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TEM and molecular simulation studies on the hydroxylapatite structure with Si and Mg impurities.

Transmission electron microscopy (TEM) and molecular simulation studies of traces of chemical elements such as Mg, Si, and OH in the hydroxylapatite (CaHAP) crystal structure obtained from the sand dollar were carried out. Two different types of CaHAP crystal morphologies in the samples synthesized by the hydrothermal method used were observed. Reflections with regular intensity in the experimental electron diffraction patterns obtained from these morphologies were observed. However, when these results were compared with a simulated electron diffraction pattern (which was obtained using the crystalline structure proposed for the hydroxylapatite) some forbidden reflections in the experimental pattern were observed. Then, in order to reproduce the experimental patterns Si and Mg atoms in the crystalline lattice were introduced. These elements in the elemental chemical analysis carried out by X-ray energy dispersive spectroscopy (EDS) in the typical CaHAP morphologies were detected. The positions of these atoms in the asymmetric unit were obtained using molecular simulation and during the relaxation process, the structure did not show changes in the lattice parameters. Subsequently, the crystalline structure was reproduced and matched the electron diffraction patterns simulated resulting in the experimental electron diffraction pattern. Experimental and simulated X-ray diffraction spectra were also matched.

Biocompatible Materials↗

Liquid crystal director fluctuations and surface anchoring by molecular simulation

We propose a simple and reliable method to measure the liquid crystal surface anchoring strength by molecular simulation. The method is based on the measurement of the long-range fluctuation modes of the director in confined geometry. As an example, molecular simulations of a liquid crystal in slab geometry between parallel walls with homeotropic anchoring have been carried out using the Monte Carlo technique. By studying different slab thicknesses, we are able to calculate separately the position of the elastic boundary condition and the extrapolation length.

Journal Article↗

Molecular simulation of the effects of alcohols on peptide structure.

The effects of alcohols on local protein structure have been simulated using computational approaches and model peptides. Molecular simulations were carried out on a 7-residue peptide created in both an extended conformation and an alpha-helix to explore alcohol-induced changes in peptide structure. It was assumed that alcohols hydrogen bond at peptide carbonyl groups with an optimum geometry and compete with water molecules at these site. Energy minimization of the peptide/alcohol assemblies revealed that alcohols induced a twist in the peptide backbone as a function of (1) the methylene chain length, (2) the hydrogen-bond geometry, (3) halogenation of the molecule, (4) concentration, and (5) the dielectric constant. The rank ordering of the potencies of the alcohols was hexafluoroisopropanol > trifluoroethanol approximately pentanol > butanol > ethanol > methanol. Helix destabilization by cosolvent was measured by examining the hydrogen-bond lengths in peptide structures that resulted from a combination of energy minimization and molecular dynamics simulations. Destabilization was also found to be dependent upon the chemical nature of the alcohol and the hydrogen-bond geometry. The data suggest that alcohols at low concentrations affect protein structure mainly through a combination of hydrogen-bonding and hydrophobic interactions that are influenced by the properties of the solvent.

Alcohols↗

Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study.

A 15-ns molecular dynamics simulation of the fully hydrated liquid-crystalline dimyristoylphosphatidylcholine-cholesterol (DMPC-Chol) bilayer containing approximately 22 mol% Chol was carried out. The generated trajectory was analysed to investigate the mechanism of the Chol condensing effect on DMPC hydrocarbon chains and the influence of Chol on the chain packing in the membrane. Chol was found to induce stronger van der Waals interactions among the chains, whereas its interactions with the chains were weak. In the DMPC-Chol bilayer, as in the DMPC bilayer, DMPC chains were regularly packed around a chosen chain but around a Chol molecule they were not. DMPC gamma chains made closer contacts with Chol than the beta chains.

Cholesterol↗

Imaging of crystal morphology and molecular simulations of surface energies in pentacene thin films.

We have investigated the crystal growth of the organic semiconductor pentacene by complementing molecular simulations of surface energies with experimental images of pentacene films. Pentacene thin films having variations in thickness and grain size were produced by vacuum sublimation. Large (approximately 20 microm) faceted crystals grew on top of the underlying polycrystalline thin film. The films were characterized using optical microscopy (OM), X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Single crystals most commonly grew in a truncated diamond shape with the largest crystal face, (001), growing parallel to the substrate. Crystal morphologies and surface energies were calculated using force field-based molecular simulations. The (001) surface was found to have the lowest energy, at 76 mJ/m(2), which was consistent with experimental observations of crystal face size. It was demonstrated that the morphology of the large faceted crystals approached the equilibrium growth shape of pentacene. From contact angle measurements, the critical surface tension of textured pentacene thin films in air was determined to be 34 mJ/m(2).

Journal Article↗

Magnetoviscosity of semidilute ferrofluids and the role of dipolar interactions: comparison of molecular simulations and dynamical mean-field theory.

Extensive molecular simulations on a model ferrofluid are performed in order to study magnetoviscous and viscoelastic phenomena in semidilute ferrofluids. Simulation results of the nonequilibrium magnetization, shear viscosity, and normal stress differences are presented. Rotational and configurational contributions to the shear viscosity are analyzed and their influence on the magnetoviscous effect is discussed. The simplified model of noninteracting magnetic dipoles describes the nonequilibrium magnetization and the rotational viscosity, but does not account for configurational viscosity contributions and normal stress differences. Improved mean-field models that overcome these limitations show good agreement with the simulation results for weak dipolar interactions where the models should apply. Comparisons to simulation results for various interaction strengths allow us to determine the range of validity of the mean-field models.

Journal Article↗

Folding and mis-folding of peptides and proteins: insights from molecular simulations.

In this paper, the main achievements and problems of the application of all-atom molecular simulations, with particular attention for Molecular Dynamics (MD), will be critically reviewed. Starting from unfolding simulations, through biased simulations, which require a knowledge of the native state conformation, to folding studies based on the simple knowledge of the protein (or peptide) sequence, the strengths and weaknesses of theoretical approaches to the study of folding and their matching with experimental observations will be discussed. Finally, we will give a critical outlook on the possible developments of this field in the near future.

Computer Simulation↗

Evaluation of force fields for molecular simulation of polyhedral oligomeric silsesquioxanes.

Polyhedral oligomeric silsesquioxanes (POSS) are nanometer-size molecules suitable for the production of organic-inorganic nanocomposite materials. These organic-inorganic nano-building blocks show promise for enabling the production of polymeric materials of exceptional mechanical properties as well as novel composite materials. While the experimental studies of these materials have rapidly evolved in the past decade, their theoretical investigation is still in its infancy. Toward the validation of force fields for the molecular simulation of POSS-containing systems, we present the charge-transfer reactive (CTR) force field for the molecular simulation of polyhedral oligomeric silsesquioxane (POSS) molecules and compare the ability of this, and several force fields taken from the literature, to predict the thermophysical properties of POSS-containing systems. The literature force fields compared include the universal force field (UFF) and the COMPASS and Hybrid-COMPASS force fields. Predictions from molecular dynamics simulations of the structural parameters (unit cell vectors), melting temperature, and FT-IR spectra of crystals of POSS monomers are presented. The POSS monomers investigated are octahydride, octamethyl, and octapropyl POSS. Predicted quantities are compared to experimental results where available and provide molecular-level physical insight into several aspects of the behavior of POSS molecules. While all the force fields tested perform reasonably well, our results indicate that the Hybrid-COMPASS and CTR force fields predict structural properties that are in good agreement with experimental data.

Journal Article↗

The rational design of amino acid sequences by artificial neural networks and simulated molecular evolution: de novo design of an idealized leader peptidase cleavage site.

A method for the rational design of locally encoded amino acid sequence features using artificial neural networks and a technique for simulating molecular evolution has been developed. De novo in machine design of Escherichia coli leader peptidase (SP1) cleavage sites serves as an example application. A modular neural network system that employs sequence descriptions in terms of physicochemical properties has been trained on the recognition of characteristic cleavage site features. It is used for sequence qualification in the design cycle, representing the sequence fitness function. Starting from a random sequence several cleavage site sequences were generated by a simulated molecular evolution technique. It is based on a simple genetic algorithm that takes the quality values calculated by the artificial neural network as a heuristic for inductive sequence optimization. Simulated in vivo mutation and selection allows the identification of predominant sequence positions in Escherichia coli signal peptide cleavage site regions (positions -2 and -6). Various amino acid distance maps are used to define metrics for the step size of mutations. Position-specific mutability values indicate sequence positions exposed to high or low selection pressure in the simulations. The use of several distance maps leads to different courses of optimization and to various idealized sequences. It is concluded that amino acid distances are context dependent. Furthermore, a method for identification of local optima during sequence optimization is presented.

Algorithms↗

Using molecular dynamics simulations on crambin to evaluate the suitability of different continuum dielectric and hydrogen atom models for protein simulations.

Molecular dynamics simulations of enzymes with enough explicit waters of solvation to realistically account for solute-solvent interactions can burden the computational resources required to perform the simulation by more than two orders of magnitude. Since enzyme simulations even with an implicit solvation model can be imposing for a supercomputer, it is important to assess the suitability of different continuum dielectric models for protein simulations. A series of 100-picosecond molecular dynamics simulations were performed on the X-ray crystal structure of the protein crambin to examine how well computed structures, obtained using seven continuum dielectric and two hydrogen atom models, agreed with the X-ray structure. The best level of agreement between computed and experimental structures was obtained using a constant dielectric of 2 and the all-hydrogen model. Continuum dielectric models of 1, 1r, and 2r also led to computed structures in reasonably good agreement with the X-ray structure. In all cases, the all-hydrogen model gave better agreement than the united atom model, although, in one case, the difference was not significant. Dielectric models of 4, 80, and 4r with either hydrogen model yielded significantly poorer fits. It is especially noteworthy that the observed trends did not semiquantitatively converge until about 50 picoseconds into the simulations, suggesting that validation studies for protein calculations based on energy minimizations or short simulations should be viewed with caution.

Computer Simulation↗

Molecular simulation of the interlayer structure and the mobility of alkyl chains in HDTMA+/montmorillonite hybrids.

Molecular simulation techniques are used to find the basal spacing of organoclay on the basis of the energy minimum, using the canonical NVT ensemble. Then, the interlayer structure and mobility of alkyl chains are explored based on the interlayer atomic density profiles. Besides the basic lateral-monolayer arrangement, lateral-bilayer accompanied by partial a pseudo-trilayer and a transition structure between the two basic lateral models are observed. The later provides an excellent explanation about the reflection at 16 angstroms on XRD patterns in the literature. The atomic density profiles reveal that nitrogen atoms show stronger layering behavior than carbon atoms do. Our simulation demonstrates that the molecular mobility of the confined alkyl chains decreases from lateral-monolayer to lateral-bilayer with the increase of the intercalated surfactant. This is in accordance with the suggestion deduced from experiments. Furthermore, our simulation indicates that the mobility of the alkyl chains strongly depends on the surfactant arrangement rather than the surfactant packing density.

Journal Article↗

Molecular simulation and theory of a liquid crystalline disclination core

Molecular simulations of a nematic liquid crystal confined in cylinder geometry with homeotropic anchoring have been carried out. The core structure of a disclination line defect of strength +1 has been examined, and comparison made with various theoretical treatments, which are presented in a unified way. It is found that excellent fits to the cylindrically symmetrized order tensor profiles may be obtained with appropriate parameter choices; notwithstanding this, on the time scales of the simulation, the cylindrical symmetry of the core is broken and two defects of strength +1 / 2 may be resolved.

Journal Article↗

Molecular simulations of aqueous electrolyte solubility: 1. The expanded-ensemble osmotic molecular dynamics method for the solution phase.

We have developed a molecular-level simulation technique called the expanded-ensemble osmotic molecular dynamics (EEOMD) method, for studying electrolyte solution systems. The EEOMD method performs simulations at a fixed number of solvent molecules, pressure, temperature, and overall electrolyte chemical potential. The method combines elements of constant pressure-constant temperature molecular dynamics and expanded-ensemble grand canonical Monte Carlo. The simulated electrolyte solution systems contain, in addition to solvent molecules, full and fractional ions and undissociated electrolyte molecular units. The fractional particles are coupled to the system via a coupling parameter that varies between 0 (no interaction between the fractional particle and the other particles in the system) and 1 (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the constant pressure-constant temperature equations of motion and accompanied by random changes in the coupling parameter. The coupling-parameter changes are accepted with a probability derived from the expanded-ensemble osmotic partition function corresponding to the prescribed electrolyte chemical potential. The coupling-parameter changes mimic insertion/deletion of particles as in a crude grand canonical Monte Carlo simulation; if the coupling parameter becomes 0, the fractional particles disappear from the system, and as the coupling parameter reaches unity, the fractional particles become full particles. The method is demonstrated for a model of NaCl in water at ambient conditions. To test our approach, we first determine the chemical potential of NaCl in water by the thermodynamic integration technique and by the expanded-ensemble method. Then, we carry out EEOMD simulations for different specified values of the overall NaCl chemical potential and measure the concentration of ions resulting from the simulations. Both computations give consistent results, validating the EEOMD methodology.

Journal Article↗

Molecular simulation of protein aggregation.

Computer simulation offers unique possibilities for investigating molecular-level phenomena difficult to probe experimentally. Drawing from a wealth of studies concerning protein folding, computational studies of protein aggregation are emerging. These studies have been successful in capturing aspects of aggregation known from experiment and are being used to refine experimental methods aimed at abating aggregation. Here we review molecular-simulation studies of protein aggregation conducted in our laboratory. Specific attention is devoted to issues with implications for biotechnology.

Binding Sites↗

Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: a continuum-electrostatics study.

Artifacts induced by the application of periodic boundary conditions and lattice-sum methods in explicit-solvent simulations of (bio-)molecular systems are nowadays a major concern in the computer-simulation community. The present article reports a first step toward the design of a modified lattice-sum algorithm emulating nonperiodic boundary conditions, and therefore exempt of such periodicity-induced artifacts. This result is achieved here in the (more simple) context of continuum electrostatics. It is shown that an appropriate modification of the periodic Poisson equation and of its boundary conditions leads to a continuum-electrostatics scheme, which, although applied under periodic boundary conditions, exactly mimics the nonperiodic situation. The possible extension of this scheme to explicit-solvent simulations is outlined and its practical implementation will be described in more details in a forthcoming article.

Algorithms↗

Thermal conductivity of diamond nanorods: Molecular simulation and scaling relations.

Thermal conductivities of diamond nanorods are estimated from molecular simulations as a function of radius, length, and degree of surface functionalization. While thermal conductivity is predicted to be lower than carbon nanotubes, their thermal properties are less influenced by surface functionalization, making them prime candidates for thermal management where heat transfer is facilitated by cross-links. A scaling relation based on phonon surface scattering is developed that reproduces the simulation results and experimental measurements on silicon nanowires.

Computer Simulation↗

Generalized-ensemble algorithms for molecular simulations of biopolymers.

In complex systems with many degrees of freedom such as peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems.

Algorithms↗