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EN
Self-assembled monolayers (SAMs) have a large variety of applications. One particular ap-plication of alkanethiol-based SAMs is tuning the work function of metallic surfaces. In a recent study, it was determined that depositing a poly(methyl methacrylate) layer on selected SAMs further shifts the work function. The effect is sensitive to tacticity and neither the reason behind this nor the exact mechanism of the interaction was determined. The aim of this work is to study the problem by use of molecular dynamics simulations.
PL
Jednym zlicznych zastosowań samoorganizujących się monowarstw (SAMs) jest mody-fikacja pracy wyjścia powierzchni metalicznych. Wliteraturze można znaleźć opracowania dotyczące depozycji cienkich warstw poli(metakrylanu metylu) na wybranych samoorganizujących się monowar-stwach na bazie alkanotioli, prowadzącej do dalszych zmian wartości pracy wyjścia całej struktury. Uzyskany efekt wydaje się być zależny od taktyczności polimeru, jednakże wbadaniach eksperymen-talnych nie udało się określić przyczyn tego zjawiska. Wniniejszej pracy wspomniany efekt zbadano za pomocą symulacji komputerowych metodą dynamiki molekularnej.
2
Content available remote Surface diffusion and cluster formation of gold on the silicon (111)
EN
Purpose: Investigation of the gold atoms behaviour on the surface of silicon by molecular dynamics simulation method. The studies were performed for the case of one, two and four atoms, as well as incomplete and complete filling of gold atoms on the silicon surface. Design/methodology/approach: Investigations were performed by the method of molecular dynamics simulation using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). MEAM potential of interatomic interaction was used for modelling. Molecular dynamic simulations were carried out in isothermal-isobaric ensemble (NpT) with a timestep 1.0 fs. Findings: As a result of studies, the preferred interaction between gold atoms and the formation of clusters at temperatures up to 800 K was revealed. Analysis of the temperature dependences of the number of large jumps of atoms made it possible to calculate the activation energy of a single jump. It was found that activation energy of single atomic displacement decreases with increasing number of gold atoms. Research limitations/implications: Only a limited number of sets of atoms were used in the study. It is possible that for another combination of atoms and a larger substrate surface, the formation of gold nanoislands on the silicon surface can be observed, which requires further research. Practical implications: The research results can be used to select the modes of gold sputtering to create gold nanoislands or nanopillars on the silicon surface. Originality/value: Computer modelling of the behaviour of gold atoms on the surface of silicon with the possibility of their self-organization and cluster formation was performed for the first time.
EN
This memoir honors the late Berni Julian Alder, who inspired both of us with his pioneering development of molecular dynamics. Berni’s work with Tom Wainwright, described in the 1959 Scientific American [1], brought Bill to interview at Livermore in 1962. Hired by Berni, Bill enjoyed over 40 years’ research at the Laboratory. Berni, along with Edward Teller, founded UC’s Department of Applied Science in 1963. Their motivation was to attract bright students to use the laboratory’s unparalleled research facilities. In 1972 Carol was offered a joint LLNL employee-DAS student appointment at Livermore. Bill, thanks to Berni’s efforts, was already a Professor there. Berni’s influence was directly responsible for our physics collaboration and our marriage in 1989. The present work is devoted to two early interests of Berni’s, irreversibility and shockwaves. Berni and Tom studied the irreversibility of Boltzmann’s “H function” in the early 1950s [2]. Berni called shockwaves the “most irreversible” of hydrodynamic processes [3]. Just this past summer, in simulating shockwaves with time-reversible classical mechanics, we found that reversed Runge-Kutta shockwave simulations yielded nonsteady rarefaction waves, not shocks. Intrigued by this unexpected result we studied the exponential Lyapunov instabilities in both wave types. Besides the Runge-Kutta and Leapfrog algorithms, we developed a precisely-reversible manybody algorithm based on trajectory storing, just changing the velocities’ signs to generate the reversed trajectories. Both shocks and rarefactions were precisely reversed. Separate simulations, forward and reversed, provide interesting examples of the Lyapunov-unstable symmetry-breaking models supporting the Second Law of Thermodynamics. We describe promising research directions suggested by this work.
EN
The effects of oxygen-containing functional groups on the structure and dynamic properties of water molecules near a lignite surface were investigated through molecular dynamics (MD) simulations. Because of its complex composition and structure, a graphite surface containing hydroxyl, carboxyl, and carbonyl groups was used to represent the lignite surface model. According to X-ray photoelectron spectroscopic (XPS) results, the composing proportion of hydroxyl, carbonyl and carboxyl is 21:13:6. The density profiles of oxygen and hydrogen atoms indicate that the brown coal surface characteristics influence the structural and dynamic properties of water molecules. The interfacial water is much more ordered than bulk water. The results of the radial distribution functions, mean square displacements, and local self-diffusion coefficients for the water molecules in the vicinity of three oxygen-containing functional groups confirmed that carboxyl groups are the preferential adsorption sites.
EN
The molecular dynamics of the well-known nematic liquid crystal 4-n-pentyl-4′-cyanobiphenyl geometrically restricted in Anopore and Synpor porous membranes with various pore structure and treated by different surfactants (namely decanoic acid and lecithin) is compared. In the Anopore membrane the chosen surfactants induce the homeotropic orientation of the molecules on the walls of the cylindrical pores and observed corresponding relaxation processes (librational modes) are practically the same. The dielectric measurements of lecithin treated Synpor membranes reveals the reorientation of the molecules from planar to homeotropic on the complex multilayer structure present in their volume. The dielectric strengths of the observed two molecular processes (δ-process and librational mode) are inversed in the ratio compared to the untreated membranes. The observed differences in molecular dynamics results from the orientation of the liquid crystal molecules in untreated and treated membranes and the structure of the membranes themselves.
EN
The thermophysical properties of metal alloys are often investigated via molecular dynamics (MD) simulations. An exact and reliable estimation of the thermophysical parameters from the MD data requires a properly and carefully elaborated methodology. In this paper, an improved two-phase sandwich method for the determination of the metal melting temperature is proposed, based on the solid-liquid equilibrium theory. The new method was successfully implemented using the LAMMPS software and the C++11 Standard Libraries and then applied to aluminum and copper systems. The results show that the proposed procedure allows more precise calculations of the melting temperature than the widely used onephase boundary methods.
EN
Results of the ab initio molecular dynamics calculations of silicon crystals are presented by means of analysis of the velocity autocorrelation function and determination of mean phonon relaxation time. The mean phonon relaxation time is crucial for prediction of the phonon-associated coefficient of thermal conductivity of materials. A clear correlation between the velocity autocorrelation function relaxation time and the coefficient of thermal diffusivity has been found. The analysis of the results obtained has indicated a decrease of the velocity autocorrelation function relaxation time t with increase of temperature. The method proposed may be used to estimate the coefficient of ther-mal diffusivity and thermal conductivity of the materials based on silicon and of other wide-bandgap semiconductors. The correlation between kinetic energy fluctuations and relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate the use of kinetic energy fluctuations for the calculation of values related to heat conductivity in silicon-based semiconductors (coefficients of thermal conductivity and diffusivity).
EN
The calculation method of the molecular dynamics has been applied to study the correlation of the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function and the phonon relaxation time in a crystal. On the basis of the molecular dynamics data for silicon crystal obtained at different temperatures in the range 200 K – 1000 K the correlation between the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate a use of the kinetic energy fluctuations for the calculation of values related to the heat conductivity in the silicon based semiconductors (coefficients of thermal conductivity and diffusivity).
PL
Obliczeniowa metoda dynamiki molekularnej została zastosowana do badania korelacji fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości i czasu relaksacji fononów w krysztale. Na bazie danych dynamiki molekularnej kryształu krzemu otrzymanych w różnych temperaturach w zakresie 200 K – 1000 K została obliczona korelacja fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości, która cechuje się stosunkowo wysokim współczynnikiem determinacji R2 = 0.9396. Otrzymana korelacja uzasadnia zastosowanie fluktuacji energii kinetycznej do badań obliczeniowych wielkości powiązanych z przewodnością cieplną półprzewodników na bazie krzemu (współczynniki przewodności i dyfuzyjności cieplnej).
9
PL
Klasyczna dynamika molekularna MD jest jedną z technik symulacji komputerowych wieloatomowych lub wielocząsteczkowych układów. Pozwala na badanie struktury oraz właściwości zarówno materiałów krystalicznych, jak i amorficznych. Opiera się na rozwiązywaniu numerycznym klasycznych równań ruchu. Nie tylko uzupełnia badania eksperymentalne, ale jest również narzędziem pozwalającym na badanie budowy materiałów na poziomie nieosiągalnym konwencjonalnymi technikami. W celu przedstawienia klasycznej dynamiki molekularnej wykonano symulacje dwóch szkieł 80SiO2-20Na2O i 85SiO2-15Na2O [%mol]. Otrzymane wyniki dobrze zgadzały się z obecnym stanem wiedzy. Wykonane symulacje świadczą o tym, że technika ta jest niezwykle użyteczna przy poznawaniu struktury szkieł. Wykorzystując tę technikę, można przewidywać wpływ modyfikatorów na więźbę szkła, a przez to możliwe jest wskazywanie kierunku dalszych badań oraz optymalizacja składów chemicznych.
EN
Molecular dynamics MD is one of computer simulation methods of multiatomic or multimolecular systems. It allows to examination of structure and properties both crystalline and amorphous materials. This technique consists of the numerical solution of the classical equation of motion. It complements not only experimental methods but also it is tool make possible examination of material structure on the unavailable level for conventional methods. In order to introduce to molecular dynamics, the simulations of two glasses 80SiO2‑20Na2O and 85SiO2-15Na2O [%mol] were performed. Obtained results corresponds well to the actual state of knowledge. Performed simulation testify that this technique is a very useful to examine glass structure. Using this method, it is possible to predict influence of modifiers on glass network, it’s make possible indication research direction and optimization of chemical composition.
EN
The micro air nucleus widely distributed in the ocean is a necessary condition for the cavitation of hydraulic machinery in seawater. In order to study the stability of air nucleus in seawater and cavitation inception, the computational domain of water molecules with air nucleus was studied using the method of molecular dynamics simulation, and the transient characteristics of air nucleus in liquid water were obtained. The key factors influencing nuclei stability were analyzed. The results showed that air nucleus with a certain mass could maintain the dynamic equilibrium in liquid water. The internal density of air nuclei had a critical value that allowed the nuclei to stably exist in water. The air nuclei mass was the decisive factor in its equilibrium volume in water, and the two were positively correlated. The internal density of air nuclei was negatively correlated with the nuclei radius when the nuclei was stable in water. Liquid surface tension was an important factor affecting the stability of the air nuclei. The larger the initial radius of nuclei, the smaller the water pressure, and the more likely the cavitation occurs.
11
Content available remote Symulacje klasycznej dynamiki molekularnej szkieł z układu P2O5-Fe2O3-FeO
PL
Szkła fosforanowe ze względu na swoje właściwości zyskały wiele zastosowań np. w medycynie czy ochronie środowiska. Wprowadzenie żelaza do więźby tych szkieł powoduje poprawę ich odporności chemicznej. Najwyższą odpornością chemiczną cechuje się szkło o składzie 40% mol. Fe2O3 – 60% mol. P2O5. Żelazo w tych szkłach może występować zarówno na III, jak i na II stopniu utleniania. Ich wzajemny stosunek zależy nie tylko od atmosfery w jakiej było topione szkło, ale również od temperatury i czasu topienia. W pracy wykorzystano symulacje klasycznej dynamiki molekularnej MD w celu określenia wpływu jonów Fe(II) na więźbę szkieł z układu P2O5–Fe2O3–FeO. Uzyskane wyniki dobrze zgadzają się z obecnym stanem wiedzy na temat tych szkieł. W symulowanych szkłach odległości między najbliższymi parami jonów P–O, Fe(II)–O, Fe(III)–O i O–O nie zależą od zawartości Fe(II) w strukturze. Wraz ze wzrostem zawartości Fe(II) wzrasta ilość Fe(II) i Fe(III) o koordynacjach większych niż 4.
EN
Due to its properties, phosphate glasses have gained many applications, e.g. in medicine or environmental protection. The incorporation of iron to the glass network causes improvement of chemical durability. The highest chemical durability among others has glass with a composition of 40 mol%Fe2O3 – 60 mo% P2O5. Iron in these glasses may occur on both III and II stage of oxidation. Their ratio depends not only on the atmosphere in which the glass was melted, but also on the temperature and melting time. The work uses the simulations of classic molecular dynamics MD to determine the effect of Fe(II) ions on network of glasses from the P2O5–Fe2O3–FeO system. The obtained results agree well with the current state of knowledge about these glasses. In simulated glasses, the distances between the closest pairs of ions P-O, Fe(II)-O, Fe(III)-O and O-O do not depend on the Fe (II) content in the structure. With the increase in the Fe (II) content, the Fe (II) and Fe (III) levels are increased with coordination greater than 4.
12
Content available remote Modelling of blood thrombosis at microscopicand mesoscopic scales
EN
Blood coagulation at the place of the complete severing of a vessel or puncturing of a vessel sidewall is usually a beneficial reaction, as it protects the body from bleeding and maintains hemostasis, while the formation of a blood clot inside the blood vessel is a pathological phenomenon, which is highly dangerous, and sometimes leads to serious complications. In this paper, two scales of modelling blood thrombosis will be introduced using numerical methods and fluid dynamics. The meso-scale model of the flow is described by Navier-Stokes equations and the blood thrombosis model is based on equations of transport and diffusion. The equations describing levels of concentrations of factors responsible for blood coagulation can be implemented into a solver solving Navier-Stokes equations, what will enable simulation of blood flow and estimation of the risk of thrombus formation related to flow conditions. The proposed micro-scale model is using molecular dynamics to simulate interactions between blood cells and vascular walls. An effective combination of both models is possible thanks to the introduction of the multiple-time stepping algorithm, which enables a full visualization of blood flow, coupling molecular interaction with the fluid mechanics equation. The goal of the paper is to present the latest literature review on the possibilities of blood coagulation modelling in two scales and the main achievements in blood thrombosis research: the key role of transport and experimental background.
EN
Non-equilibrium molecular dynamics method (NEMD) is applied to investigate a formation process of water nanovortex in 7 nm wide nanocavity (aspect ratio of which was equal to 3.6). The flow in the nanocavity was induced by Poiseuille 2D water nanoflow in a main nanochannel, to which the nanocavity is situated perpendicularly. The wall of main channel and the nanocavity is made from quartz. Flow is induced by applying constant force to molecules inside the main channel. Based on NEMD simulation data, the sequence of images representing water velocity vector fields was obtained at constant time intervals equal to 1 ns, which shows vortex formation mechanism. Flow field images analysis indicates that the shape and centre position of the nanovortex vary slightly each nanosecond, nevertheless, the structure remains stable in the flow field at the entrance to the nanocavity.
14
Content available remote Central-force decomposition of the Tersoff potential
EN
Central forces play important role in the analysis of results obtained with particle simulation methods, since they allow evaluating stress fields. In this work we derive expressions for a central-force decompositon of the Tersoff potential, which is often used to describe interatomic interactions in covalently bonded materials. We simplify the obtained expressions and discuss their properties.
EN
Results of the ab initio molecular dynamics for pure silicon and phosphorus doped silicon crystals have been presented. The relation between the phonon lifetime and the root mean square deviation  of atoms based on the condition of the interferometric minimum has been proposed. The relation approximates adequately the temperature dependence of the heat conductivity of pure silicon. However, that relation has not reproduced properly the reference experimental magnitude of the phonon conductivity coefficient of silicon for the phosphorus content nP = 51020 cm-3. This result indicates that the additional kind of the phonon scattering on the local phosphorus stimulated defects should be taken into consideration.
PL
Przedstawiono wyniki obliczeń z pierwszych zasad dynamiki molekularnej niedomieszkowanych i domieszkowanych fosforem kryształów krzemu i zaproponowano wzór relacji między czasem życia fononów i odchyleniem standardowym atomów , bazujący na interferencyjnym warunku minimum fal fononowych. Zaproponowany wzór adekwatnie opisuje temperaturową zależność współczynnika przewodnictwa cieplnego niedomieszkowanego krzemu. Jednak zaproponowany wzór nie odtwarza zadowalająco referencyjnej doświadczalnej wartości przewodności cieplnej krzemu dla koncentracji fosforu nP = 51020 cm-3. Ten wynik wskazuje na to, że dla adekwatnego odtwarzania wartości doświadczalnych należy uwzględnić dodatkowy kanał rozpraszania fononów, związany z lokalnymi około fosforowymi defektami.
EN
In this work, two collectors sodium oleate (NaOL) and benzohydroxamic acid (BHA) were used to study the synergic effect in wolframite flotation. The flotation behaviour of these collectors was investigated at various NaOL:BHA ratios. Results show that the mixtures of NaOL with BHA of different ratios result in large improvements in the recovery of wolframite and the 9:1 NaOL:BHA ratio of collector mixture produced the highest wolframite recovery. The amount of NaOL and BHA adsorbed on wolframite was measured for these various reagent mixtures. Compared with pure NaOL, the addition of a certain proportion of BHA is beneficial for NaOL adsorption. Molecular dynamics simulations indicate the formation of HOL–HA (oleic acid–benzohydroxamic acid) complex can take place spontaneously in NaOL–BHA system. Additionally, HOL–HA complex interact with the huebnerite (MnWO4) surface more easily than NaOL–HOL (the highest surface active composition in sodium oleate) and the addition of BHA enable the H of carboxyl group in HOL to generate hydrogen bonds with O atoms of huebnerite surface, resulting in a stronger affinity of mixed surfactants. These results reveal that in a binary NaOL–BHA system, the BHA can encourage greater adsorption of the NaOL.
17
Content available remote Thermal conductivity of silicon doped by phosphorus: ab initio study
EN
An original approach to the theoretical calculations of the heat conductivity of crystals based on the first principles molecular dynamics has been proposed. The proposed approach exploits the kinetic theory of phonon heat conductivity and permits calculating several material properties at certain temperature: specific heat, elastic constant, acoustic velocity, mean phonon scattering time and coefficient of thermal conductivity. The method has been applied to silicon and phosphorus doped silicon crystals and the obtained results have been found to be in satisfactory agreement with corresponding experimental data. The proposed computation technique may be applied to the calculations of heat conductivity of pure and doped semiconductors and isolators.
EN
Thermo-fluid properties are required for numerical modeling of nano/micro devices. These properties are mostly obtained from the results of molecular dynamics (MD) simulations. Therefore, efforts have been made to develop methods for numerical evaluation of fluid properties such as pressure and velocity. One of the main challenges faced by numerical simulations is to simulate steady molecular flow in channels with non-equal inlet and outlet boundaries. Currently, periodic boundary conditions at the inlet and outlet boundaries are an inevitable condition in many steady flow molecular dynamics simulations. As a result, a nano-channel with different cross sectional areas at the inlet and outlet could not be simulated easily. Here, a method is presented to generate and control steady molecular flow in a nano-channel with different cross sectional areas at the inlet and outlet. The presented method has been applied to a converging-diverging channel, and its performance has been studied through qualitative and quantitative representation of flow properties.
19
Content available remote Yokohama to Ruby Valley : Around the World in 80 Years. II.
EN
We two had year-long research leaves in Japan, working together fulltime with several Japanese plus Tony De Groot back in Livermore and Harald Posch in Vienna. We summarize a few of the high spots from that very productive year (1989-1990), followed by an additional fifteen years’ work in Livermore, with extensive travel. Next came our retirement in Nevada in 2005, which has turned out to be a long-term working vacation. Carol narrates this part of our history together.
EN
A one-component Lennard-Jones/spline fluid at equilibrium was perturbed by a sudden change of the temperature at one of the system’s boundaries. The system’s response was determined by non-equilibrium molecular dynamics (NEMD). The results show that heat was transported by two mechanisms: (1) Heat diffusion and conduction, and (2) energy dissipation associated with the propagation of a pressure (shock) wave. These two processes occur at different time scales, which makes it possible to separate them in one single NEMD run. The system was studied in gas, liquid, and supercritical states with various forms and strengths of the thermal perturbation. Near the heat source, heat was transported according to the transient heat equation. In addition, there was a much faster heat transport, correlated with a pressure wave. This second mechanism was similar to the thermo-mechanical “piston effect” in near-critical fluids and could not be explained by the Joule-Thomson effect. For strong perturbations, the pressure wave travelled faster than the speed of sound, turning it into a shock wave. The system’s local measurable heat flux was found to be consistent with Fourier’s law near the heat source, but not in the wake of the shock. The NEMD results were, however, consistent with the Cattaneo-Vernotte model. The system was found to be in local equilibrium in the transient phase, even with very strong perturbations, except for a low-density gas. For dense systems, we did not find that the local equilibrium assumption used in classical irreversible thermodynamics is inconsistent with the Cattaneo-Vernotte model.
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