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PubMed2001

Molecular dynamics simulations of hard sphere solidification at constant pressure.

Molecular dynamics simulations in the NPT ensemble are used to study the dynamics of crystallization processes in hard sphere systems. The simulation method used permits us to follow the dynamics after a sudden pressure or temperature quench in a one-step process without the need of extra densification methods. During the quench a strong correlation between the system density and the crystalline order parameter Q(6) is found. The growth of fcc order in the system over time is observed in detail and compared to Q(6)(t). We compare results for the equation of state on the metastable fluid branch with previous results from constant volume molecular dynamics simulations. Some results for the crystallization of binary hard sphere mixtures are also presented for a number of different size ratios.

Journal Article↗
PubMed2002

Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study.

From three 2.4-ns molecular dynamics simulations of the r(CpG)(12) duplex conducted at 5, 25 and 37 degrees C, a strong temperature dependence of the dynamics of the water molecules and ions located in the first nucleic acid coordination shell is observed. At 5 degrees C, the highest residence times of bound water molecules exceed 1 ns while, at 37 degrees C, they decrease to 0.5 ns in agreement with available NMR data. Similar temperature dependencies are observed for the potassium ions bound to the duplex. In this temperature range, the structure of the RNA helix remains essentially unchanged. Thus, the observed alterations correspond to a 'premelting' of the solvent structure around the duplex. It is proposed that, before the nucleic acid structure melts, the entropy of the solvent increases to a point where it is no longer compensated by the enthalpic contribution of solute-solute and solute-solvent interactions. At this stage, the weakest structural elements start to melt. In other terms, the experimentally observed melting processes are preceded by a melting of the more labile solvent structure.

Computer Simulation↗
PubMed1997

Effect of lithium and sodium ions on a charged membrane of dipalmitoylphosphatidylserine: a study by molecular dynamics simulation.

We describe a series of molecular dynamics simulations performed on a model of charged lipid bilayer (dipalmitoylphosphatidylserine) and water, in presence of sodium and lithium ions, with an atomic detail. The structure of the lipid membranes was strongly affected by the presence of lithium, as manifested by the observation of a transition from a disordered to a gel state. Concerning the mechanism of such a transition, it was associated to the dehydration that we detected in the lipid-water interface in the presence of lithium. This dehydration introduced an increase in the lipid-lipid interactions, and as a consequence, a diminution of the disorder of the membrane. When both types of ions are present in the aqueous phase, lithium shown a special affinity for the lipid membrane displacing almost all the sodium ions toward the middle of the water layer. As a result, we observed remarkable differences in the atom and electric field distributions across the lipid membrane. Concerning the diffusion and orientation of water molecules across the lipid-water interface, we also observed a strong dependency of the type ion. On the other hand, the mobility and the hydration shell of lithium and sodium ions are strongly perturbed by the presence of the charged lipid bilayer. The lipid layer was responsible for a dehydration of the ions compared to bulk water. This dehydration was compensated by an increase of coordination number of the ions with the lipid oxygens. Also, the residence times of water in the first hydration shell of lithium and sodium ions are perturbed by the presence of the lipid membrane.

Diffusion↗
PubMed1999

Molecular dynamics simulations of beta-hairpin folding.

Molecular dynamics simulations of beta-hairpin folding have been carried out with a solvent-referenced potential at 274 K. The model peptide V4DPGV4 formed stable beta-hairpin conformations and the beta-hairpin ratio calculated by the DSSP algorithm was about 56% in the 50-ns simulation. Folding into beta-hairpin conformations is independent of the initial conformations. The simulations provided insights into the folding mechanism. The hydrogen bond often formed in a beta-turn first, and then propagated by forming more hydrogen bonds along the strands. Unfolding and refolding occurred repeatedly during the simulations. Both the hydrogen bonding and the hydrophobic interaction played important roles in forming the ordered structure. Without the hydrophobic effect, stable beta-hairpin conformations did not form in the simulations. With the same energy functions, the alanine-based peptide (AAQAA)3Y folded into helical conformations, in agreement with experiments. Folding into an alpha-helix or a beta-hairpin is amino acid sequence-dependent.

Algorithms↗
PubMed2003

Free energy of solvation from molecular dynamics simulations for low dielectric solvents.

Using molecular dynamics simulation, we present new results for the free energy of solvation for solvents with low dielectric constants (CCl(4), CHCl(3), benzene). The solvation free energy is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent repulsion and dispersion interactions, and the electrostatic solvation of the solute. The cavitational contribution has been obtained from the Claverie-Pierotti model applied to excluded volumes obtained from distances for nearest neighbor configurations between the solute's atoms and a spherical solvent description. An electrostatic continuum model has been adapted for the computation of the electrostatic free energy of solvation, whereas the van der Waals contribution has been calculated directly from the intermolecular interactions defined by the force fields applied to the simulations. For each solvent, a large set of solute molecules containing most of the chemically interesting functionalities has been treated. The simulated solvation free energies are in very good agreement with experimental data, although a small systematical overestimation of the free energy of solvation indicates a failure of the spherical approach to the solvent molecules in the case of benzene.

Journal Article↗
PubMed2007

A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations.

Cell lists are ubiquitous in molecular dynamics simulations--be it for the direct computation of short-range inter-atomic potentials, the short-range direct part of a long-range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary interparticle distance calculations. In this paper, an algorithm is presented which reduces the number of spurious distance calculations by first sorting the particles along the cell pair axis and then only interacting two particles if their distance along the axis is smaller than the cutoff distance of the interaction. This approach is shown to be more efficient than the conventional approach and similar approaches using smaller cells.

Journal Article↗
PubMed2005

Protein flexibility: multiple molecular dynamics simulations of insulin chain B.

Multiple molecular dynamics simulations totaling more than 100 ns were performed on chain B of insulin in explicit solvent at 300 K and 400 K. Despite some individual variations, a comparison of the protein dynamics of each simulation showed similar trends and most structures were consistent with NMR experimental values, even at the elevated temperature. The importance of packing interactions in determining the conformational transitions of the protein was observed, sometimes resulting in conformations induced by localized hydrophobic interactions. The high temperature simulation generated a more diverse range of structures with similar elements of secondary structure and populated conformations to the simulations at room temperature. A broad sampling of the conformational space of insulin chain B illustrated a wide range of conformational states with many transitions at room temperature in addition to the conformational states observed experimentally. The T-state conformation associated with insulin activity was consistently present and a possible mechanism of behavior was suggested.

Computer Simulation↗
PubMed2005

Molecular dynamics simulation of a phosphatidylglycerol membrane.

Although molecular dynamics simulations are an important tool for studying membrane systems, relatively few simulations have used anionic lipids. This paper reports the first simulation of a pure phosphatidylglycerol (PG) bilayer. The properties of this equilibrated palmitoyloleoylphosphatidylglycerol membrane agree with experimental observations of PG membranes and with previous simulations of monolayers and mixed bilayers containing PG lipids. These simulations also provide interesting insights into hydrogen bonding interactions in PG membranes. This equilibrated membrane will be a useful starting point for simulations of membrane proteins interacting with PG lipids.

Hydrogen Bonding↗
PubMed1996

Molecular dynamics simulations of silicon-fluorine etching.

Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)n adsorbates on the Si(100) - (2 x 1) surface are performed using the SW potential and compared to simulations with the WWC reparameterization of the SW potential. Theoretical and experimental work has demonstrated that the reactive fluorosilyl layer during silicon-fluorine etching is composed of tower-like adspecies of SiF, SiF2 and SiF3 groups. The objective of the simulations is to determine how the chemical composition, mechanism of formation, and energy distribution of the etched gas-phase products depend on the identity of the reacting adsorbate, the incident kinetic energy, and the parameterization of the potential energy function. Three reactions are simulated: F(g) + SiF3(a), F(g) + SiF2-SiF3(a), and F(g) + SiF2-SiF2-SiF3(a). SiF4 is the major product and Si2F6 and Si3F8 are minor products. In Si2F6 and Si3F8, the silicon-fluorine bond that is formed is stronger than the silicon-silicon bond in the molecule and, therefore, the majority of these products have enough energy to dissociate and will fragment before reaching the detector. An SN2-like mechanism is the primary mechanism responsible for the formation of SiF4, Si2F6, and Si3F8. In addition, at higher energies, the simulations have discovered a previously unknown mechanism for the formation of SiF4, which involves an insertion between a silicon-silicon bond. The results of the simulations with the two potentials differ quite substantially in their prediction of the reactivity of the adsorbates. The SW potential predicts a 2- to 3-eV lower energy threshold for reaction and a much higher reaction cross-section, especially for the SiF4 product. These results are explained in terms of the differences in the potential energy functions used to describe the silicon-fluorine interactions. In addition, the results are compared to experimental data on silicon-fluorine etching.

Computer Graphics↗
PubMed2000

Hydration of T-antigen Gal beta(1-3)GalNAc and the isomer Gal beta(1-3)GlcNAc by molecular dynamics simulations.

We present a 250 ps molecular dynamics simulation of the T-antigen Gal beta(1-3)GalNAc and its isomer Gal beta(1-3)GlcNAc in the classic Gibbs Ensemble, Number of particles, Pressure and Temperature (NPT) with explicit representation of 432 water molecules. We computed the radial distribution function, equilibrium conformation, intramolecular and intermolecular hydrogen bonds, and water residence time to characterize the hydration pattern of these sugars, which are not very different and exhibit hydrophilic behavior. Based on hydration dynamics, it was concluded that these sugars should be classified as negative hydrated. Formation of an intramolecular hydrogen bond between the ring oxygen atom O5 of the first unit and the OH4' group of glycoside of the second unit might influence interaction with the antigenic receptor and could explain the main difference of affinities between them.

Antigens, Tumor-Associated, Carbohydrate↗
PubMed2005

Molecular dynamics simulations of polymer transport in nanocomposites.

Molecular dynamics simulations on the Kremer-Grest bead-spring model of polymer melts are used to study the effect of spherical nanoparticles on chain diffusion. We find that chain diffusivity is enhanced relative to its bulk value when polymer-particle interactions are repulsive and is reduced when polymer-particle interactions are strongly attractive. In both cases chain diffusivity assumes its bulk value when the chain center of mass is about one radius of gyration R(g) away from the particle surface. This behavior echoes the behavior of polymer melts confined between two flat surfaces, except in the limit of severe confinement where the surface influence on polymer mobility is more pronounced for flat surfaces. A particularly interesting fact is that, even though chain motion is strongly speeded up in the presence of repulsive boundaries, this effect can be reversed by pinning one isolated monomer onto the surface. This result strongly stresses the importance of properly specifying boundary conditions when the near surface dynamics of chains are studied.

Journal Article↗
PubMed2005

Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study.

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.

Journal Article↗
PubMed2006

Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations.

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.

Computer Simulation↗
PubMed2006

Discontinuous molecular dynamics simulation study of polymer collapse.

Discontinuous molecular dynamics simulations were used to study the coil-globule transition of a polymer in an explicit solvent. Two different versions of the model were employed, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. For each case, a model parameter lambda determines the degree of hydrophobicity of the monomers by controlling the degree of energy mismatch between the monomers and solvent particles. We consider a lambda-driven coil-globule transition at constant temperature. The simulations are used to calculate average static structure factors, which are then used to determine the scaling exponents of the system in order to determine the theta-point values lambda(theta) separating the coil from the globule state. For each model we construct coil-globule phase diagrams in terms of lambda and the particle density rho. Additionally, we explore for each model the effects of varying the range of the attractive interactions on the phase boundary separating the coil and globule phases. The results are analyzed in terms of a simple Flory-type theory of the collapse transition.

Journal Article↗
PubMed2005

Growth of carbon nanotubes on metal nanoparticles: a microscopic mechanism from ab initio molecular dynamics simulations.

We report on ab initio molecular dynamics simulations of the early stages of single-walled carbon nanotube (SWCNT) growth on metal nanoparticles. Our results show that a sp2 bonded cap is formed on an iron catalyst, following the diffusion of C atoms from hydrocarbon precursors on the nanoparticle surface. The weak adhesion between the cap and iron enables the graphene sheet to "float" on the curved surface, as additional C atoms covalently bonded to the catalyst "hold" the tube walls. Hence the SWCNT grows capped. At the nanoscale, we did not observe any tendency of C atoms to penetrate inside the catalyst, consistent with total energy calculations showing that alloying of Fe and C is very unlikely for 1 nm particles. Root growth was observed on Fe but not on Au, consistent with experiment.

Journal Article↗
PubMed2004

Overcoming free energy barriers using unconstrained molecular dynamics simulations.

Association of unconstrained molecular dynamics (MD) and the formalisms of thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)] have been employed to determine potentials of mean force. When implemented in a general MD code, the additional computational effort, compared to other standard, unconstrained simulations, is marginal. The force acting along a chosen reaction coordinate xi is estimated from the individual forces exerted on the chemical system and accumulated as the simulation progresses. The estimated free energy derivative computed for small intervals of xi is canceled by an adaptive bias to overcome the barriers of the free energy landscape. Evolution of the system along the reaction coordinate is, thus, limited by its sole self-diffusion properties. The illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, the dimerization of methane in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method.

Journal Article↗
PubMed2006

Stability and migration of metal ions in G4-wires by molecular dynamics simulations.

We present a molecular dynamics investigation of guanine quadruple helices based on classical force fields. We analyze the dependence of the helical conformation on various compositional factors, such as the length of the G4-wire, as well as the incorporation into the helix channel of alkali ions of different species and in different amounts. In compliance with previous indications, our results suggest that monovalent alkali cations assist the stability of the quadruplex arrangement against disruption on the few nanoseconds time scale in the order of increasing van der Waals radius. Whereas very short G4-wire fragments immediately unfold in the absence of coordinating metal ions or in the presence of tiny ions (e.g., Li+) in agreement with the experimental evidence that empty short guanine quadruplexes are not formed in any synthetic conditions, our simulations show that longer empty helices do not discompose. This finding supports the possibility of producing long G4-wires with different guanine-cation stoichiometries than those routinely known. The classical trajectories allow us to identify different stationary axial sites for the different metal species, which are confirmed by complementary quantum calculations.

Journal Article↗
PubMed2006

Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation.

The structure and molecular packing density of a "mismatched" solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data on comparable systems. The local density or molecular packing in DMPC-hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested a positive volume change, DeltaV(m), of 4 cm(3) mol(-1) hexanol partitioned at 310 K in good accordance with experimental values. Analysis of the apparent volumes of each component in the pure and mixed states further showed that DeltaV(m) reflects a balance between a substantial increase in the packing density of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8) is stretched by about 4%. Concomitantly, the average lateral area per chain decreases and these two effects compensate so that the overall packing density in the outer region, where the hexanol molecules are located, remains practically constant. The core of the bilayer (C9-C13) is slightly thinned. The average lateral area per chain in this region expands, resulting in a looser packing density. The net effect in the core is a 2-3% decrease in density corresponding to a total volume increase of approximately 14 cm(3) mol(-1) hexanol partitioned.

Computer Simulation↗