Structure and magnetic properties of polydisperse ferrofluids: a molecular dynamics study

We study by Langevin molecular dynamics simulations systematically the influence of polydispersity in the particle size, and subsequently in the dipole moment, on the physical properties of ferrofluids. The polydispersity is in a first approximation modeled by a bidisperse system that consists of small and large particles at different ratios of their volume fractions. In the first part of our investigations the total volume fraction of the system is fixed, and the volume fraction phi(L) of the large particles is varied. The initial susceptibility chi and magnetization curve of the systems show a strong dependence on the value of phi(L). With the increase of phi(L), the magnetization M of the system has a much faster increment at weak fields, and thus leads to a larger chi. We performed a cluster analysis that indicates that this is due to the aggregation of the large particles in the systems. The average size of these clusters increases with increasing phi(L). In the second part of our investigations, we fixed the volume fraction of the large particles, and increased the volume fraction phi(S) of the small particles in order to study their influence on the chain formation of the large ones. We found that the average aggregate size formed by large particles decreases when phi(S) is increased, demonstrating a significant effect of the small particles on the structural properties of the system. A topological analysis of the structure reveals that the majority of the small particles remain nonaggregated. Only a small number of them are attracted to the ends of the chains formed by large particles.

Molecular dynamics study on the equilibrium magnetization properties and structure of ferrofluids

We investigate in detail the initial susceptibility, magnetization curves, and microstructure of ferrofluids in various concentration and particle dipole moment ranges by means of molecular dynamics simulations. We use the Ewald summation for the long-range dipolar interactions, take explicitly into account the translational and rotational degrees of freedom, coupled to a Langevin thermostat. When the dipolar interaction energy is comparable with the thermal energy, the simulation results on the magnetization properties agree with the theoretical predictions very well. For stronger dipolar couplings, however, we find systematic deviations from the theoretical curves. We analyze in detail the observed microstructure of the fluids under different conditions. The formation of clusters is found to enhance the magnetization at weak fields and thus leads to a larger initial susceptibility. The influence of the particle aggregation is isolated by studying ferro-solids, which consist of magnetic dipoles frozen in at random locations but which are free to rotate. Due to the artificial suppression of clusters in ferrosolids the observed susceptibility is considerably lowered when compared to ferrofluids.

Mode-specific chemisorption of CH4 on Pt{110}-(1 x 2) explored by first-principles molecular dynamics

The chemisorption of CH4 on Pt{110}-(1 x 2) has been studied by vibrational analysis of the reaction pathway defined by the potential energy surface and, in time reversal, by first-principles molecular dynamics simulations of CH4 associative desorption, with the electronic structure treated explicitly using density functional theory. We find that the symmetric stretch vibration ν1 is strongly coupled to the reaction coordinate; our results therefore provide a firm theoretical basis for recently reported state-resolved reactivity measurements, which show that excitation of the ν1 normal mode is the most efficient way to enhance the reaction probability

Bond-selective energy redistribution in the chemisorption of CH3D and CD3H on Pt{1 1 0}-(1 2): a first-principles molecular dynamics study

We have investigated the chemisorption of CH3D and CD3H on Pt{11 0}-(1 2) by performing first-principles molecular dynamics simulations of the recombinative desorption of CH3D (from adsorbed methyl and deuterium) and of CD3H (from adsorbed trideuteromethyl and hydrogen). Vibrational analysis of the symmetry adapted internal coordinates of the desorbing molecules shows that excitation of the single C– D (C–H) bond in the parent molecule is strongly correlated with energy excess in the reaction coordinate. The results of the molecular dynamics simulations are consistent with observed mode- and bond-specific reactivity measurements for chemisorption of methane and its isotopomers on platinum and nickel surfaces.

Polymer brushes under shear: molecular dynamics simulations compared to experiments

Surfaces coated with polymer brushes in a good solvent are known to exhibit excellent tribological properties. We have performed coarse-grained equilibrium and nonequilibrium molecular dynamics (MD) simulations to investigate dextran polymer brushes in an aqueous environment in molecular detail. In a first step, we determined simulation parameters and units by matching experimental results for a single dextran chain. Analyzing this model when applied to a multichain system, density profiles of end-tethered polymer brushes obtained from equilibrium MD simulations compare very well with expectations based on self-consistent field theory. Simulation results were further validated against and correlated with available experimental results. The simulated compression curves (normal force as a function of surface separation) compare successfully with results obtained with a surface forces apparatus. Shear stress (friction) obtained via nonequilibrium MD is contrasted with nanoscale friction studies employing colloidal-probe lateral force microscopy. We find good agreement in the hydrodynamic regime and explain the observed leveling-off of the friction forces in the boundary regime by means of an effective polymer–wall attraction.

GSHMC: an efficient method for molecular simulation

The hybrid Monte Carlo (HMC) method is a popular and rigorous method for sampling from a canonical ensemble. The HMC method is based on classical molecular dynamics simulations combined with a Metropolis acceptance criterion and a momentum resampling step. While the HMC method completely resamples the momentum after each Monte Carlo step, the generalized hybrid Monte Carlo (GHMC) method can be implemented with a partial momentum refreshment step. This property seems desirable for keeping some of the dynamic information throughout the sampling process similar to stochastic Langevin and Brownian dynamics simulations. It is, however, ultimate to the success of the GHMC method that the rejection rate in the molecular dynamics part is kept at a minimum. Otherwise an undesirable Zitterbewegung in the Monte Carlo samples is observed. In this paper, we describe a method to achieve very low rejection rates by using a modified energy, which is preserved to high-order along molecular dynamics trajectories. The modified energy is based on backward error results for symplectic time-stepping methods. The proposed generalized shadow hybrid Monte Carlo (GSHMC) method is applicable to NVT as well as NPT ensemble simulations.

Studying reactive processes with classical dynamics: rebinding dynamics in MbNO

A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mu s of total simulation time) for the rebinding of NO to myoglobin. The unbound surface ((FeNO)-N-...) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

Molecular insights of p47phox phosphorylation dynamics in the regulation of NADPH oxidase activation and superoxide production

Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47phox is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47phox phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47phox protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47phox is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22phox binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47phox_/_ coronary microvascular cells. Compared with wild-type p47phoxcDNAtransfected cells, the single mutation of S379A completely blocked p47phox membrane translocation, binding to p22phox and endothelial O2 . production in response to acute stimulation of PKC. p47phox C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47phox conformational changes and NADPH oxidase-dependent superoxide production by cells.

Molecular dating and biogeography of fig-pollinating wasps

Figs and fig-pollinating wasps are obligate mutualists that have coevolved for over 60 million years. But when and where did pollinating fig wasps (Agaonidae) originate? Some studies suggest that agaonids arose in the Late Cretaceous and the current distribution of fig-wasp faunas can be explained by the break-up of the Gondwanan landmass. However, recent molecular-dating studies suggest divergence time estimates that are inconsistent with the Gondwanan vicariance hypothesis and imply that long distance oceanic dispersal could have been an important process for explaining the current distribution of both figs and fig wasps. Here, we use a combination of phylogenetic and biogeographical data to infer the age, the major period of diversification, and the geographic origin of pollinating fig wasps. Age estimates ranged widely depending on the molecular-dating method used and even when using the same method but with slightly different constraints, making it difficult to assess with certainty a Gondwanan origin of agaonids. The reconstruction of ancestral areas suggests that the most recent common ancestor of all extant fig-pollinating wasps was most likely Asian, although a southern Gondwana origin cannot be rejected. Our analysis also suggests that dispersal has played a more important role in the development of the fig-wasp biota than previously assumed. (C) 2009 Elsevier Inc. All rights reserved.

Computer simulations of structures, energetics and dynamics of myoglobin center dot center dot center dot ligand complexes

Myoglobin has been studied in considerable detail using different experimental and computational techniques over the past decades. Recent developments in time-resolved spectroscopy have provided experimental data amenable to detailed atomistic simulations. The main theme of the present review are results on the structures, energetics and dynamics of ligands ( CO, NO) interacting with myoglobin from computer simulations. Modern computational methods including free energy simulations, mixed quantum mechanics/molecular mechanics simulations, and reactive molecular dynamics simulations provide insight into the dynamics of ligand dynamics in confined spaces complementary to experiment. Application of these methods to calculate and understand experimental observations for myoglobin interacting with CO and NO are presented and discussed.

Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

Ligand dynamics in myoglobin: calculation of infrared spectra for photodissociated NO

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Modeling entangled dynamics: comparison between stochastic single-chain and multichain models

To test the effectiveness of stochastic single-chain models in describing the dynamics of entangled polymers, we systematically compare one such model; the slip-spring model; to a multichain model solved using stochastic molecular dynamics(MD) simulations (the Kremer-Grest model). The comparison involves investigating if the single-chain model can adequately describe both a microscopic dynamical and a macroscopic rheological quantity for a range of chain lengths. Choosing a particular chain length in the slip-spring model, the parameter values that best reproduce the mean-square displacement of a group of monomers is determined by fitting toMDdata. Using the same set of parameters we then test if the predictions of the mean-square displacements for other chain lengths agree with the MD calculations. We followed this by a comparison of the time dependent stress relaxation moduli obtained from the two models for a range of chain lengths. After identifying a limitation of the original slip-spring model in describing the static structure of the polymer chain as seen in MD, we remedy this by introducing a pairwise repulsive potential between the monomers in the chains. Poor agreement of the mean-square monomer displacements at short times can be rectified by the use of generalized Langevin equations for the dynamics and resulted in significantly improved agreement.

Temperature dependence of protein dynamics simulated with three different water models

The effect of variation of the water model on the temperature dependence of protein and hydration water dynamics is examined by performing molecular dynamics simulations of myoglobin with the TIP3P, TIP4P, and TIP5P water models and the CHARMM protein force field at temperatures between 20 and 300 K. The atomic mean-square displacements, solvent reorientational relaxation times, pair angular correlations between surface water molecules, and time-averaged structures of the protein are all found to be similar, and the protein dynamical transition is described almost indistinguishably for the three water potentials. The results provide evidence that for some purposes changing the water model in protein simulations without a loss of accuracy may be possible.