Investigation of moisture diffusion in cross-linked epoxy moulding compound by molecular dynamics simulation

Molecular dynamics (MD) simulation was carried out to study the moisture diffusion in cross-linked epoxy resin, with the influence of temperature, water concentration and polymer conversion taken into account. The simulation results showed that the moisture diffusion coefficients increased with the increase in temperature. And generally, with the increased moisture concentration or decreased polymer conversion, the moisture diffusion coefficients reduced. However, the moisture diffusion was strongly inhibited when the number of epoxy groups in completely reacted epoxy resins was equal to the number of water molecules.     

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.     

Molecular dynamics simulation of intrinsically disordered proteins

Intrinsically disordered proteins are biomolecules that do not have a definite 3D structure; therefore, their dynamical simulation cannot start from a known list of atomistic positions, such as a Protein Data Bank file. We describe a method to start a computer simulation of these proteins. The first step of the procedure is the creation of a multi-rod configuration of the molecule, derived from its primary sequence. This structure is dynamically evolved in vacuo until its gyration radius reaches the experimental average value; at this point solvent molecules, in explicit or implicit implementation, are added to the protein and a regular molecular dynamics simulation follows. We have applied this procedure to the simulation of tau, one of the largest totally disordered proteins.     

Molecular dynamics investigation of nitric oxide (II) interaction with a model biological membrane

Nitric oxide (II) diffusion through a model two-component (phosphatidylcholine and phosphatidylethanolamine molecules) biological membrane is investigated using the molecular dynamics method. It is shown that NO molecules are rotating in the process of diffusion into the phospholipid bilayer. The calculated diffusion coefficient D[NO] = 0.35 (±0.23) × 10^?5 (cm²/s) is in a good agreement with literature data. This testifies that free diffusion of NO molecules may be a plausible mechanism of the NO permeation through the membranes.     

Molecular dynamics simulation of hydration in myoglobin

This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After solvation of the protein, energy minimization and equilibration of the system, 50 ps of Newtonian dynamics was performed. This data showed that only 4 water molecules are continously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water. © 1995 Wiley-Liss, Inc.     

Molecular dynamics simulation of interactions in glycolytic enzymes

Two glycolytic enzymes, phosphoglycerate mutase (PGM) and enolase from Saccharomyces cerevisiae, have been chosen to detect complex formation and possible channeling, using molecular dynamics simulation. The enzymes were separated by 10 angstroms distance and placed in a water-filled box of size 173 x 173 x 173 angstroms. Three different orientations have been investigated. The two initial 3-phosphoglycerate substrate molecules near the active centers of the initial structure of PGM have been replaced with final product (2-phosphoglycerate) molecules, and 150 mM NaCl together with three Mg2+ ions have been added to the system to observe post-catalytic activity under near-physiological conditions. Analysis of interaction energies and conformation changes for 3 nsec simulation indicates that PGM and enolase do show binding affinity between their near active regions, which is necessary for channeling to occur. Interaction of the C-terminal residues Ala239 and Val240 of PGM (which partially "cap" the 2-phosphoglycerate) with enolase also favors the existence of channeling.     

Molecular dynamics simulation of self-assembled nanocubes in methanol

Molecular dynamics simulations were performed for the hexameric nanocubes of methylated (1₆) and demethylated (2₆) gear-shaped amphiphiles in pure methanol to reveal the difference in structural fluctuation between 1₆ and 2₆. Within our simulation time of 2.0 ns, the cubic structure of 1₆ in methanol is maintained, whereas that of 2₆ is collapsed. We found that the triple π-stacking moieties consisting of the three 3-pyridyl groups in 2₆ are more fluctuated than those in 1₆. This suggests that methyl groups serve to reduce structural fluctuation for nanocubes. We also found that the existence of the solvent molecules near the nanocube is an important factor for the collapse of the 2₆ structure.     

Molecular dynamics simulation,binding free energy calculation and molecular docking of human D-amino acid oxidase (DAAO) with its inhibitors

Schizophrenia is a mental illness; most affected people live in developing countries, and neither appropriate treatment nor commercial drugs are currently available. One possibility is to inhibit human-d-amino acid oxidase (h-DAAO). In this study, molecular dynamic simulations of the monomer, dimer and tetramer forms of h-DAAO complexed with the inhibitor 3-hydroxyquinolin-2(1H)-one(2) were performed. Seven residues, Leu51, Gln53, Leu215, Tyr228, Ile230, Arg283 and Gly313, were identified as essential for interacting with the inhibitor. Molecular docking of h-DAAO with pyrrole, quinoline and kojic acid derivatives, representing 69 known or potential h-DAAO inhibitors, was also performed. The results indicated that the activity of the inhibitor can be improved by modifying the compounds to have a substituent group capable of interacting with the side chain of Tyr228. Van der Waals interactions of the inhibitor with the hydrophobic pocket of h-DAAO and electrostatic interactions or H-bonds with Arg283 and Gly313 were important elements in determining the efficiency of the inhibitor. These results provide information on the interaction between h-DAAO and its inhibitors at the molecular level and can aid in the design of novel inhibitors against h-DAAO for new drug development in the treatment of schizophrenia.     

Molecular dynamics simulation of the Al2O3 film structure during atomic layer deposition

Based on an understanding of atomic layer deposition (ALD) from prior experimental and computational results, all-atom molecular dynamics (MD) simulations are used to model the Al₂O₃ film structure and composition during ALD processing. By separating the large time-scale surface reactions from the small time-scale structural relaxation, we have focused on the growth dynamics of amorphous Al₂O₃ films at the atomic scale. The simulations are able to reproduce some important properties and growth mechanisms of Al₂O₃ ALD films, and hence provide a bridge between atomic-level information and experimental measurements. Information about the evolution of the microscopic structures of the Al₂O₃ films is generated, and the influence of operation parameters on the Al₂O₃ ALD process. The simulations predict a strong influence of the initial surface composition and process temperature on the surface roughness, growth rate and growth mode of the deposited films.     

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.     

Transport diffusivities of fluids in nanopores by non-equilibrium molecular dynamics simulation

We present a method to study fluid transport through nanoporous materials using highly efficient non-equilibrium molecular dynamics simulations. A steady flow is induced by applying an external field to the fluid particles within a small slab of the simulation cell. The external field generates a density gradient between both sides of the porous material, which in turn triggers a convective flux through the porous medium. The heat dissipated by the fluid flow is released by a Gaussian thermostat applied to the wall particles. This method is effective for studying diffusivities in a slit pore as well as more natural, complex wall geometries. The dependence of the diffusive flux on the external field sheds light on the transport diffusivities and allows a direct calculation of effective diffusivities. Both pore and fluid particle interactions are represented by coarse-grained molecular models in order to present a proof-of-concept and to retain computational efficiency in the simulations. The application of the method is demonstrated in two different scenarios, namely the effective mass transport through a slit pore and the calculation of the effective self-diffusion through this system. The method allows for a distinction between diffusive and convective contributions of the mass transport.     

Molecular dynamics simulation of methane hydrate dissociation by depressurisation

Methane (CH₄) hydrate dissociation and the mechanism by depressurisation are investigated by molecular dynamics (MD) simulation. The hydrate decomposition processes are studied by the ‘vacuum removal method’ and the normal method. It is found that the hydrate decomposition is promoted by depressurisation. The quasi-liquid layer is formed in the hydrate surface layer. The driving force of dissociation is found to be controlled by the concentration gradient between the H₂O molecules of the hydrate surface layer and the H₂O molecules of the hydrate inner layer. The clathrates collapse gradually, and the hydrate decomposes layer by layer. Relative to our previous MD simulation results, this study shows that the rate of the hydrate dissociation by depressurisation is slower than that by the thermal stimulation and the inhibitor injection. This study illustrated that MD simulation can play a significant role in investigating the hydrate decomposition mechanisms.     

Molecular dynamics simulation of isothermal crystallisation of polymer chains around single polymer lamella

The isothermal crystallisation of polyethylene (PE) chains around single PE lamella in vacuum is investigated by molecular dynamic simulation. The crystallisation process is analysed in terms of the orientational order parameters, principal moments of inertia for the simulated systems. The effects of charge interactions between the polymer chains and lamella are discussed. It is found that the crystallisation process for uncharged systems can be divided into three stages: (1) adsorption, (2) orientation and (3) arrangement. The single polymer lamella changes a little during the three stages. PE chains are arranged parallel to the chain direction of the stems in the crystalline state. When considering the effect of charge interactions between the polymer chains and lamella, a different crystallisation process appears. The single polymer lamella is affected by the charged polymer chains.     

Molecular dynamics simulation of lactate dehydrogenase adsorption onto pristine and carboxylic-functionalized graphene

ABSTRACT

Lactate dehydrogenase (LDH) is a tetrameric enzyme which is composed of two subunits known as LDHA and LDHB, which are encoded by the LDHA and LDHB genes respectively. LDH catalyses the last step in anaerobic glycolysis through the reversible conversion of pyruvate to lactate via coupled oxidation of NADH cofactor. The LDHA plays an important regulatory role in anaerobic glycolysis, by catalysing the final step of the process. Therefore, it is likely that increases in the expression level of LDHA in cancer cells could facilitate the efficiency of anaerobic glycolysis. Measuring the level of serum LDHA is a key step in the diagnosis of many cancer types. In this study, the adsorption, stability, and dynamics of LDHA on the surface of pristine graphene (PG) and carboxylated graphene (COOH-Graphene) were investigated using its molecular dynamics simulation. Variations in root mean square deviation, root mean square fluctuation, solvent accessible surface area and adsorption energy of the LDHA during the simulation were calculated to analyse the effect of PG and COOH-Graphene on the overall conformation of LDHA. Results showed that the adsorption of LDHA on COOH-Graphene is mostly mediated by electrostatic interactions, whereas on the PG, both Van der Waals and π-π interactions are prominent.     

Molecular dynamics simulation of hydrated d(CGGGTACCCG)4 as a four-way DNA Holliday junction and comparison with the crystallographic structure

Molecular dynamics (MD) simulation of decamer sequence (CGGGTACCCG)₄ as a four-way Holliday junction is reported here for 15.0 ns at three different temperatures 100, 200 and 300 K, respectively, using AMBER force field. Particle mesh Ewald method has been utilised to deal long-range interaction potentials. After MD simulation, various parameters of the junction model including backbone and helical parameters have been worked out and the dynamical pathway is discussed. Structural analysis and geometrical calculations were carried out through X3DNA. The computational results obtained are compared with the previously reported crystallographic outcomes. The width and depth of the major and minor grooves of the duplex of the four arms of the DNA junction have been calculated. The variations in the C1′–C1′ distances between the two complementary strands are discussed in detail. A close observation of the results reveals that the conformation of the average simulated structure at low temperature is of ‘B’ form and the structural integrity of the DNA junction having a twofold sequence symmetry is temperature dependent. It also seems that besides the other parameters (i.e. presence of ions, solvents, etc.), temperature may be playing a key role in preserving the structural integrity of the DNA junction.     

Molecular dynamics simulation of primary detonation process of TATB crystal under shock loading

Molecular dynamics simulations were performed to gain fundamental insights into the mechanisms for the primary detonation process of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under shock wave loading using self-consistent charge density-functional tight binding(SCC-DFTB) calculations combined with the multiscale shock technique (MSST). The primary process starts with shock loading and ends with the formation of dynamically stable heterocyclic clusters, which could inhibit the reactivity of TATB. The results show that the initial step of shocked TATB decomposition is the N–O bond cleavage; then carbon rings aggregate and connect by N atoms to form clusters; after the carbon rings open, heterocyclic clusters with nitrogen are formed, and persist throughout the simulation. This is a new mechanism for the primary processes of shocked TATB and this initiation mechanism is independent of the initial shock speeds.     

Molecular dynamics simulation of thermal conductivity of an argon liquid layer confined in nanospace

Molecular dynamics simulations were used to study the thermal conductivity of liquid argon ultra thin films confined between two plates spaced several nanometres apart. The research focused on the dependence of the liquid argon thermal conductivity on the liquid layer thickness and the interaction between liquid and solid. The results show that the thermal conductivity of liquid argon ultra thin films confined between two plates depends on the distance between the two plates and the existence of solid-like liquid layering at the liquid–solid interface and the average migration frequency of all liquid molecules. Stronger interactions between the liquid and the solid resulted in a larger number of atoms in the solid-like liquid layer along the surface and hence smaller thermal resistance between the liquid and the solid. However, as the strength of the interaction with the solid increased, the thermal conductivity was reduced due to fewer atoms near the hot solid boundary and less molecular migration.     

Molecular dynamics simulation of the docking of substrates to proteins

A simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using transrational temperatures of the substrate in the range of 1300–1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search (“helicopter view”) is obtained, which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed. © 1994 Wiley-Liss, Inc.     

Molecular dynamics simulation of content of bound water in ethylene glycol and glycerol solution

In this paper, the content of bound water was studied to evaluate the cryoprotective properties of ethylene glycol and glycerol solution. Molecular dynamic models for the solution were built, the classification principle and statistical methods of water molecules in solutions were presented, respectively. The content of bound water with various hydroxyl molarity at different temperatures was obtained through molecular dynamic simulation. The results reveal that the content of bound water increases with increasing hydroxyl molarity, but decreases with increasing temperature. It was found that, the content of bound water in ethylene glycol solution is always slightly more than that in glycerol solution, regardless of whether the temperature increases or not.