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.     

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.     

Influence of doped nitrogen and vacancy defects on the thermal conductivity of graphene nanoribbons

A systematic investigation of the thermal conductivity of zigzag graphene nanoribbons (ZGNRs) doped with nitrogen and containing a vacancy defect was performed using reverse nonequilibrium molecular dynamics (RNEMD). The investigation showed that the thermal conductivity of the ZGNRs was significantly reduced by nitrogen doping. The thermal conductivity dropped rapidly when the nitrogen doping concentration was low. Also, the presence of a vacancy defect was found to significantly decrease the thermal conductivity. Initially, as the vacancy moved from the heat sink to the heat source, the phonon frequency and the phonon energy increased, and the thermal conductivity decreased. When the distance between the vacancy in the ZGNR and the edge of the heat sink reached 2.214 nm, tunneling began to occur, allowing high-frequency phonons to pass through the vacancies and transfer some energy. The curve of the thermal conductivity of the ZGNRs versus the vacancy position was found to be pan-shaped, with the thermal conductivity of the ZGNRs controlled by the phonon. These findings could be useful when attempting to control heat transfer on the nanoscale using GNR-based thermal devices.     

Non-equilibrium molecular dynamics study of nanoscale thermal contact resistance

Interfaces play an important role in microscale and nanoscale heat transfer processes with molecular dynamics (MD) simulations often used to study these interfacial phenomena. In this study, two models were used to simulate thermal conduction across micro contact points and the thermal contact resistance using non-equilibrium molecular dynamics simulations with consideration of the near field radiation. When the ratio of the length of the micro contact to the length of the conduction region is less than 0.125, the influence of the near field radiation should be considered; but when the ratio is larger than 0.2, it can be neglected. When the computational domain sizes are 8.50 × 10.62 × 8.50 nm and 10.62 × 10.62 × 10.62 nm, the MD results show that the thermal contact resistance exponentially increases with decreasing area of the micro contact point and increases with increasing micro contact layer thickness. The MD thermal contact resistances in nanoscale are much larger than that of the classical thermal analysis since the material thermal conductivity reduction is ignored in the classical model. The results also show that material defects increase the thermal resistance.     

The surface of evaporated carbon films is an insulating, high-bandgap material

The electrical conductance and the optical density of evaporated carbon films are measured as a function of the thickness of the films. The resulting data show that up to a thickness of approximately 4 nm, carbon films are optically transparent and electrically insulating. The same data also suggest that this insulating character persists near to the surface when the overall thickness is further increased. Since a support film with poor surface conductivity is undesirable for many applications in electron microscopy, we suggest that the usefulness of evaporated carbon films in electron microscopy might be further improved by doping or by other methods that improve the electrical conductivity near the surface.     

A molecular dynamics simulation on the effect of different parameters on thermal resistance of graphene-argon interface

Molecular dynamics simulations of argon molecules confined between two parallel graphene sheets are carried out to investigate the parameters affecting heat transfer and thermal properties. These parameters include wall–fluid interaction strength, fluid density and wall temperature. For constant wall temperature simulations, we show that the first two parameters have influence on near-wall fluid density. As a result, the heat transfer at wall–fluid interfaces and thus through argon molecules across the domain will change. Also, we demonstrate that variations in wall temperature rarely affects the density profiles of argon molecules next to the walls. Therefore, in these cases, the variations in thermal resistance at the interface is most dominantly due to wall temperature itself. To analyse the results, the density and temperature profiles and also other parameters including heat flux and temperature gradient of bulk of argon molecules, Kapitza length and argon thermal conductivity are considered. The Kapitza length describes thermal resistance at liquid–solid interface. According to the results, increasing wall–fluid interaction strength leads to greater molecular aggregation of argon molecules near the walls and, consequently, decreasing the Kapitza length. Furthermore, higher fluid density leads to greater thermal resistance at wall–fluid interactions and therefore greater temperature jumps are observed in temperature profiles.     

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.     

High Thermoelectric Performance in p‐type Polycrystalline Cd‐doped SnSe Achieved by a Combination of Cation Vacancies and Localized Lattice Engineering

Herein, a high figure of merit (ZT) of ≈1.7 at 823 K is reported in p‐type polycrystalline Cd‐doped SnSe by combining cation vacancies and localized‐lattice engineering. It is observed that the introduction of Cd atoms in SnSe lattice induce Sn vacancies, which act as p‐type dopants. A combination of facile solvothermal synthesis and fast spark plasma sintering technique boosts the Sn vacancy to a high level of ≈2.9%, which results in an optimum hole concentration of ≈2.6 × 10¹⁹ cm^?3 and an improved power factor of ≈6.9 µW cm^?1 K^?2. Simultaneously, a low thermal conductivity of ≈0.33 W m^?1 K^?1 is achieved by effective phonon scattering at localized crystal imperfections, as observed by detailed structural characterizations. Density functional theory calculations reveal that the role of Cd atoms in the SnSe lattice is to reduce the formation energy of Sn vacancies, which in turn lower the Fermi level down into the valence bands, generating holes. This work explores the fundamental Cd‐doping mechanisms at the nanoscale in a SnSe matrix and demonstrates vacancy and localized‐lattice engineering as an effective approach to boosting thermoelectric performance. The work provides an avenue in achieving high‐performance thermoelectric properties of materials.     

Molecular dynamics simulations of thermal expansion properties of single layer graphene sheets

The area coefficients of thermal expansion (CTEs) of perfect single layer graphene sheet (SLGS) and SLGS with vacancy defects of different distributions were calculated in this work through molecular dynamics (MD) simulations. The effects of some parameters such as temperature, SLGS size, sample area size, vacancy fraction and vacancy distribution on CTE were investigated extensively. Numerical results clearly revealed that for both perfect and defective SLGSs, the area CTEs are negative and nonlinear with the temperature variation within a wide temperature range. Moreover, the area CTEs tend to be more insensitive to the temperature when temperature is higher than 600 K. The area CTE of a perfect SLGS converges only when the SLGS size and the ratio of the sample size to the SLGS size is above a critical value. When the SLGS size or the sample size is small, the area CTE shows distinct size-dependence. In addition, a set of empirical formulations is proposed for evaluating the area CTEs of perfect SLGSs within a wide temperature range. For the SLGS with vacancy defects, the area CTE decreases with the increase of vacancy fraction within the temperature range considered. Furthermore, compared with a decentralised distribution of vacancy defects, a concentrated distribution leads to a smaller value of area CTE of SLGS, especially for the case of high vacancy fraction.     

Controlling Hierarchy in Solution‐processed Polymer Solar Cells Based on Crosslinked P3HT

Understanding and controlling the morphology of donor/acceptor blends is critical for the development of solution processable organic solar cells. By crosslinking a poly(3‐n‐hexylthiophene‐2,5‐diyl) (P3HT) film we have been able to spin‐coat [6,6]‐phenyl‐C₆₁‐butyric acid methyl ester (PCBM) onto the film to form a structure that is close to a bilayer, thus creating an ideal platform for investigating interdiffusion in this model system. Neutron reflectometry (NR) demonstrates that without any thermal treatment a smaller amount of PCBM percolates throughout the crosslinked P3HT when compared to a non‐crosslinked P3HT film. Using time‐resolved NR we also show thermal annealing increases the rate of diffusion, resulting in a near‐uniform distribution of PCBM throughout the polymer film. XPS measurements confirm the presence of both P3HT and PCBM at the annealed film's surface indicating that the two components are intermixed. Photovoltaic devices fabricated using this bilayer approach and suitable annealing conditions yielded comparable power conversion efficiencies to bulk heterojunction devices made from the same materials. The crosslinking procedure has also enabled the formation of patterned P3HT films by photolithography. Pillars with feature sizes down to 2 μm were produced and after subsequent deposition of PCBM and thermal annealing devices with efficiencies of up to 1.4% were produced.     

Harvesting graphics power for MD simulations

We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a congruential shift random number generator are presented. The performance of the GPU's is compared to their main processor counterpart. We achieve speedups of up to 40, 80 and 150 fold, respectively. With the latest generation of GPU's one can run standard MD simulations at 10⁷ flops/$.     

Refilling Nitrogen to Oxygen Vacancies in Ultrafine Tungsten Oxide Clusters for Superior Lithium Storage

Morphological engineering of nanosized transitional metal oxides shows great promise for performance improvement, yet limited efforts have been attempted to engineer the atomic structure. Oxygen vacancy (V_O) can boost charge transfer leading to enhanced performance; yet excessive V_O may impair the conductivity. Herein, tungsten oxide is atomically tailored by incorporating nitrogen heteroatoms into the oxygen vacancies. The efficient nitrogen‐filling into the oxygen vacancies is evidenced by the electron paramagnetic resonance spectroscopy and X‐ray absorption spectroscopy. The coordinated N atoms play a crucial role in facilitating the charge transfer and maintaining efficient lithium‐ion diffusion. Consequently, the tungsten oxide with N‐filled oxygen vacancies exhibits superior lithium‐ion storage performance.     

Coupled intra- and interdomain dynamics support domain cross-talk in Pin1

The functional mechanisms of multidomain proteins often exploit interdomain interactions, or “cross-talk.” An example is human Pin1, an essential mitotic regulator consisting of a Trp–Trp (WW) domain flexibly tethered to a peptidyl-prolyl isomerase (PPIase) domain, resulting in interdomain interactions important for Pin1 function. Substrate binding to the WW domain alters its transient contacts with the PPIase domain via means that are only partially understood. Accordingly, we have investigated Pin1 interdomain interactions using NMR paramagnetic relaxation enhancement (PRE) and molecular dynamics (MD) simulations. The PREs show that apo-Pin1 samples interdomain contacts beyond the range suggested by previous structural studies. They further show that substrate binding to the WW domain simultaneously alters interdomain separation and the internal conformation of the WW domain. A 4.5-μs all-atom MD simulation of apo-Pin1 suggests that the fluctuations of interdomain distances are correlated with fluctuations of WW domain interresidue contacts involved in substrate binding. Thus, the interdomain/WW domain conformations sampled by apo-Pin1 may already include a range of conformations appropriate for binding Pin1''s numerous substrates. The proposed coupling between intra-/interdomain conformational fluctuations is a consequence of the dynamic modular architecture of Pin1. Such modular architecture is common among cell-cycle proteins; thus, the WW–PPIase domain cross-talk mechanisms of Pin1 may be relevant for their mechanisms as well.     

Conformational dynamics of α-1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP

α-1 acid glycoprotein (AGP) is one of the most abundant plasma proteins. It fulfills two important functions: immunomodulation, and binding to various drugs and receptors. These different functions are closely associated and modulated via changes in glycosylation and cancer missense mutations. From a structural point of view, glycans alter the local biophysical properties of the protein leading to a diverse ligand-binding spectrum. However, glycans can typically not be observed in the resolved X-ray crystallography structure of AGP due to their high flexibility and microheterogeneity, so limiting our understanding of AGP's conformational dynamics 70 years after its discovery. We here investigate how mutations and glycosylation interfere with AGP's conformational dynamics changing its biophysical behavior, by using molecular dynamics (MD) simulations and sequence-based dynamics predictions. The MD trajectories show that glycosylation decreases the local backbone flexibility of AGP and increases the flexibility of distant regions through allosteric effects. We observe that mutations near the glycosylation site affect glycan's conformational preferences. Thus, we conclude that mutations control glycan dynamics which modulates the protein's backbone flexibility directly affecting its accessibility. These findings may assist in the drug design targeting AGP's glycosylation and mutations in cancer.     

Thermophysical Properties of Lignocellulose: A Cell-Scale Study Down to 41K

Thermal energy transport is of great importance in lignocellulose pyrolysis for biofuels. The thermophysical properties of lignocellulose significantly affect the overall properties of bio-composites and the related thermal transport. In this work, cell-scale lignocellulose (mono-layer plant cells) is prepared to characterize their thermal properties from room temperature down to ∼40 K. The thermal conductivities of cell-scale lignocellulose along different directions show a little anisotropy due to the cell structure anisotropy. It is found that with temperature going down, the volumetric specific heat of the lignocellulose shows a slower decreasing trend against temperature than microcrystalline cellulose, and its value is always higher than that of microcrystalline cellulose. The thermal conductivity of lignocellulose decreases with temperature from 243 K to 317 K due to increasing phonon-phonon scatterings. From 41 K to 243 K, the thermal conductivity rises with temperature and its change mainly depends on the heat capacity''s change.     

Integrating experimental data with molecular simulations to investigate RNA structural dynamics

Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule Förster resonance energy transfer, or even thermal or mechanical denaturation experiments probe RNA dynamics at different time and space resolutions. Their combination with accurate atomistic molecular dynamics (MD) simulations paves the way for quantitative and detailed studies of RNA dynamics. First, experiments provide a quantitative validation tool for MD simulations. Second, available data can be used to refine simulated structural ensembles to match experiments. Finally, comparison with experiments allows for improving MD force fields that are transferable to new systems for which data is not available. Here we review the recent literature and provide our perspective on this field.     

MD simulations reveal alternate conformations of the oxyanion hole in the Zika virus NS2B/NS3 protease

Recent crystallography studies have shown that the binding site oxyanion hole plays an important role in inhibitor binding, but can exist in two conformations (active/inactive). We have undertaken molecular dynamics (MD) calculations to better understand oxyanion hole dynamics and thermodynamics. We find that the Zika virus (ZIKV) NS2B/NS3 protease maintains a stable closed conformation over multiple 100-ns conventional MD simulations in both the presence and absence of inhibitors. The S1, S2, and S3 pockets are stable as well. However, in two of eight simulations, the A132-G133 peptide bond in the binding pocket of S1' spontaneously flips to form a 3₁₀-helix that corresponds to the inactive conformation of the oxyanion hole, and then maintains this conformation until the end of the 100-ns conventional MD simulations without inversion of the flip. This conformational change affects the S1' pocket in ZIKV NS2B/NS3 protease active site, which is important for small molecule binding. The simulation results provide evidence at the atomic level that the inactive conformation of the oxyanion hole is more favored energetically when no specific interactions are formed between substrate/inhibitor and oxyanion hole residues. Interestingly, however, transition between the active and inactive conformation of the oxyanion hole can be observed by boosting the valley potential in accelerated MD simulations. This supports a proposed induced-fit mechanism of ZIKV NS2B/NS3 protease from computational methods and provides useful direction to enhance inhibitor binding predictions in structure-based drug design.     

Extracting Curvature Preferences of Lipids Assembled in Flat Bilayers Shows Possible Kinetic Windows for Genesis of Bilayer Asymmetry and Domain Formation in Biological Membranes

Studies on the assembly of pure lipid components allow mechanistic insights toward understanding the structural and functional aspects of biological membranes. Molecular dynamic (MD) simulations on membrane systems provide molecular details on membrane dynamics that are difficult to obtain experimentally. A large number of MD studies have remained somewhat disconnected from a key concept of amphipathic assembly resulting in membrane structures—shape parameters of lipid molecules in those structures in aqueous environments. This is because most of the MD studies have been done on flat lipid membranes. With the above in view, we analyzed MD simulations of 26 pure lipid patches as a function of (1) lipid type(s) and (2) time of MD simulations along with 35–40 ns trajectories of five pure lipids. We report, for the first time, extraction of curvature preferences of lipids from MD simulations done on flat bilayers. Our results may lead to mechanistic insights into the possible origins of bilayer asymmetries and domain formation in biological membranes.     

Predicting Atomic Details of the Unfolding Pathway for YibK,a Knotted Protein from the SPOUT Superfamily

Abstract

Several protein structures have been reported to contain intricate knots of the polypeptide backbone but the mechanism of the (un)folding process of knotted proteins remains unknown. The members of the SPOUT superfamily of RNA methyltransferases are some of the most intensely studied systems for investigation of the knot formation and function. YibK (whose biochemical function remains unknown) is the representative protein of the SPOUT superfamily. This protein exhibits a deep trefoil knot at the C-terminus.

We conducted an extensive computational analysis of the unfolding process for the monomeric form of YibK. In order to predict the (un)folding pathway of YibK, we have calculated the order of secondary structure disassembly using UNFOLD, and performed thermal unfolding simulations using classical Molecular Dynamics (MD), as well as simulations employing reduced representation of the peptide chain using either MD with the UNRES method or the Monte Carlo (MC) unfolding with the REFINER method.

Results obtained from all methods used in this work are in qualitative agreement. We found that YibK unfolds through four intermediate states. The trefoil knot in YibK disappears at the end of the unfolding process, long after the protein loses its native topology. We observed that the C-terminus leaves the knotting loop folded into a hairpin-like structure, in agreement with the results of coarse-grained simulation reported earlier. We propose that the folding pathway of YibK corresponds to the reversed sequence of events observed in the unfolding pathway elucidated in this study. Thus, we predict that the knot formation is the slowest part of the YibK folding process.     

Characterization of the water defect at the HIV-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations

The membrane spanning domain (MSD) of human immunodeficiency virus 1 (HIV-1) envelope glycoprotein gp41 is important for fusion and infection. We used molecular dynamics (MD) simulations (3.4 μs total) to relate membrane and peptide properties that lead to water solvation of the α-helical gp41 MSD's midspan arginine in pure dipalmitoylphosphatidylcholine (DPPC) and in 50/50 DPPC/cholesterol membranes. We find that the midspan arginine is solvated by water that penetrates the inner leaflet, leading to a so-called water defect. The water defect is surprisingly robust across initial conditions and membrane compositions, but the presence of cholesterol modulates its behavior in several key ways. In the cholesterol-containing membranes, fluctuations in membrane thickness and water penetration depth are localized near the midspan arginine, and the MSD helices display a tightly regulated tilt angle. In the cholesterol-free membranes, thickness fluctuations are not as strongly correlated to the peptide position and tilt angles vary significantly depending on protein position relative to boundaries between domains of differing thickness. Cholesterol in an HIV-1 viral membrane is required for infection. Therefore, this work suggests that the colocalized water defect and membrane thickness fluctuations in cholesterol-containing viral membranes play an important role in fusion by bringing the membrane closer to a stability limit that must be crossed for fusion to occur.