazioni sono state effettuate con il modello alla mesoscala "Weather Research and Forecasting" (WRF), accoppiato con le parametrizzazioni urbane "Building Effect Parametrization" (BEP) e "Building Energy Model" (BEM), che agiscono a vari livelli verticali urbani. Il periodo di studio riguarda sei giorni caldi e senza copertura nuvolosa durante un periodo di heat wave dell’anno 2015. La copertura urbana è stata definita con il "World Urban Databes and Access Portal Tools" (WUDAPT), un metodo che permette di classificare le aree urbane in dieci "urban climate zones" (UCZ), attraverso l’uso combinato di immagini satellitari e "training areas" manualmente definite con il software Google Earth. Sono state svolte diverse simulazioni a domini innestati, con risoluzione per il dominio più piccolo di 500 m, centrato sulla città di Bologna. Le differenze fra le simulazioni riguardano la presenza o l’assenza delle strutture urbane, il metodo di innesto e tipo di vegetazione rurale. Inoltre, è stato valutato l’effetto dovuto alla presenza di pannelli fotovoltaici sopra i tetti di ogni edificio e le variazioni che i pannelli esercitano sullo strato limite urbano. Per verificare la bontà del modello, i dati provenienti dalle simulazioni sono stati confrontati con misure provenienti da 41 stazioni all’interno dell’area di studio. Le variabili confrontate sono: temperatura, umidità relativa, velocità e direzione del vento. Le simulazioni sono in accordo con i dati osservativi e riescono a riprodurre l’effetto isola di calore: la differenza di temperatura fra città e zone rurali circostanti è nulla durante il giorno; al contrario, durante la notte l’isola di calore è presente, e in media raggiunge il massimo valore di 4°C alle 1:00. La presenza dei pannelli fotovoltaici abbassa la temperatura a 2 metri dell’aria al massimo di 0.8°C durante la notte, e l’altezza dello strato limite urbano dell’ordine 200mrispetto al caso senza pannelli. I risultati mostrano come l’uso di pannelli fotovoltaici all’interno del contesto urbano ha molteplici benefici: infatti, i pannelli fotovoltaici riescono a ridurre la temperatura durante un periodo di heat wave, e allo stesso tempo possono parzialmente sopperire all’alto consumo energetico, con una conseguente riduzione del consumo di combustibili fossili.

LPJ-LMfire simulations for Europe for the Last Glacial Maximum and preindustrial control, link to netCDF files

This data sets contains LPJ-LMfire dynamic global vegetation model output covering Europe and the Mediterranean for the Last Glacial Maximum (LGM; 21 ka) and for a preindustrial control simulation (20th century detrended climate). The netCDF data files are time averages of the final 30 years of the model simulation. Each netCDF file contains four or five variables: fractional cover of 9 plant functional types (PFTs; cover), total fractional coverage of trees (treecover), population density of hunter-gatherers (foragerPD; only for the "people" simulations), fraction of the gridcell burned on 30-year average (burnedf), and vegetation net primary productivity (NPP). The model spatial resolution is 0.5-degrees For the LGM simulations, LPJ-LMfire was driven by the PMIP3 suite of eight GCMs for which LGM climate simulations were available. Also provided in this archive is the result of an LPJ-LMfire run that was forced by the average climate of all GCMs (the "GCM-mean" files), and the average of each of the individual LPJ-LMfire runs over the eight LGM scenarios individually (the "LPJ-mean" files). The model simulations are provided that include the influence of human presence on the landscape (the "people" files), and in a "world without humans" scenario (the "natural" files). Finally this archive contains the preindustrial reference simulation with and without human influence ("PI_reference_people" and "PI_reference_nat", respectively). There are therefore 22 netCDF files in this archive: 8 each of LGM simulations with and without people (total 16) and the "GCM mean" simulation (2 files) and the "LPJ mean" aggregate (2 files), and finally the two preindustrial "control" simulations ("PI"), with and without humans (2 files). In addition to the LPJ-LMfire model output (netCDF files), this archive also contains a table of arboreal pollen percent calculated from pollen samples dated to the LGM at sites throughout (lgmAP.txt), and a table containing the location of archaeological sites dated to the LGM (LGM_archaeological_site_locations.txt).