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.     

Simulated dynamics of Ne@C60 aggregates beyond dissociation

Molecular dynamics (MD) computer simulations are utilized to better understand the dynamics of small (N = 5) endohedral Ne@C₆₀ aggregates. Multiple runs at various temperatures are used to increase the reliability of our statistics. The aggregate holds together until somewhere between T = 1150 and 1200 K, where it dissociates, showing no intermediate sign of melting or fullerene disintegration. When the temperature is increased to around T = 4000 K, the encapsulated neon atoms begin to leave the aggregate, with the fullerene molecules still remaining intact. At temperatures near T = 4400 K, thermal disintegration of the fullerenes preempts the aggregate dissociation. Above this temperature neon atoms are more quickly released and the fullerenes form a larger connected structure, with bonding taking place in atom pairs from different original fullerene molecules. Escape constants and half lives are calculated for the temperature range 4000 K ≤ T ≤ 5000 K. The agreements and disagreements of results of this work with experiments suggest that classical MD simulations are useful in describing fullerene systems at low temperatures and near disintegration, but require development of new techniques before it is possible to accurately model windowing at temperatures below T = 3000 K.     

Ab initio and molecular dynamics studies of solid β-HMX: effects of hydrostatic pressure and high temperature

Using first-principles density functional theory and classical molecular dynamics (MD), the structural, electronic and mechanical properties of the energetic material β-HMX have been studied. The crystal structure optimised by the local density approximation calculations compares reasonably with the experimental data. Electronic band structure and density of states indicate that β-HMX is an insulator with a band gap of 3.059 eV. The pressure effect on the crystal structure and physical properties has been investigated in the range of 0–40 GPa. The crystal structure and electronic properties change slightly as the pressure increases from 0 to 2.5 GPa; when the pressure is above 2.5 GPa, further increment of the pressure results in significant changes in crystal structure. There is a larger compression along the b-axis than along the a- and c-axes. Isothermal–isobaric MD simulations on β-HMX were performed in the temperature range of 5–400 K. Phase transition at 360 K, corresponding to a volume interrupt, was found. The computed thermal expansion coefficients show anisotropic behaviour with a slightly larger expansion along the b- and c-axes than along the a-axis. In the temperature range of 5–360 K, β-HMX possesses good plasticity and its stiffness decreases with increasing the temperature.     

Effects of the nitrogen doping configuration and site on the thermal conductivity of defective armchair graphene nanoribbons

The influence of the nitrogen (N) doping configuration on the thermal conductivity (TC) of armchair graphene nanoribbons (AGNRs) of size 15.7 nm × 7.26 nm was investigated using classical molecular dynamics (MD) simulations with the optimized Tersoff potential at room temperature. The effect of changing the N-doping site in defects on the TC of AGNRs was also investigated in detail. The variations with N concentration of the TCs of AGNRs presenting graphitic N (quarternary N), pyridinic N, and pyrrolic N doping configurations were studied. Results of MD simulations showed that, among these three doping configurations, pyridinic N was associated with the highest TC, and pyrrolic N with the lowest TC. The highest TC values were obtained when the N dopant atoms were located at the edges and at defects in the AGNR. The presence of both pyrrolic N and Stone–Wales type 1 (SW-1) defects led to a higher TC than the presence of both pyrrolic N and SW-2 defects. Phonon–defect scattering was found to be influenced by changes in C–C bond orientation. SW-1 defects were found to exert a greater influence on the TC than graphitic N doping. Furthermore, the influence on the TC of the N-doping site location in SW-1 defects was examined. Doping the central sites of SW-1 defects was found to yield higher TC values than doping the edge sites of defects. Graphitic-N doping of the more central sites in a SW-1 defect led to a higher TC than the random graphitic-N doping of sites in a SW-1 defect.     

Simulation of heat conduction in nanocomposite using energy-conserving dissipative particle dynamics

We report on the simulation of heat conduction in nanocomposite by using a novel mesoscopic particle method, the energy-conserving dissipative particle dynamics (eDPD) method. The original eDPD method is extended to account for the interfacial thermal resistance occurs at the angstrom-wide interface between materials, and we also investigated the choice of time step in eDPD simulations. For nanocomposite with randomly dispersed nanoparticles, the eDPD simulations predict that the thermal conductivity of matrix material can be enhanced by embedding high thermal conductivity nanoparticles, but the effectiveness of such a strategy diminishes as the interfacial thermal resistance between the nanoparticle and matrix material increases. These results are in quantitative agreement with the classical Maxwell–Garnett model. Further simulations indicate that the enhancement of thermal conductivity can be affected by the alignment of nanoparticles with respect to the temperature gradient, which cannot be predicted by the classical models. These simulation results indicate that eDPD method can be a versatile method for studying thermal transport in heterogeneous materials and complex systems.     

Curcumin specifically binds to the human calcium–calmodulin-dependent protein kinase IV: fluorescence and molecular dynamics simulation studies

Calcium–calmodulin-dependent protein kinase IV (CAMK4) plays significant role in the regulation of calcium-dependent gene expression, and thus, it is involved in varieties of cellular functions such as cell signaling and neuronal survival. On the other hand, curcumin, a naturally occurring yellow bioactive component of turmeric possesses wide spectrum of biological actions, and it is widely used to treat atherosclerosis, diabetes, cancer, and inflammation. It also acts as an antioxidant. Here, we studied the interaction of curcumin with human CAMK4 at pH 7.4 using molecular docking, molecular dynamics (MD) simulations, fluorescence binding, and surface plasmon resonance (SPR) methods. We performed MD simulations for both neutral and anionic forms of CAMK4-curcumin complexes for a reasonably long time (150 ns) to see the overall stability of the protein–ligand complex. Molecular docking studies revealed that the curcumin binds in the large hydrophobic cavity of kinase domain of CAMK4 through several hydrophobic and hydrogen-bonded interactions. Additionally, MD simulations studies contributed in understanding the stability of protein–ligand complex system in aqueous solution and conformational changes in the CAMK4 upon binding of curcumin. A significant increase in the fluorescence intensity at 495 nm was observed (λ_exc = 425 nm), suggesting a strong interaction of curcumin to the CAMK4. A high binding affinity (K_D = 3.7 × 10^?8 ± .03 M) of curcumin for the CAMK4 was measured by SPR further indicating curcumin as a potential ligand for the CAMK4. This study will provide insights into designing a new inspired curcumin derivatives as therapeutic agents against many life-threatening diseases.     

The impact of line tension on the contact angle of nanodroplets

The line tension for a Lennard–Jones (LJ) fluid on a (9, 3) solid of varying strength was calculated using Monte Carlo simulations. A new perturbation method was used to determine the interfacial tension between liquid–vapour, solid–liquid and solid–vapour phases for this system to determine the Young's equation contact angle. Cylindrical and spherical nanodroplets were simulated for comparison. The contact angles from the cylindrical drops and Young's equation agree very well over the range of surface strengths and cylindrical drop sizes, except on a very weak surface. Tolman length effects were not observable for cylindrical drops. This shows that quite small systems can reproduce macroscopic contact angles. For spherical droplets, a deviation between the contact angle of spherical droplets and Young's equation was evident, but decreased with increasing interaction strengths to be negligible for contact angles less than 90°. Linear fitting of the contact angle data for varying droplet sizes showed no clear effect by line tension on contact angle. All calculated line tension values have a magnitude less than 4 × 10^? 12 J/m with both negative and positive signs. The best estimate of line tension for this system of LJ droplets was 1 × 10^? 13 J/m, which is smaller than the reported estimations in the literature, and is too small to be conclusively positive or negative in value.     

Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data

Molecular dynamics (MD) simulation combined with inelastic neutron scattering can provide information about the thermal dynamics of proteins, especially the low-frequency vibrational modes responsible for large movement of some parts of protein molecules. We performed several 30-ns MD simulations of cytochrome c (Cyt c) in a water box for temperatures ranging from 110 to 300 K and compared the results with those from experimental inelastic neutron scattering. The low-frequency vibrational modes were obtained via dynamic structure factors, S(Q, ω), obtained both from inelastic neutron scattering experiments and calculated from MD simulations for Cyt c in the same range of temperatures. The well known thermal transition in structural movements of Cyt c is clearly seen in MD simulations; it is, however, confined to unstructured fragments of loops Ω₁ and Ω₂; movement of structured loop Ω₃ and both helical ends of the protein is resistant to thermal disturbance. Calculated and experimental S(Q, ω) plots are in qualitative agreement for low temperatures whereas above 200 K a boson peak vanishes from the calculated plots. This may be a result of loss of crystal structure by the protein–water system compared with the protein crystal.     

Propagation Properties of Nanoscale Three-Dimensional Plasmonic Waveguide Based on Hybrid of Two Fundamental Planar Optical Metal Waveguides

In this paper, a nanoscale three-dimensional plasmonic waveguide (TDPW), created by depositing an Ag stripe on a SiO₂ layer with an Ag substrate, is introduced and theoretically investigated at visible and telecom wavelengths. By applying the effective index method and finite-difference time-domain numerical simulations, the authors find that the propagation properties of surface plasmon polaritons (SPPs) in the TDPW, including the propagation length and beam width, are mainly decided by the core (the SiO₂ layer just under the Ag stripe) itself, due to the much stronger localization of SPPs in the core than in the two side claddings (the SiO₂ layer without the covered Ag stripe). And propagating SPPs in the TDPW are strongly confined in the core region, even with a very small waveguide cross section. Furthermore, based on the stronger localization of propagation SPPs in the TDPW, two kinds of bending waveguides, oblique bending and 90° circular bending waveguides, are also investigated. For wavelength of 1550 nm, the 90° circular bending guide with a minimum radius as small as 2.6 μm show nearly zero radiation loss, even with a small waveguide cross section of 70?×?80 nm². The proposed TDPW is suitable for planar integration and provides a possible way for constructing various nanoscale counterparts of conventional integrated devices such as splitter, resonator, sensor, and optical switch.     

GPU-accelerated replica exchange molecular simulation on solid–liquid phase transition study of Lennard-Jones fluids

Determining the solid–liquid phase transition point by conventional molecular dynamics (MD) simulations is difficult because of the tendency of the system to get trapped in local minimum energy states at low temperatures and hysteresis during cooling and heating cycles. The replica exchange method, used in performing many MD simulations of the system at different temperature conditions simultaneously and performs exchanges of these temperatures at certain intervals, has been introduced as a tool to overcome this local-minimum problem. However, around the phase transition temperature, a greater number of different temperatures are required to adequately find the phase transition point. In addition, the number of different temperature values increases when treating larger systems resulting in huge computation times. We propose a computational acceleration of the replica exchange MD simulation on graphics processing units (GPUs) in studying first-order solid–liquid phase transitions of Lennard-Jones (LJ) fluids. The phase transition temperature for a 108-atom LJ fluid has been calculated to validate our new code. The result corresponds with that of a previous study using multicanonical ensemble. The computational speed is measured for various GPU-cluster sizes. A peak performance of 196.3 GFlops with one GPU and 8.13 TFlops with 64 GPUs is achieved.     

The solvation of bromide anion in acetonitrile: a structural study based on the combination of theoretical calculations and X-ray absorption spectroscopy

This work studies the solvation of bromide in acetonitrile by combining quantum mechanics, computer simulations and X-ray absorption near edge structure (XANES) spectroscopy. Three different sets of interaction potentials were tested, one of them derived from literature and the other two are simple modifications of the previous one to include specificities of the bromide–acetonitrile interactions. Results for microsolvation of bromide were obtained by quantum mechanical optimization and classical minimization of small clusters [Br(ACN) _n ]^?  (n = 9, 20). Analysis of molecular dynamics (MD) simulations has provided structural, dynamic and energetic aspects of the solvation phenomenon. The theoretical computation of Br K-edge XANES spectrum in solution using the structural information obtained from the different simulations has allowed the comparison among the three different potentials, as well as the examination of the main structural and dynamic factors determining the shape of the experimental spectrum.     

Electrodissociation of clathrate-like structures

In the present work, we develop molecular dynamics (MD) simulations in the NPT (isobaric–isothermic) ensemble to analyse the effect of an external electrostatic field over a cubic methane hydrate crystallite. The amplitude of the field is in the range 0.5–3.0 V/nm. For the simulations, we used the SPC/E rigid water model and a single-site model for methane at a temperature of 248 K and a pressure of 20 bar. When the external electrostatic field is applied, the water dipoles are oriented in such a way that the methane molecules can diffuse far away from the water cages, hence the clathrate dissociation takes place. This last phenomenon was observed for intensities above 1.5 V/nm. Taking the final configuration of each run as input, we develop a new set of MD simulations, and we observe that the stable clathrate is not recovered immediately when the external electrostatic field is turned off due to limitations in the simulation time.     

Development of a transient large strain contact method for biological heart valve simulations

A new 2D method to implement transient contact using Comsol Multiphysics (finite element analysis software that enables multiphysics simulations) is described, which is based on Hertzian contact. This method is compared to the existing (default) contact method that does not enable real transient simulations, but instead performs steady-state solutions where time is a constant. The two types of contact modelling have been applied to simple 2D biological heart valve models, undergoing strains in the region of 10% under 20 kPa pressure (applied over 0.3 s). Both the methods predicted comparable stress patterns, locations of peak stresses, deformations and directions of principal stress. The default contact method predicted slightly greater contact stresses, but spreads over a shorter surface length than the new contact method. The default contact method is useful for contact systems with little transient dependency, due to ease of use. However, where transient conditions are important the new contact method is preferred.     

Probing the interaction between cHAVc3 peptide and the EC1 domain of E-cadherin using NMR and molecular dynamics simulations

The goal of this work is to probe the interaction between cyclic cHAVc3 peptide and the EC1 domain of human E-cadherin protein. Cyclic cHAVc3 peptide (cyclo(1,6)Ac-CSHAVC-NH₂) binds to the EC1 domain as shown by chemical shift perturbations in the 2D ¹H,-¹⁵N-HSQC NMR spectrum. The molecular dynamics (MD) simulations of the EC1 domain showed folding of the C-terminal tail region into the main head region of the EC1 domain. For cHAVc3 peptide, replica exchange molecular dynamics (REMD) simulations generated five structural clusters of cHAVc3 peptide. Representative structures of cHAVc3 and the EC1 structure from MD simulations were used in molecular docking experiments with NMR constraints to determine the binding site of the peptide on EC1. The results suggest that cHAVc3 binds to EC1 around residues Y36, S37, I38, I53, F77, S78, H79, and I94. The dissociation constants (K_d values) of cHAVc3 peptide to EC1 were estimated using the NMR chemical shifts data and the estimated K_ds are in the range of .5 × 10^?5–7.0 × 10^?5 M.     

A coarse grained molecular dynamics study on the structure and stability of small-sized liposomes

The dependence of geometric structure and thermal stability of liposomes on their component phospholipid molecules and distribution of molecules in the inner and the outer layers of the liposome is investigated by conducting molecular simulations in explicit water for the eight types of liposomes constructed from different phospholipids. Using molecular mechanics structure-relaxation based on the coarse grained (CG) model, stable structures of the solvated liposomes are obtained. In addition, the molecular dynamics (MD) simulations based on the CG model are carried out at 310 and 360 K for elucidating the change in structure of the solvated liposomes. The MD simulations reveal that liposomes having the same number of lipids (SNL) in both the inner and the outer layers keep their spherical structures even at 360 K. In particular, the SNLs composed of palmitoyloleoyl-phosphatidyl-ethanolamine1 or dimyristoylglycero-phosphatidyl-choline lipid exhibit a compact spherical shape. In contrast, liposomes having the same density of lipids in the inner and the outer layers cannot keep their spherical shapes at 360 K. The obtained results contribute toward developing novel liposomes with enhanced thermal stability.     

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

Wide-angle x-ray scattering (WAXS) experiments of biomolecules in solution have become increasingly popular because of technical advances in light sources and detectors. However, the structural interpretation of WAXS profiles is problematic, partly because accurate calculations of WAXS profiles from structural models have remained challenging. In this work, we present the calculation of WAXS profiles from explicit-solvent molecular dynamics (MD) simulations of five different proteins. Using only a single fitting parameter that accounts for experimental uncertainties because of the buffer subtraction and dark currents, we find excellent agreement to experimental profiles both at small and wide angles. Because explicit solvation eliminates free parameters associated with the solvation layer or the excluded solvent, which would require fitting to experimental data, we minimize the risk of overfitting. We further find that the influence from water models and protein force fields on calculated profiles are insignificant up to q ≈ 15 nm^?1. Using a series of simulations that allow increasing flexibility of the proteins, we show that incorporating thermal fluctuations into the calculations significantly improves agreement with experimental data, demonstrating the importance of protein dynamics in the interpretation of WAXS profiles. In addition, free MD simulations up to one microsecond suggest that the calculated profiles are highly sensitive with respect to minor conformational rearrangements of proteins, such as an increased flexibility of a loop or an increase of the radius of gyration by  <  1%. The present study suggests that quantitative comparison between MD simulations and experimental WAXS profiles emerges as an accurate tool to validate solution ensembles of biomolecules.     

Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens

Previous experimental studies on thermostable lipase from Shewanella putrefaciens suggested the maximum activity at higher temperatures, but with little information on its conformational profile. In this study, the three-dimensional structure of lipase was predicted and a 60 ns molecular dynamics (MD) simulation was carried out at temperatures ranging from 300 to 400 K to better understand its thermostable nature at the molecular level. MD simulations were performed in order to predict the optimal activity of thermostable lipase. The results suggested strong conformational temperature dependence. The thermostable lipase maintained its bio-active conformation at 350 K during the 60 ns MD simulations.     

DRF90: a polarizable force field

The direct reaction field (DRF) approach has proven to be a useful tool to investigate the influence of solvents on the quantum/classical behaviour of solute molecules. In this paper, we report the latest extension of this DRF approach, which consists of the gradient of the completely classical energy expressions of this otherwise QM/MM method. They can be used in (completely classical) molecular dynamics (MD) simulations and geometry optimizations, that can be followed by a number of single point QM/MM calculations on configurations obtained in these simulations/optimizations. We report all energy and gradient expressions, and results for a number of interesting (model) systems. They include geometry optimization of the benzene dimer as well as MD simulations of some solvents. The most stable configuration for the benzene dimer is shown to be the parallel-displaced form, which is slightly more stable (0.3 kcal/mol) than the T-shaped dimer.     

Molecular dynamics study on deformation and mechanics of nanoscale Au/Cu multilayers under indentation

The effects of individual layer thickness, indentation velocity, and temperature on the mechanical properties and mechanics of nanoscale Au/Cu multilayers under indentation were studied using molecular dynamics simulations based on the many-body embedded-atom potential. The simulation results show that layer interfaces act as strong barriers that resist the propagation of dislocations, even at an extremely small individual layer thickness of 3 nm. The number of dislocations increases significantly and the growth of dislocations decreases with decreasing individual layer thickness. There is no clear relationship between the magnitude of the required indentation force and the number of film layers; however, the average required indentation force increases with increasing indentation velocity and decreasing temperature. During indentation at a relatively low velocity, dislocation propagation is more significant; the number of disordered atoms significantly increases at a relatively high indentation velocity.     

Effect of chirality,length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study

We carried out molecular dynamics simulations to study the adsorption of all the 20 amino acids (AAs; aromatic, polar and non-polar) on the surface of chiral, zigzag and armchair single-walled carbon nanotubes. The adsorption was occurring in all systems. In the aromatic AAs, the π–π stacking and the semi-hydrogen bond formation cause a strong interaction with the carbon nanotubes (CNTs). We also investigated the chirality, length and diameter dependencies on adsorption energies. We found that all AAs have more tendency to adsorption on the chiral and zigzag CNTs over the armchair. The results show that increasing both the diameter and the length causes the enhancement of the adsorption energy. But, the effect of the length is more than of the diameter. For example, the adsorption energy of Trp on the surface of CNT (4,1), with 2 nm length, is 20.4 kcal/mol. When the length of CNT becomes twice, the adsorption energy increases by 24 ± 0.3%. But by doubling the diameter, the adsorption energy increased only by 9.8 ± 0.25%.