Molecular dynamics simulation of film size and vacancy defect effects on the thermal conductivities of argon thin films

It is well known that there is a size effect for the thermal conductivity of thin films and that vacancy defects in film reduce the film's thermal conduction. In this paper, the film size and vacancy defect effects on the thermal conductivities of argon thin films were studied by molecular dynamics simulations. The results show the existence of phonon boundary scattering. The results also confirm that the theoretical model based on the Boltzmann equation can accurately model the thermal conduction of thin argon films. Both the theoretical and MD results illustrate that, although, both the defect and the thickness of the thin film deduce the thermal conductivity, their physical mechanisms differ.     

Non-equilibrium molecular dynamics study on radial thermal conductivity and thermal rectification of graphene

In the present study, the radial thermal rectification and thermal conductivity of the graphene were investigated by non-equilibrium molecular dynamics simulation and then corrected by quantum correction to make it closer to the fact. The Optimised three-body Tersoff potential is employed in order to simulate the interactions between the carbon atoms in the graphene sheet. A circular region in the centre and the one at the graphene edge are selected as hot and cold bath to generate radial temperature gradient. It is observed that the heat current passes through radially inward direction than outward with the same temperature gradient and hence there is a radial thermal rectification in graphene. Also, temperature distribution and heat flux are theoretically introduced as a function of distance from the graphene centre and then it is confirmed by the molecular dynamics simulation data. Finally, the influence of temperature gradient and size of graphene on radial thermal rectification and the impact of size on the radial thermal conductivity is investigated.     

Molecular dynamics study of the thermal conductivity of nanoscale argon films

Non-equilibrium molecular dynamics (MD) simulations were used to study the thermal conductivity of thin argon films. The MD simulations show that the argon film's thermal conductivity is affected by the thickness up to thickness of about 100 nm, which agrees with theoretical estimates. The results show that the MD method is very effective for modeling nanoscale thermal conduction. Besides pure argon films, the effect of vacancies on the argon film's thermal conductivity was also studied. The vacancies greatly reduce the thermal conductivity as a function of the vacancy concentration but not as a function of the vacancy distribution when the film's temperature is constant.     

The effect of alumina nanoparticles on the thermal properties of PMMA: a molecular dynamics simulation

Metal oxides, as one of the most promising flame retardant additives, improve the fire retardant and the thermal stability properties of polymers. In the present study, molecular dynamics (MD) simulations based on the united atom model were applied to study the effect of alumina nanoparticles on the density, thermal conductivity, heat capacity, and thermal diffusivity of isotactic poly(methyl methacrylate) (is-PMMA). Thermal diffusivity of PMMA and PMMA/alumina nanocomposite were investigated through calculating thermal conductivity, density and heat capacity in the range of 300–700?K. Heat capacity can be calculated using fluctuations properties of energy. Thermal conductivity was calculated through the nonequilibrium molecular dynamics (NEMD) simulation by Fourier’s law approach. Our results show that the addition of alumina nanoparticles decreases the heat capacity and increases the glass transition temperature (T_g), thermal conductivity and thermal diffusivity of the PMMA. Therefore, the addition of alumina nanoparticles to PMMA improves the fire retardancy of the polymer. In addition, we illustrate the links between the intermolecular and bulk properties of PMMA in the presence of the alumina nanoparticles.     

Molecular dynamics studies in nanoscale liquid structures: geometry and thermal effects on nanojet development

Conventional macroscopic jet theory relies heavily on experimental correlations which cannot be easily extended to the nanoscale regime. Moreover, the fluid dynamic effects at small length scales and their contribution to the development of nanoscale liquid structures are fundamentally different from their macroscopic counterparts. This coupled with the high spatial and temporal resolution requirements at nanoscale domains make molecular dynamics (MD) an excellent tool for studying such structures. In this study, the formation and breakup of nanojets (NJs) developing from high pressure into vacuum is investigated using MD based on non-Hamiltonian formulations. By ejecting the equilibrated argon atoms through various nozzle geometries and diameters, nanoscale jet flows were generated. The dependence of the jet structure on nozzle geometry and diameter is studied. The influence of geometry on NJ formation is also studied along with issues involved in the equilibration and thermostat coupling parameter. Various thermostats are compared to understand the role they play in MD simulations of liquid nanostructures. Tuning of the thermostat coupling parameter has also been discussed. The jet breakup phenomenon is analysed and a comparative study, vis-à-vis, well-established continuum and stochastic models, is attempted.     

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 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 simulations of heat conduction in multi-walled carbon nanotubes

Heat conduction in multi-walled carbon nanotubes (MWNTs) was studied using non-equilibrium molecular dynamics simulations. This research focuses on the effects of the multi-wall structure of the MWNTs on the heat conduction. The results show that the thermal conductivity of a MWNT is almost the same as that of the corresponding single-walled carbon nanotubes (SWNTs) rather than much smaller as has been suggested. Thus, the multi-wall structure does not significantly affect the thermal conduction in the MWNTs. Analysis of the temperature profiles and the phonon density of states confirms that there is almost no heat transport between the MWNT layers and that each layer conducts heat nearly independently along parallel channels. This is physically reasonable since the weak inter-wall interactions and large interfacial thermal resistances make the MWNT layers behave like parallel thermal circuits.     

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 simulations of the thermal stability of tteRBP and ecRBP

Molecular dynamics simulations were performed for investigating the thermal stability of the extremely thermophilic Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) and the mesophilic homologous Escherichia coli ribose binding protein (ecRBP). The simulations for the two proteins were carried out under the room temperature (300?K) and the optimal activity temperature (tteRBP 375?K and ecRBP 329?K), respectively. The comparative analyses of the trajectories show that the two proteins have stable overall structures at the two temperatures; further analyses indicate that they both have strong side-chain interactions and different backbone flexibilities at the different temperatures. The tteRBP 375?K and ecRBP 329?K have stronger internal motion and higher flexibility than tteRBP 300?K and ecRBP 300?K, respectively, it is noted that the flexibility of tteRBP is much higher than that of ecRBP at the two temperatures. Therefore, tteRBP 375?K can adapt to high temperature due to its higher flexibility of backbone. Combining with the researches by Cuneo et al., it is concluded that the side-chain interactions and flexibility of backbone are both the key factors to maintain thermal stability of the two proteins.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:22     

Molecular dynamics simulation of single-walled carbon nanotubes inside liquid crystals

Molecular dynamic simulations of systems of single-walled carbon nanotubes (CNTs) in liquid crystalline solvents were performed, in order to investigate the effect of the molecular structure and phase of the liquid crystal (LC) on the interactions between the CNTs. Three different LC molecules (5CB, 8CB and 5CF) were considered in our study. Our results with 5CB and 8CB suggest that increasing the chain length of the hydrophobic part of the LC molecule by three carbon atoms is insufficient to decrease the tendency for the CNTs to aggregate in the LCs. Additionally, varying the phase of the LC is also insufficient to decrease the aggregation tendency of the CNTs. However, simulations with 5CF (which has fluorine atoms in the head group of the LC molecule) suggest that this LC solvent can decrease the tendency of the CNTs to aggregate. This study is relevant to assist experimentalists with the development of high-quality dispersions of large concentrations of CNTs in the LCs.     

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 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 dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change

The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40 ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10 ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins.     

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 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 simulation of a human thiopurine S-methyltransferase complexed with 6-mercaptopurine model

Human thiopurine S-methyltransferase (TPMT) is an essential protein in 6-mercaptopurine (6MP) drug metabolism. To understand thepharmacogenetics of TPMT and 6MP, X-ray co-crystal structures of TPMT complexes with S-adenosyl-L-methionine (AdoMet) and 6MPare required. However, the co-crystal structure of this complex has not been reported because 6MP is poorly water soluble. We usedmolecular dynamics (MD) simulation to predict the structure of the complex of human TPMT-AdoHcy(CH₂)6MP, where the sulfur atoms ofAdoHcy and 6MP were linked by a CH₂ group. After 1300 picoseconds of MD simulation, the trajectory showed that 6MP was stabilized inthe TPMT active site by formation of non-bonded interactions between 6MP and Phe40, Pro196 and Arg226 side chains of TPMT. Theintersulfur distance between AdoHcy and 6MP as well as the binding modes and the interactions of our TPMT-AdoHcy model areconsistent with those observed in the X-ray crystal structure of murine TPMT-AdoHcy-6MP complex. The predicted binding modes ofAdoHcy and 6MP in our model are consistent with those observed in murine TPMT X-ray crystal structures, which provides structuralinsights into the interactions of TPMT, AdoHcy, and 6MP at the atomic level and may be used as a starting point for further study ofthiopurine drug pharmacogenetics.     

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 chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity

Abstract

The fungal chitinase I obtained from Thermomyces lanuginosus SSBP, a thermophilic deuteromycete, has an optimum growth temperature and pH of 323.15 K and 6.5, respectively. This enzyme plays an important task in the defence mechanism of organisms against chitin-containing parasites by hydrolysing β-1, 4-linkages in chitin. It acts as both anti-fungal and biofouling agents, with some being thermostable and suitable for the industrial applications. Three-dimensional model of chitinase I enzyme was predicted and analysed using various bioinformatics tools. The structure of chitinase I exhibited a well-defined TIM barrel topology with an eight-stranded α/β domain. Structural analysis and folding studies at temperatures ranging from 300 to 375 K using 10 ns molecular dynamics simulations clearly showed the stability of the protein was evenly distributed even at higher temperatures, in accordance with the experimental results. We also carried out a number of 20 ns constant pH molecular dynamics simulations of chitinase I at a pH range 2–6 in a solvent. This work was aimed at establishing the optimum activity and stability profiles of chitinase I. We observed a strong conformational pH dependence of chitinase I and the enzyme retained their characteristic TIM barrel topology at low pH.