Effect of Pt and Sn on the adsorption of n-heptane in γ-Al2O3 catalyst models

The Grand Canonical Monte-Carlo (GCMC) method has been used to carry out simulations of the adsorption of n-heptane in models of naphtha-reforming catalysts. Models used in the study differed in the number and distribution of metal atoms—Pt and Sn. The number of adsorbed n-heptane molecules grows linearly with increasing number of metal atoms. The effect of Pt content on the adsorption of n-heptane molecules is most distinct at approximately 100 kPa and within the lower range of the temperatures investigated. In the models of bimetallic catalysts, the effect of the two metals is additive.Figure Effect of Pt and Sn on number of n-heptane molecules adsorbed in Al₂O₃ catalyst in 773 K and 1000 kPa.      

Self-assembly of two-patch particles in solution: a Brownian dynamics simulation study

We study the self-assembly behaviour of two-patch particles with D_∞h symmetry by using Brownian dynamics simulations. The self-assembly process of two-patch particles with diverse patch coverage in two selective solvent conditions is investigated. The patchy particles in a solvent that is bad for patches but good for matrix form linear thread-like structures with low patch coverage, whereas they form 3D network structures with relatively high patch coverage on surface. For patchy particles in a solvent which is good for patches but bad for body, monolayer structures are obtained at high patch coverage, and some cluster structures emerge when surface patch coverage is low.     

Replacing xylene with n-heptane for paraffin embedding

Abstract

In standard histological technique, aromatic solvents such as xylene and toluene are used as clearing agents between ethanol dehydration and paraffin embedding. In addition, these solvents are used for de-waxing paraffin sections. Unfortunately, these solvents are harmful and therefore adequate substitutes would be useful. We suggest the use of n-heptane as a convenient substitute for xylene. Paraffin sections of rat tissues processed with n-heptane and stained with hematoxylin-eosin or Masson's trichrome showed proper embedment, well preserved morphology and excellent staining.     

A molecular dynamics investigation of buckling behaviour of hydrogenated graphene

Molecular dynamics simulations have been performed to characterise the stability behaviour of graphene nanoribbons having different hydrogen coverage, subject to a uniaxial compressive load. The temperature is set at a very low value to circumvent the contribution of thermal agitations. The results show that hydrogen coverage promotes to a rapid drop in the strain of buckling onset due to the effects of easy rotation of newly unsupported sp³ bonds. Furthermore, we have also found a critical value of the hydrogen adsorption above which the declining trend in the stability behaviour of hydrogenated graphene nanoribbons is reversed.     

Thermal stability of carbon [n,5] prismanes (n = 2–4): a molecular dynamics study

Tight-binding molecular dynamics simulations are carried out to analyse the thermal stability of the carbon [n,5] prismanes with n = 2–4 over a wide temperature range. The results obtained demonstrate that the isomerisation activation energy as well as the frequency factor in the Arrhenius equation of these metastable nanostructures rapidly decreases with an increase of n. Therefore, the increase in the effective length of [n,5] prismane leads to the decrease in its lifetime up to the moment of its isomerisation. Nevertheless, the stability of [n,5] prismanes is confirmed to be sufficient for their existence at the liquid-nitrogen temperature. The main identified mechanism of [n,5] prismanes isomerisation is the interlayer C–C bond breaking leading to their transformation to the hypostrophene-based molecular systems.     

A population dynamics perspective on effect of irrigation regimes and plant densities on greenbug abundance in grain sorghum using regression

• 1 A dataset generated from previous experiments on greenbug Schizaphis graminum (Rondani) (Hemiptera: Aphididae) response to irrigation and plant density in grain sorghum was reanalyzed using a recently‐developed mechanistic ecological model for describing aphid population density curves. The model was used to estimate seven response variables: observed peak aphid abundance, predicted peak aphid abundance, time of peak abundance, per capita birthrate, death rate coefficient, final cumulative density and duration of substantial aphid infestation across three irrigation regimes and five plant densities.
• 2 Using regression, the observed peak aphid abundance, predicted peak aphid abundance, per capita birthrate and final cumulative abundance were shown to decrease significantly, whereas the death rate coefficient and duration of the infestation were shown to increase significantly for each 100 000 plant/ha increase.
• 3 Although significant results were found for a number of variables generated from the specific data set used in the analyses, of perhaps greater importance is the potential use of these equations in future predictions of aphid population dynamics. An example of projecting population curves based on estimated peak and cumulative counts and an example of projecting population curves based on estimated birth and death rate coefficients are provided.

     

Impact of high-pressure processing on diffusion in polyethylene based on molecular dynamics simulation

Abstract

The impact of high-pressure processing (HPP) on dissusion of antioxidant butylated hydroxytoluene (BHT) in polyethylene (PE) was discussed via the molecular dynamics method. Furthermore, the glass transition temperatures (T_g), the accessible free volumes of PE and the diffusion coefficients of BHT in PE at different HPP treatments were calculated, and the diffusion trajectories of the BHT molecules in PE were also presented. Finally, the diffusion mechanism of BHT in PE under HPP was analyzed based on the aforementioned simulation results. The results show that the T_g of PE increases under high pressure while the fractional free volume (FFV) reduces, and the diffusion coefficient decreases with the pressure on the rise. The diffusion trajectories of BHT in PE under HPP indicate that the BHT molecules are trapped and slowly wriggle in a narrow path among PE molecular chains due to the extreme high pressure. However, the high temperature has an opposite effect on the diffusion behavior of BHT in PE compared with high pressure. As the temperature rises, the FFV of PE and the diffusion coefficient of BHT in PE are elevated. This study is helpful to the research of high-pressure food safety and packaging migration.     

Static and dynamic properties of mid-size liquid n- alkanes,C12∼C400: a molecular dynamics simulation study

ABSTRACT

In this paper, we have extended our previous study of the static and dynamic properties (self-diffusion coefficient D_self and friction coefficient ζ) of liquid n-alkane systems up C₄₀₀ at several temperatures (～2300?K) using molecular dynamics (MD) simulations in the canonical ensembles. For the small n-alkanes with n?≤?120 (n: the chain length), the chains are clearly ?R² _ee?/6?R² _g? ≥ 1 (1.06 ～ 1.44), which leads to the conclusion that the liquid n-alkanes are far away from the ideal chain regime. But for the n-alkanes of n?≥?160, the chains are ?R² _ee?/6?R² _g? ≈ 1, indicating that they are Gaussian. It is found that the long chains of these n-alkanes at high temperatures show abnormalities in density and friction coefficient. We observed a clear transition in the power law dependence of n-alkane self-diffusion coefficient on the molecular weight (M) of n-alkane, D_self ～ M^?γ, occurs in the range C₁₂₀～C₁₆₀ at temperatures of 318, and 618?K, corresponding to a crossover from the ‘oligomer’ to the ‘Rouse’ regime. The entanglement lengths (N_e) are calculated by the Z1 code and discussed shortly.     

Hydrogen sequential dissociative chemisorption on Nin(n = 2~9,13) clusters: comparison with Pt and Pd

Hydrogen dissociative chemisorption and desorption on small lowest energy Ni_n clusters up to n = 13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy path calculations suggest that H₂ dissociative chemisorption is both thermodynamically and kinetically favorable and the H atoms on the clusters are mobile. Calculations on the sequential H₂ dissociative chemisorption on the clusters indicate that the edge sites are populated first and subsequently several on-top sites and hollow sites are also occupied upon full cluster saturation. In all cases, the average hydrogen capacity on Ni_n clusters is similar to that of Pd_n clusters but considerably smaller than that of Pt_n clusters. Comparison of hydrogen dissociative chemisorption energies and H desorption energies at full H-coverage among the Ni family clusters was made.     

Polylepis woodland dynamics during the last 20,000 years

Aim

To determine the palaeoecological influences of climate change and human land use on the spatial distribution patterns of Polylepis woodlands in the Andes.

Location

Tropical Andes above 2,900 m between 2°S and 18°S of latitude.

Methods

Pollen and charcoal data were gathered from 13 Andean lake sediment records and were rescaled by the maximum value in each site. The rescaled pollen data were used to estimate a mean abundance and coefficient of variation to show woodland expansions/contractions and woodland fragmentation over the last 20,000 years. The rescaled charcoal was displayed as a 200‐year moving median using 500‐year bins to infer the influence of fire on woodland dynamics at landscape scale. Pollen and charcoal were compared with speleothem, clastic flux and archaeological data to assess the influence of moisture balance, glacial activity and human impact on the spatial distribution of Polylepis woodlands.

Results

Woodland expansion and fire were correlated with precipitation changes and glacier dynamics from c. 20 to 6 kcal bp (thousands of calibrated years before present). Charcoal abundances between 20 and 12 kcal bp were less common than from 12 kcal bp to modern. However, human‐induced fires were unlikely to be the main cause of a woodland decline centred at 11 kcal bp , as woodlands recovered from 10.5 to 9.5 kcal bp (about twofold increase). Charcoal peaks analogous to those that induced the woodland decline at 11 kcal bp were commonplace post‐9.5 kcal bp but did not trigger an equivalent woodland contraction. An increase in the coefficient of variation after c. 5.5 kcal bp suggests enhanced fragmentation and coincided with the shift from logistic to exponential growth of human populations. Over the last 1,000 years, Polylepis became hyper‐fragmented with over half of sites losing Polylepis from the record and with coefficients of variation paralleling those of glacial times.

Main conclusions

Polylepis woodlands formed naturally patchy woodlands, rather than a continuous vegetation belt, prior to human occupation in the Andes. The main factors controlling pre‐human woodland dynamics were precipitation and landscape heterogeneity. Human activity led to hyper‐fragmentation during the last c. 1,000 years.     

Energetics,kinetics and dynamics of self-interstitial clusters in bcc tungsten

The configuration, slipping and rotation of self-interstitial atoms cluster along <111> crystal orientation with different sizes in a tungsten are investigated systematically with molecular dynamics. It is found that (I) the SIA clusters with high symmetry are always favoured; (II) the SIA clusters can undergo one-dimensional fast migration along <111> direction, and their migration barriers are no more than 0.07?eV, which is expected due to the strong interaction in the SIA clusters; (III) the rotation energy barriers of the SIA clusters are rather high and they are basically positively correlated with the size of the cluster. For example, the reorientation barrier is 0.66?eV for 1 SIA, 1.2–1.8?eV for SIA_n (2?≤?n?≤?5) clusters and over 2.7?eV for SIA_n (6?≤?n?≤?7) clusters. Compared with slipping of SIA clusters, is an infrequent event, especially for larger SIAs cluster, the vast majority SIAs cluster would have already recombination with vacancies or annihilates at surface and grain boundary through slipping before rotation, which explained that there are very low density of SIAs cluster found in the experiment.     

Kinetics of protein adsorption and desorption on surfaces with grafted polymers

The kinetics of protein adsorption are studied using a generalized diffusion approach which shows that the time-determining step in the adsorption is the crossing of the kinetic barrier presented by the polymers and already adsorbed proteins. The potential of mean-force between the adsorbing protein and the polymer-protein surface changes as a function of time due to the deformation of the polymer layers as the proteins adsorb. Furthermore, the range and strength of the repulsive interaction felt by the approaching proteins increases with grafted polymer molecular weight and surface coverage. The effect of molecular weight on the kinetics is very complex and different than its role on the equilibrium adsorption isotherms. The very large kinetic barriers make the timescale for the adsorption process very long and the computational effort increases with time, thus, an approximate kinetic approach is developed. The kinetic theory is based on the knowledge that the time-determining step is crossing the potential-of-mean-force barrier. Kinetic equations for two states (adsorbed and bulk) are written where the kinetic coefficients are the product of the Boltzmann factor for the free energy of adsorption (desorption) multiplied by a preexponential factor determined from a Kramers-like theory. The predictions from the kinetic approach are in excellent quantitative agreement with the full diffusion equation solutions demonstrating that the two most important physical processes are the crossing of the barrier and the changes in the barrier with time due to the deformation of the polymer layer as the proteins adsorb/desorb. The kinetic coefficients can be calculated a priori allowing for systematic calculations over very long timescales. It is found that, in many cases where the equilibrium adsorption shows a finite value, the kinetics of the process is so slow that the experimental system will show no adsorption. This effect is particularly important at high grafted polymer surface coverage. The construction of guidelines for molecular weight/surface coverage necessary for kinetic prevention of protein adsorption in a desired timescale is shown. The time-dependent desorption is also studied by modeling how adsorbed proteins leave the surface when in contact with a pure water solution. It is found that the kinetics of desorption are very slow and depend in a nonmonotonic way in the polymer chain length. When the polymer layer thickness is shorter than the size of the protein, increasing polymer chain length, at fixed surface coverage, makes the desorption process faster. For polymer layers with thickness larger than the protein size, increases in molecular weight results in a longer time for desorption. This is due to the grafted polymers trapping the adsorbed proteins and slowing down the desorption process. These results offer a possible explanation to some experimental data on adsorption. Limitations and extension of the developed approaches for practical applications are discussed.     

Drivers of longitudinal telomere dynamics in a long‐lived bat species,Myotis myotis

Age‐related telomere shortening is considered a hallmark of the ageing process. However, a recent cross‐sectional ageing study of relative telomere length (rTL) in bats failed to detect a relationship between rTL and age in the long‐lived genus Myotis (M. myotis and M. bechsteinii), suggesting some other factors are responsible for driving telomere dynamics in these species. Here, we test if longitudinal rTL data show signatures of age‐associated telomere attrition in M. myotis and differentiate which intrinsic or extrinsic factors are likely to drive telomere length dynamics. Using quantitative polymerase chain reaction, rTL was measured in 504 samples from a marked population, from Brittany, France, captured between 2013 and 2016. These represent 174 individuals with an age range of 0 to 7+ years. We find no significant relationship between rTL and age (p = .762), but demonstrate that within‐individual rTL is highly variable from year to year. To investigate the heritability of rTL, a population pedigree (n = 1744) was constructed from genotype data generated from a 16‐microsatellite multiplex, designed from an initial, low‐coverage, Illumina genome for M. myotis. Heritability was estimated in a Bayesian, mixed model framework, and showed that little of the observed variance in rTL is heritable (h² = 0.01–0.06). Rather, correlations of first differences, correlating yearly changes in telomere length and weather variables, demonstrate that, during the spring transition, average temperature, minimum temperature, rainfall and windspeed correlate with changes in longitudinal telomere dynamics. As such, rTL may represent a useful biomarker to quantify the physiological impact of various environmental stressors in bats.     

Modeling the interaction between anti-cancer drug penicillamine and pristine and functionalized carbon nanotubes for medical applications: density functional theory investigation and a molecular dynamics simulation

Abstract

The present study focuses on the prediction and investigation of binding properties of penicillamine with pure (5,5) single-walled carbon nanotube (SWCNT) and functionalized SWCNT (f-SWCNT) through the B3LYP and M06-2X functionals using the 6-31G** basis set. The electronic and structural properties, adsorption energy and frontier molecular orbitals of various configurations are examined. Our theoretical results indicated that the interaction of the nanotubes with penicillamine molecule is weak so that the drug adsorption process is typically physisorption. Also, results of theoretical calculations show that the adsorption of the drug molecule on f-SWCNT is stronger with shorter intermolecular distances in comparison to pure SWCNT. The natural bond orbital (NBO) analysis of studied systems demonstrates that the charge is transferred from penicillamine molecule to the nanotubes. Furthermore, molecular dynamics (MD) simulation is employed to evaluate the dynamic and diffusion behavior of drug molecule on SWCNT and f-SWCNT. Energy results show that drug molecule spontaneously moves toward the carriers, and the van der Waals energy contributions in drug adsorption are more than electrostatic interaction. The obtained results from MD simulation confirm that the functionalization of SWCNT leads to increase in the solubility of the carrier in aqueous solution.

Communicated by Ramaswamy H. Sarma     

A three‐dimensional numerical model investigation of the impact of submerged macrophytes on flow dynamics in a large fluvial lake

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Calculation of the diffusion coefficient of thiophene oligomers using molecular dynamics

Electropolymerisation is a very useful methodology for conducting polymers synthesis. A total comprehension of this process will help on the designing of new materials with improved optical and electrical properties. In this sense, computational simulations can deliver important information at atomic scale. Within a kinetic Monte Carlo scheme, diffusion rates are crucial to obtain accurate predictions; however, experimental values of this dynamic property for different oligomers are very scarce among literature. In this study, the diffusion coefficient (D) of thiophene oligomers (1Th–6Th) has been calculated using molecular dynamics simulations coupled with the Einstein expression. Results are in the order of experimental values, demonstrating that this methodology is a fast and reliable alternative to calculate diffusion coefficients with low computational costs.     

New developments in first-principles excited-state dynamics simulations: unveiling the solvent specificity of excited anionic cluster relaxation and electron solvation

Charge-transfer-to-solvent excited iodide–polar solvent molecule clusters, [I^? (Solv)_n]^*, have attracted substantial interest over the past 20 years as they can undergo intriguing relaxation processes leading ultimately to the formation of gas-phase molecular analogues of the solvated electron. In this review article, we present a comprehensive overview of the development and application of state-of-the-art first-principles molecular dynamics simulation approaches to understand and interpret the results of femtosecond photoelectron spectroscopy experiments on [I^? (Solv)_n]^* relaxation, which point to a high degree of solvent specificity in the electron solvation dynamics. The intricate molecular details of the [I^? (Solv)_n]^* relaxation process are presented, and by contrasting the relaxation mechanisms of clusters with several different solvents (water, methanol and acetonitrile), the molecular basis of the solvent specificity of electron solvation in [I^? (Solv)_n]^* is uncovered, leading to a more refined view of the manifestation of electron solvation in small gas-phase clusters.     

Complex nonlinear dynamics of the Hodgkin-Huxley equations induced by time scale changes

 The Hodgkin–Huxley equations with a slight modification are investigated, in which the inactivation process (h) of sodium channels or the activation process of potassium channels (n) is slowed down. We show that the equations produce a variety of action potential waveforms ranging from a plateau potential, such as in heart muscle cells, to chaotic bursting firings. When h is slowed down – differently from the case of n variable being slow – chaotic bursting oscillations are observed for a wide range of parameter values although both variables cause a decrease in the membrane potential. The underlying nonlinear dynamics of various action potentials are analyzed using bifurcation theory and a so-called slow–fast decomposition analysis. It is shown that a simple topological property of the equilibrium curves of slow and fast subsystems is essential to the production of chaotic oscillations, and this is the cause of the large difference in global firing characteristics between the h-slow and n-slow cases. Received: 9 August 2000 / Accepted in revised form: 10 January 2001     

Monte Carlo simulation of the adsorption of C2–C7 linear alkanes in aluminophosphate AlPO4-11

The adsorption behaviors of linear alkanes ranging in length from C₂ to C₇ in AlPO₄-11 have been simulated by using configurational-bias Monte Carlo technique at 313 K. The calculated heats of adsorption at zero coverage for linear alkanes, estimated by Henry coefficients, are consistent well with previously reported experimental and simulation results. The simulated isotherms for n-hexane in AlPO₄-11 at 298 K agree with the experimental data. The isotherms of C₂–C₇ linear alkane were predicted, in which butane presents a substep. The adsorbed alkane molecules are only localized in 10-membered ring channels, and adsorbed phase structures for each alkane were investigated. Total potentials for individual alkane molecule decrease with increasing number of carbon atoms. A linear change in total potential is observed for each linear alkane with increasing loading per unit cell, except that an increasing trend is found in the total potential curve of butane as the loading per unit cell is higher than two molecules.     

Impact-induced desorption of large molecular structures from graphitic substrates

We use molecular dynamics computer simulation to show how the impact of a C₆₀ molecule on a graphite surface can cause an acoustic wave across the surface of the substrate that is strong enough to desorb a neighbouring C₆₀ molecule that has already been adsorbed. This could have potential implications for experimentalists attempting to grow fullerene-based structures on graphite-like materials using an energetic deposition technique. It suggests that unlike normal growth conditions, where sticking probabilities are the principle concern, an extra problem of deposition induced desorption may further slow a growth process.