Molecular dynamics simulation of diffusion behaviour of gas molecules within oil–paper insulation system

The diffusion behaviour of hydrogen, carbon monoxide, carbon dioxide, methane, acetylene, ethylene and ethane in oil and paper medium was examined using molecular dynamics to reveal the diffusion mechanism of gas molecules in transformer oil–paper insulation system at the microscopic level. These compounds are commonly used in the dissolved gas analysis of power transformers and produced during the ageing process of oil–paper composite insulating material. Two groups of models were constructed using molecular dynamics simulation software to simulate the diffusion behaviour of the aforementioned seven types of small gas molecules in oil and paper. The diffusion coefficients, displacement features, free volume characteristics and interaction energies of the gas molecules were investigated. In particular, the diffusion micro-mechanism of the gas molecules was observed. The differences in diffusion features among the gas molecules were discussed, and the factors influencing the diffusion of the gas molecules were compared. Simulation results indicate that the diffusion coefficients of gas molecules in cellulose is an order of magnitude lower than that in oil, and the diffusion coefficients of these gas molecules in the two types of insulation media have different orders. Free volume of gas molecules is the main factor that influences the diffusion behaviour in oil, whereas intermolecular interaction is the main influencing factor of diffusion behaviour in cellulose.     

Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions

β₂‐Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂‐microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β₂‐microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂‐microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis‐trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native‐like trans‐conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis‐trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β₂‐microglobulin provides details of the binding modes of the drug and a rationale for its effect. Proteins 2011. © 2010 Wiley‐Liss, Inc.     

Molecular dynamics simulation of the reciprocal fused LiF–KBr mixture: local structure and self-diffusion coefficients

This paper describes the molecular dynamics simulation of the reciprocal fused LiF–KBr mixture, which is located above the critical mixing point, in the temperature range 1280–1450 K. The first coordination sphere is found to form as follows: a smaller ion is formed around a smaller counter-ion, and a larger ion is formed around a larger counter-ion. The calculated concentration dependence of the self-diffusion coefficients and the radial distribution functions of all ion pairs indicate that the degree of association of the Li–F pair increases as the lithium fluoride fraction in the mixture decreases.     

Molecular dynamics simulation of diffusion of hydrogen in binary hydrogen–tetrahydrofuran hydrate

The binary structure II hydrogen–tetrahydrofuran (THF) hydrate was studied with molecular dynamics simulation. The simulations were carried out at 300, 310 K and 10.1 MPa, and with various contents of hydrogen and THF. The migrations of hydrogen molecules from cage to cage were observed. The migration process of hydrogen was also analysed, and the diffusion coefficients of hydrogen in the hydrate were calculated. The calculated diffusion coefficients qualitatively agreed with the experimental data. Double and quintet occupancies of hydrogen molecules were observed in the small and large cages, respectively, without changing the hydrate structure.     

Molecular dynamics simulation of the melting processes of core–shell and pure nanoparticles

Core–shell nanoparticles are nanosized particles that consist of a core and a shell, constructed from different metallic elements. Core–shell nanoparticles have received extensive attention, owing to their various potential applications such as paints, optical films and catalysts. Herein, we investigate the melting behaviours of different core–shell nanoparticles under continuous heating using molecular dynamics simulation. Different metallic elements were examined as core–shell and pure nanoparticles. Five different processes were observed during the melting of core–shell nanoparticles. In contrast, only one process was identified during the melting of pure nanoparticles. These processes were influenced by the nanoparticle size, shell thickness and differences between the lattice constants and melting point temperatures of the metallic elements. Our simulation provides microscopic insights into the melting behaviours of existing and proposed core–shell nanoparticles that would be highly beneficial towards the fabrication of materials with different chemical coatings.     

Molecular dynamics simulation of Axillaridine–A: A potent natural cholinesterase inhibitor

Molecular Dynamics (MD) simulations were carried out for human acetylcholinesterase (hAChE) and its complex with Axillaridine–A, in order to dynamically explore the active site of the protein and the behaviour of the ligand at the peripheral binding site. Simulation of the enzyme alone showed that the active site of AChE is located at the bottom of a deep and narrow cavity whose surface is lined with rings of aromatic residues while Tyr72 is almost perpendicular to the Trp286, which is responsible for stable π -π interactions. The complexation of AChE with Axillaridine-A, results in the reduction of gorge size due to interaction between the ligand and the active site residues. The gorge size was determined by the distance between the center of mass of Glu81 and Trp286. As far as the geometry of the active site is concerned, the presence of ligand in the active site alters its specific conformation, as revealed by stable hydrogen bondings established between amino acids. With the increasing interaction between ligand and the active amino acids, size of the active site of the complex decreases with respect to time. Axillaridine-A, forms stable π -π interactions with the aromatic ring of Tyr124 that results in inhibition of catalytic activity of the enzyme. This π -π interaction keeps the substrate stable at the edge of the catalytic gorge by inhibiting its catalytic activity. The MD results clearly provide an explanation for the binding pattern of bulky steroidal alkaloids at the active site of AChE.     

Molecular dynamics simulation of the gGAPDH–NAD+ complex from Trypanosoma cruzi

A 50-ns molecular dynamics simulation has been used to study the homotetramer of the enzyme glycosomal glyceraldehyde 3-phosphate dehydrogenase (gGAPDH) complexes, from Trypanosoma cruzi, with nicotinamide adenine dinucleotide (NAD⁺) cofactors in aqueous solution. The root mean square deviation indicates that the overall structure of the homotetramer does not undergo significant change. The largest structural change observed was in the NAD⁺ binding domain of subunit (chain) D; as a consequence, the NAD⁺ cofactor was dislocated from its initial position. However, the other subunits were not affected, suggesting that the gGAPDH enzyme exhibits non-cooperative behaviour. Our simulation estimates that the NAD⁺ binding domain rotates about 4.8° relative to the catalytic domain in the apo–holo form transition. The hydrogen bond analysis reveals that the residues R12, I13, D38 and M39 are essential for gGAPDH–NAD⁺ interaction. Furthermore, two promising cavities to be explored in drug design were found: one formed by residues I13, R12, T197, T199, E336 and Y339, and the other by residues C166, H194, R249, I13, R12, T197, T199, E336 and Y339. The results presented in this paper offer new insight into the search for inhibitors of the gGAPDH enzyme of T. cruzi protozoan.     

Molecular dynamics simulation of the graphene–water interface: comparing water models

In this work, different water models (i.e. SPC/E, TIP3P, TIP4P/2005, TIP5P, SPC/Fw, TIP4P/2005f and SWM4_DP) are implemented to simulate water on neutral, negatively charged and positively charged graphene. In all cases ambient conditions are considered. Structural and dynamical properties for water are calculated to quantify the differences among various water models. The results show that SPC/E, TIP4P/2005, SPC/Fw, TIP4P/2005f and SWM4_DP water models yield a similar structure for interfacial water on graphene, whether it is neutral, negatively charged or positively charged. TIP5P is the model whose predictions for the structure of the interface deviate the most from those of the other models. Although qualitatively the results are for the most part similar, a large quantitative variation is observed among the dynamical properties predicted when various water models are implemented. Although experimental data are not available to discriminate the most/least accurate of the model predictions, our results could be useful for comparing results for interfacial water obtained implementing different models. Such critical comparison will benefit practical applications such as the development of energy-storage and water-desalination devices (e.g. electric double-layer capacitors), among others.     

Molecular dynamics simulation approach for the prediction of transmembrane helix–helix heterodimers assembly

Computational methods are useful to identify favorable structures of transmembrane (TM) helix oligomers when experimental data are not available or when they cannot help to interpret helix-helix association. We report here a global search method using molecular dynamics (MD) simulations to predict the structures of transmembrane homo and heterodimers. The present approach is based only on sequence information without any experimental data and is first applied to glycophorin A to validate the protocol and to the HER2-HER3 heterodimer receptor. The method successfully reproduces the experimental structures of the TM domain of glycophorin A (GpA(TM)) with a root mean square deviation of 1.5 A. The search protocol identifies three energetically stable models of the TM domain of HER2-HER3 receptor with favorable helix-helix arrangement, including right-handed and left-handed coiled-coils. The predicted TM structures exhibit the GxxxG-like motif at the dimer interface which is presumed to drive receptor oligomerization. We demonstrate that native structures of TM domain can be predicted without quantitative experimental data. This search protocol could help to predict structures of the TM domain of HER heterodimer family.     

Molecular simulation of solid–solid phase transitions

Applications of dl_poly to solid–solid phase transitions are reviewed, with particular attention to how details of the mechanisms of the transitions may be extracted from molecular dynamics simulations. Two examples in molecular crystals are discussed: the order–disorder transition of p-terphenyl initiated at around 200 K by the unlocking of ring flipping; and the rotator phases of n-alkanes with around 20 carbon atoms per chain, showing distinct molecular mechanisms in the dynamics just below the melting points of odd and even chains. Covalent-ionic materials are represented by an application to an aluminophophate molecular sieve, AlPO₄-5.     

Molecular insight into activated sludge producing polyhydroxyalkanoates under aerobic–anaerobic conditions

One of the options enabling more economic production of polyhydroxyalkanoates compared to pure cultures is the application of mixed cultures. The use of a microbial community in a sequencing batch reactor has a few advantages: a simple process control, no necessity for sterile processing, and possibilities of using cheap substrates as a source of carbon. Nevertheless, while cultivation methods to achieve high PHAs biomass concentration and high productivity in wild and recombinant strains are defined, knowledge about the cultivation strategy for PHAs production by mixed culture and species composition of bacterial communities is still very limited. The main object of this study was to characterize on the molecular level the composition and activity of PHAs producing microorganism in activated sludge cultivated under oxygen limitation conditions. PHAs producers were detected using a PCR technique and the created PHA synthase gene library was analyzed by DNA sequencing. The obtained results indicate that PHAs-producers belonged to Pseudomonas sp., and possessed genes coding for mcl-PHA synthase. The kinetics of mcl-PHA synthase expression was relatively estimated using real-time PCR technology at several timepoints. Performed quantitative and qualitative analysis of total bacterial activity showed that there were differences in total activity during the process but differential expression of various groups of microorganisms examined by using DGGE was not observed.     

Molecular dynamics simulation of six β-blocker drugs passing across POPC bilayer

Six selected β-blocker drugs (alprenolol, atenolol, metoprolol, nadolol, pindolol and propranolol) passing across 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer were studied using all-atom molecular dynamics simulation. The free energy profiles can be divided into two groups, according to their shapes: the free energy curve of group one (atenolol, nadolol and pindolol) has an obvious minimum while that of the other group (propranolol, metoprolol and alprenolol) is flat inside membrane. Energy analysis shows that electrostatic interaction plays an important role for the first group drugs. The hydrogen bond analysis results also certify that the first group drugs form more hydrogen bonds than the other β-blockers. The calculated permeability sequence agrees with the experimental ones. Our calculation suggests that the permeability model using potential of mean force (PMF) method can be also applied to chemically similar compounds besides chemically diverse compounds.     

Fate and dynamics of recently fixed C in pasture plant–soil system under field conditions

The flow of photosynthetically fixed C from plants to selected soil C pools was studied after ¹³CO₂ pulse labeling of pasture plants under field conditions, dynamics of root-derived C in soil was assessed and turnover times of the soil C pools were estimated. The transport of the fixed C from shoots to the roots and into the soil was very fast. During 27 h, net C belowground allocation reached more than 10% of the fixed C and most of the C was already found in soil. Soil microbial biomass (C_MIC) was the major sink of the fixed C within soil C pools (ca 40–70% of soil ¹³C depending on sampling time). Significant amounts of ¹³C were also found in other labile soil C pools connected with microbial activity, in soluble organic C and C associated with microbial biomass (hot-water extract from the soil residue after chloroform fumigation-extraction) and the ¹³C dynamics of all these pools followed that of the shoots. When the labelling (2 h) finished, the fixed ¹³C was exponentially lost from the plant–soil system. The loss had two phases; the first rapid phase corresponded to the immediate respiration of ¹³C during the first 24 h and the second slower loss was attributable to the turnover of ¹³C assimilated in C_MIC. The corresponding turnover times for C_MIC were 1.1 days and 3.4 days respectively. Such short turnover times are comparable to those measured by growth kinetics after the substrate amendment in other studies, which indicates that microbial growth in the rhizosphere is probably not limited by substrate availability. Our results further confirmed the main role of the soil microbial community in the transformation of recently fixed C, short turnover time of the easily degradable C in the rhizosphere, and its negligible contribution to more stable soil C storage.     

Investigating the effects of wettability and gaseous nanobubbles on roughened wall–fluid interface using molecular dynamics simulation

This paper reports on the use of molecular dynamics (MD) simulation to investigate the coupling effects of wettability, surface roughness and interfacial nanobubbles (INBs) on wall–fluid interfaces. The fluid properties close to the wall–fluid interface, such as potential energy, density, diffusion coefficients of fluid molecules and effective slip length are simulated. In the cases without surface nanobubbles, regions with lower potential energy have a higher probability of hosting water molecules. The local translational and rotational diffusion coefficients of water within the cavities are strongly influenced by wettability but largely unaffected by hydrodynamic effects. In cases where INBs exist, variations in wettability result in distinctly different argon morphologies. Argon nanobubbles form a convex shape on Wenzel-like interfaces but a shallow concave shape on Cassie-like interfaces. The phenomenon of water molecules invading grooves tends to occur on Wenzel-like interfaces; however, this depends largely on the morphology of the grooves. The high mobility and high density of argon molecules indicate that the state of the argon molecules within the grooves may require further investigation. Our results also show that the effective slip length is significantly influenced by wall–fluid wettability as well as the morphology of INBs.     

Molecular dynamics simulation of α-melanocyte stimulating hormone in a water-membrane model interface

The conformation of the tridecapeptide α-melanocyte stimulating hormone in the presence of a double water-membrane interface was studied by molecular dynamics simulation, using the computational package THOR. In this program the solvent is represented by a continuous medium with dielectric constant ɛ, and the interface between different media is simulated by a surface of discontinuity of the dielectric constant. The electrostatic image method was used to write down the terms, added to the force field, that describe the polarisation effects induced in the interface by the atomic charges. The program was further improved by the introduction of a second surface, parallel to the first one, to mimic the membrane. A conformational search using the software Prelude was employed to find an initial geometry for the peptide in water. The molecular dynamics simulation performed during 10 ns showed that the peptide structure is flexible in water, without stabilisation of any preferential conformation. In the presence of the model membrane, the peptide moved to the medium representing the interior of the membrane. Inside the low dielectric constant medium, the structure of the peptide showed a turn in the central sequence of amino acids and a packed conformation remained stabilised during more than 7.0 ns of simulation. Received: 27 November 1998 / Revised version: 11 March 1999 / Accepted: 8 April 1999     

Quantum chemical molecular dynamics simulation of carbon nanotube–graphene fusion

Abstract

Here we report a quantum mechanical molecular dynamics (QM/MD) study of a fusion process of an open-ended carbon nanotube on a graphene hole, which results in the formation of a so-called pillared graphene structure – a three-dimensional nanomaterial consisting entirely of sp²-carbons. The self-consistent-charge density-functional tight-binding potential was adopted in this study. Two different sizes of graphene holes with 12 or 24 central carbon atoms removed from a graphene flake, and a (6,6) carbon nanotube with a compatible diameter were adopted. Formations of 6–7–6/5–8–5 defect structures were found on the fusion border between tube and graphene hole. The 6–7–6 structure was found to bear less curvature-induced strain energy and therefore to be more stable and much easier to form than the 5–8–5 structure.     

Molecular dynamics simulation integrating the inhibition kinetics of hydroxysafflor yellow A on α-glucosidase

Inhibition of α-glucosidase has attracted the attention of researchers due to its connection to type-2 diabetes. Hydroxysafflor yellow A (HSYA) extracted from Carthamus tinctorius L. is a natural antioxidant used in traditional Chinese medicine. In this study, the effect of HSYA on α-glucosidase was evaluated using inhibitory kinetics based on the antioxidant properties of HSYA and by performing computational simulation integration methods. HSYA reversibly inhibited α-glucosidase in a competitive inhibition manner and the evaluated kinetic parameters were IC₅₀ = 1.1 ± 0.22 mM and K_i = 1.04 ± 0.23 mM, respectively. The results of spectrofluorimetry showed that the inner hydrophobic regions of α-glucosidase, which are mostly in the active site, were exposed to the surface with increasing HSYA concentrations, indicating that the inactivation of α-glucosidase by HSYA was accompanied by regional unfolding. The molecular dynamics simulations indicated that the four rings of HSYA interact with four residues such as G217, A278, H279, and G280 at the entrance of the active site. Our study provides insight into the inhibition of α-glucosidase and the accompanying structural changes by HSYA. Based on its α-glucosidase-inhibiting effect and its potential as a natural antioxidant, HSYA is a potential agent for treating α-glucosidase-associated type-2 diabetes.