Showing papers in "Faraday Discussions in 2010"

Mori–Zwanzig formalism as a practical computational tool

Abstract: An operational procedure is presented to compute explicitly the different terms in the generalized Langevin equation (GLE) for a few relevant variables obtained within Mori-Zwanzig formalism. The procedure amounts to introducing an artificial controlled parameter which can be tuned in such a way that the so-called projected dynamics becomes explicit and the GLE reduces to a Markovian equation. The projected dynamics can be realised in practice by introducing constraints, and it is shown that the Green-Kubo formulae computed with these dynamics do not suffer from the plateau problem. The methodology is illustrated in the example of star polymer molecules in a melt using their center of mass as relevant variables. Through this example, we show that not only the effective potentials, but also the friction forces and the noise play a very important role in the dynamics.

Mapping hydrophobicity at the nanoscale: Applications to heterogeneous surfaces and proteins

Abstract: Approaches to quantify wetting at the macroscale do not translate to the nanoscale, highlighting the need for new methods for characterizing hydrophobicity at the small scale. We use extensive molecular simulations to study the hydration of homo and heterogeneous self-assembled monolayers (SAMs) and of protein surfaces. For homogeneous SAMs, new pressure-dependent analysis shows that water displays higher compressibility and enhanced density fluctuations near hydrophobic surfaces, which are gradually quenched with increasing hydrophilicity, consistent with our previous studies. Heterogeneous surfaces show an interesting context dependence – adding a single –OH group in a –CH3 terminated SAM has a more dramatic effect on water in the vicinity compared to that of a single –CH3 group in an –OH background. For mixed –CH3/–OH SAMs, this asymmetry leads to a non-linear dependence of hydrophobicity on the surface concentration. We also present preliminary results to map hydrophobicity of protein surfaces by monitoring local density fluctuations and binding of probe hydrophobic solutes. These molecular measures account for the behavior of protein's hydration water, and present a more refined picture of its hydrophobicity map. At least for one protein, hydrophobin-II, we show that the hydrophobicity map is different from that suggested by a commonly used hydropathy scale.

Multiscale simulation of soft matter systems.

Abstract: This paper gives a short introduction to multiscale simulation approaches in soft matter science. This paper is based on and extended from a previous review.1 (1. C. Peter and K. Kremer, Soft Matter, 2009, DOI:10.1039/b912027k.) It also includes a discussion of aspects of soft matter in general and a short account of one of the historically underlying concepts, namely renormalization group theory. Some different concepts and several typical problems are shortly addressed, including a (more personal) view on challenges and chances.

The search for the hydrophobic force law

Abstract: After nearly 30 years of research on the hydrophobic interaction, the search for the hydrophobic force law is still continuing. Indeed, there are more questions than answers, and the experimental data are often quite different for nominally similar conditions, as well as, apparently, for nano-, micro-, and macroscopic surfaces. This has led to the conclusion that the experimentally observed force–distance relationships are either a combination of different ‘fundamental’ interactions, or that the hydrophobic force-law, if there is one, is complex – depending on numerous parameters. The only unexpectedly strong attractive force measured in all experiments so far has a range of D ≈ 100–200 A, increasing roughly exponentially down to ∼10–20 A and then more steeply down to adhesive contact at D = 0 or, for power-law potentials, effectively at D ≈ 2 A. The measured forces in this regime (100–200 A) and especially the adhesive forces are much stronger, and have a different distance-dependence from the continuum VDW force (Lifshitz theory) for non-conducting dielectric media. We suggest a three-regime force-law for the forces observed between hydrophobic surfaces: In the first, from 100–200 A to thousands of angstroms, the dominating force is created by complementary electrostatic domains or patches on the apposing surfaces and/or bridging vapour cavities; a ‘pure’ but still not well-understood ‘long-range hydrophobic force’ dominates the second regime from ∼150 to ∼15 A, possibly due to an enhanced Hamaker constant associated with the ‘proton-hopping’ polarizability of water; while below ∼10–15 A to contact there is another ‘pure short-range hydrophobic force’ related to water structuring effects associated with surface-induced changes in the orientation and/or density of water molecules and H-bonds at the water–hydrophobic interface. We present recent SFA and other experimental results, as well as a simplified model for water based on a spherically-symmetric potential that is able to capture some basic features of hydrophobic association. Such a model may be useful for theoretical studies of the HI over the broad range of scales observed in SFA experiments.

Systematic coarse-graining of molecular models by the Newton inversion method.

Abstract: Systematic construction of coarse-grained molecular models from detailed atomistic simulations, and even from ab initio simulations is discussed. Atomistic simulations are first performed to extract structural information about the system, which is then used to determine effective potentials for a coarse-grained model of the same system. The statistical-mechanical equations expressing the canonical properties in terms of potential parameters can be inverted and solved numerically according to the iterative Newton scheme. In our previous applications, known as the Inverse Monte Carlo, radial distribution functions were inverted to reconstruct pair potential, while in a more general approach the targets can be other canonical averages. We have considered several examples of coarse-graining; for the united atom water model we suggest an easy way to overcome the known problem of high pressure. Further, we have developed coarse-grained models for L- and D-prolines, dissolved here in an organic solvent (dimethylsulfoxide), keeping their enantiomeric properties from the corresponding all-atom proline model. Finally, we have revisited the previously developed coarse-grained lipid model based on an updated all-atomic force field. We use this model in large-scale meso-scale simulations demonstrating spontaneous formation of different structures, such as vesicles, micelles, and multi-lamellar structures, depending on thermodynamical conditions.

Contact angle hysteresis: a different view and a trivial recipe for low hysteresis hydrophobic surfaces

Abstract: Contact angle hysteresis is addressed from two perspectives. The first is an analysis of the events that occur during motion of droplets on superhydrophobic surfaces. Hysteresis is discussed in terms of receding contact line pinning and the tensile failure of capillary bridges. The sign of the curvature of the solid surface is implicated as playing a key role. The second is the report of a new method to prepare smooth low hysteresis surfaces. The thermal treatment of oxygen plasma-cleaned silicon wafers with trimethylsilyl-terminated linear poly(dimethylsiloxane) (PDMS - commercial silicone oils) in disposable glass vessels is described. This treatment renders silicon/silica surfaces that contain covalently attached PDMS chains. The grafted layers of nanometre scale thickness are liquid-like (rotationally dynamic at room temperature), decrease activation barriers for contact line motion and minimize water contact angle hysteresis. This simple method requires neither sophisticated techniques nor substantial laboratory skills to perform.

Oxidation of alcohols using supported gold and gold–palladium nanoparticles

Abstract: A key discovery in the last two decades has been the realisation that gold, when prepared as supported nanoparticles, is exceptionally effective as an oxidationcatalyst, particularly for the oxidation of carbon monoxide at sub-ambient temperature but also for a number of organic reactions of synthetic significance. To some extent this observation is counterintuitive since extended gold surfaces do not chemisorb oxygen, nor do they corrode. For some oxidation reactions, the catalytic activity is markedly enhanced by the addition of palladium. This paper is concerned with recent advances in understanding the mechanism of catalysis by gold–palladium alloy nanoparticles of one such organic reaction, the oxidation of alcohols to the corresponding carbonyl compounds by molecular oxygen. We report detailed reaction studies using a high activity catalyst prepared by sol-immobilisation on a titania support. Using solvent-free conditions, benzyl alcohol is oxidised primarily to benzaldehyde but small amounts of toluene are also formed. The origin of these products is explored using initial rate measurements, deuterium labelling and kinetic isotope effects, and by the study of substituent effects. The effect of changing the nature of the catalyst support is also briefly examined. On the basis of all the results, we consider that we have evidence for multiple reaction pathways in this heterogeneous system. We put forward general mechanisms for the overall processes and describe confirmatory experiments in support of these, and we suggest possible reaction intermediates involved in the heterogeneously catalysed reaction.

Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

Abstract: Antimicrobial peptides (AMPs) comprise a large family of peptides that include small cationic peptides, such as magainins, which permeabilize lipid membranes. Previous atomistic level simulations of magainin-H2 peptides show that they act by forming toroidal transmembrane pores. However, due to the atomistic level of description, these simulations were necessarily limited to small system sizes and sub-microsecond time scales. Here, we study the long-time relaxation properties of these pores by evolving the systems using a coarse-grain (CG) description. The disordered nature and the topology of the atomistic pores are maintained at the CG level. The peptides sample different orientations but at any given time, only a few peptides insert into the pore. Key states observed at the CG level are subsequently back-transformed to the atomistic level using a resolution-transformation protocol. The configurations sampled at the CG level are stable in the atomistic simulation. The effect of helicity on pore stability is investigated at the CG level and we find that partial helicity is required to form stable pores. We also show that the current CG scheme can be used to study spontaneous poration by magainin-H2 peptides. Overall, our simulations provide a multi-scale view of a fundamental biophysical membrane process involving a complex interplay between peptides and lipids.

Untangling the chemical evolution of Titan's atmosphere and surface–from homogeneous to heterogeneous chemistry

Abstract: In this article, we first explored the chemical dynamics of simple diatomic radicals (dicarbon, methylidyne) utilizing the crossed molecular beams method. This versatile experimental technique can be applied to study reactions relevant to the atmospheres of planets and their moons as long as intense and stable supersonic beam sources of the reactant species exist. By focusing on reactions of dicarbon with hydrogen cyanide, we untangled the contribution of dicarbon in its singlet ground and first excited triplet states. These results were applied to understand and re-analyze the data of crossed beam reactions of the isoelectronic dicarbon plus acetylene reaction. Further, we investigated the interaction of ionizing radiation in form of energetic electrons with organic molecules ethane and propane sequestered on Titan’s surface. These experiments presented compelling evidence that even at irradiation exposures equivalent to about 44 years on Titan’s surface, aliphatic like organic residues can be produced on Titan’s surface with thicknesses up to 1.5 m. Finally, we investigated how Titan’s nascent chemical inventory can be altered by an external influx of matter as supplied by (micro)meteorites and possibly comets. For this, we simulated the ablation process in Titan’s atmosphere, which can lead to ground and electronically excited atoms of, for instance, the principal constituents of silicates like iron, silicon, and magnesium, in laboratory experiments. By ablating silicon species and seeding the ablated species in acetylene carrier gas, which also acts as a reactant, we produced organo silicon species, which were then photoionized utilizing tunable VUV radiation from the Advanced Light Source. In combination with electronic structure calculations, the structures and ionization energies of distinct organo-silicon species were elucidated.

Water reorientation, hydrogen-bond dynamics and 2D-IR spectroscopy next to an extended hydrophobic surface

Abstract: The dynamics of water next to hydrophobic groups is critical for several fundamental biochemical processes such as protein folding and amyloid fiber aggregation. Some biomolecular systems, like melittin or other membrane-associated proteins, exhibit extended hydrophobic surfaces. Due to the strain these surfaces impose on the hydrogen (H)-bond network, the water molecules shift from the clathrate-like arrangement observed around small solutes to an anticlathrate-like geometry with some dangling OH bonds pointing toward the surface. Here we examine the water reorientation dynamics next to a model hydrophobic surface through molecular dynamics simulations and analytic modeling. We show that the water OH bonds lying next to the hydrophobic surface fall into two subensembles with distinct dynamical reorientation properties. The first is the OH bonds tangent to the surface; these exhibit a behavior similar to the water OHs around small hydrophobic solutes, i.e. with a moderate reorientational slowdown explained by an excluded volume effect due to the surface. The second is the dangling OHs pointing toward the surface: these are not engaged in any H-bond, reorient much faster than in the bulk, and exhibit an unusual anisotropy decay which becomes negative for delays of a few picoseconds. The H-bond dynamics, i.e. the exchanges between the different configurations, and the resulting anisotropy decays are analyzed within the analytic extended jump model. We also show that a recent spectroscopy technique, two-dimensional time resolved vibrational spectroscopy (2D-IR), can be used to selectively follow the dynamics of dangling OHs, since these are spectrally distinct from H-bonded ones. By computing the first 2D-IR spectra of water next to a hydrophobic surface, we establish a connection between the spectral dynamics and the dynamical properties that we obtain directly from the simulations.

Mesoscopic modelling of colloids in chiral nematics

Abstract: We present numerical modelling of colloidal particles in chiral nematics with cubic symmetry (blue phases) within the framework of the Landau-de Gennes free energy. The interaction potential of a single, nano-sized colloidal particle with a −1/2 disclination line is calculated as a generic trapping mechanism for particles within the cholesteric blue phases. The interaction potential is shown to be highly anisotropic and have threefold rotational symmetry. We discuss the equilibration of the colloidal texture with respect to particle positions and the unit cell size of the blue phase. We also describe how preservation of the liquid crystal volume and the number of particles allows blue phase colloidal structures with different unit cell sizes and configurations to be compared numerically.

Concerted diffusion of lipids in raft-like membranes.

Abstract: Currently, there is no comprehensive model for the dynamics of cellular membranes. The understanding of even the basic dynamic processes, such as lateral diffusion of lipids, is still quite limited. Recent studies of one-component membrane systems have shown that instead of single-particle motions, the lateral diffusion is driven by a more complex, concerted mechanism for lipid diffusion (E. Falck et al., J. Am. Chem. Soc., 2008, 130, 44-45), where a lipid and its neighbors move in unison in terms of loosely defined clusters. In this work, we extend the previous study by considering the concerted lipid diffusion phenomena in many-component raft-like membranes. This nature of diffusion phenomena emerge in all the cases we have considered, including both atom-scale simulations of lateral diffusion within rafts and coarse-grained MARTINI simulations of diffusion in membranes characterized by coexistence of raft and non-raft domains. The data allows us to identify characteristic time scales for the concerted lipid motions, which turn out to range from hundreds of nanoseconds to several microseconds. Further, we characterize typical length scales associated with the correlated lipid diffusion patterns and find them to be about 10 nm, or even larger if weak correlations are taken into account. Finally, the concerted nature of lipid motions is also found in dissipative particle dynamics simulations of lipid membranes, clarifying the role of hydrodynamics (local momentum conservation) in membrane diffusion phenomena.

Superhydrophobic surfaces by hybrid raspberry-like particles

Abstract: Surface roughness on different length scales is favourable for superhydrophobic behaviour of surfaces. Here we report (i) an improved synthesis for hybrid raspberry-like particles and (ii) a novel method to obtain superhydrophobic films of good mechanical stability. Polystyrene spheres with a diameter of 400 nm–1 μm are decorated with silica colloids < 100 nm in size, thus introducing surface asperities on a second length scale. To improve mechanical resistance, we then coated the polystyrene core and attached silica colloids with a smooth silica shell of 10 nm to 40 nm thickness. All three steps of this synthesis procedure can be sensitively tuned so that the average size and number of the silica colloids as well as the morphology of the resulting raspberry particles can be predicted. As the particles disperse in water, either monolayers can be prepared by dip coating or multilayers by drop casting. Although mechanically stable, the shells are porous enough to allow for leakage of molten or dissolved polystyrene from the core. In tetrahydrofuran vapour polystyrene bridges form between the particles that render the multilayer-film stable. Leaked polystyrene that masks some asperities can be removed by plasma cleaning. Surface roughness on larger scales can be tuned by the drying procedure. The films are hydrophobized by silanization with a semi-fluorinate silane.

Ab initio transition state theory for polar reactions in solution

Abstract: New ab initio calculations are reported for two typical organic reactions of polar species, the Wittig reaction of the stabilized ylide Ph3PCHCO2CH3 with benzaldehyde, and the Morita–Baylis–Hillman reaction of the Michael acceptor methyl acrylate with benzaldehyde, catalyzed by quinuclidine. The vacuum ab initio data is combined with continuum solvent models in an attempt to predict solution rate constants. The results show (a) that calculations can now be carried out using accurate local correlation methods with large basis sets for systems with over fifty atoms; (b) that many ‘standard’ computational methods, while qualitatively useful, and known to give accurate results for small molecular systems, can be very inaccurate for large reactive partners; and (c) that predicting rate constants quantitatively is very difficult.

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

Abstract: Recent years have seen dramatic improvements in computer power, allowing ever more challenging problems to be approached. In light of this, it is imperative to have a quantitative model for examining chemical reactivity, both in the condensed phase and in solution, as well as to accurately quantify physical organic chemistry (particularly as experimental approaches can often be inconclusive). Similarly, computational approaches allow for great progress in studying enzyme catalysis, as they allow for the separation of the relevant energy contributions to catalysis. Due to the complexity of the problems that need addressing, there is a need for an approach that can combine reliability with an ability to capture complex systems in order to resolve long-standing controversies in a unique way. Herein, we will demonstrate that the empirical valence bond (EVB) approach provides a powerful way to connect the classical concepts of physical organic chemistry to the actual energies of enzymatic reactions by means of computation. Additionally, we will discuss the proliferation of this approach, as well as attempts to capture its basic chemistry and repackage it under different names. We believe that the EVB approach is the most powerful tool that is currently available for studies of chemical processes in the condensed phase in general and enzymes in particular, particularly when trying to explore the different proposals about the origin of the catalytic power of enzymes.

Interfacial thermodynamics of confined water near molecularly rough surfaces.

Abstract: We study the effects of nanoscopic roughness on the interfacial free energy of water confined between solid surfaces. SPC/E water is simulated in confinement between two infinite planar surfaces that differ in their physical topology: one is smooth and the other one is physically rough on a sub-nanometre length scale. The two thermodynamic ensembles considered, with constant pressure either normal or parallel to the walls, correspond to different experimental conditions. We find that molecular-scale surface roughness significantly increases the solid–liquid interfacial free energy compared to the smooth surface. For our surfaces with a water-wall interaction energy minimum of −1.2 kcal mol−1, we observe a transition from a hydrophilic surface to a hydrophobic surface at a roughness amplitude of about 3 A and a wavelength of 11.6 A, with the interfacial free energy changing sign from negative to positive. In agreement with previous studies of water near hydrophobic surfaces, we find an increase in the isothermal compressibility of water with increasing surface roughness. Interestingly, average measures of the water density and hydrogen-bond number do not contain distinct signatures of increased hydrophobicity. In contrast, a local analysis indicates transient dewetting of water in the valleys of the rough surface, together with a significant loss of hydrogen bonds, and a change in the dipole orientation toward the surface. These microscopic changes in the density, hydrogen bonding, and water orientation contribute to the large increase in the interfacial free energy, and the change from a hydrophilic to a hydrophobic character of the surface.

H3+ cooling in planetary atmospheres.

Abstract: We review the role of H3+ in planetary atmospheres, with a particular emphasis on its effect in cooling and stabilising, an effect that has been termed the “H3+ thermostat” (see Miller et al., Philos. Trans. R. Soc. London, Ser. A, 2000, 58, 2485). In the course of our analysis of this effect, we found that cooling functions that make use of the partition function, Q(T) based on the calculated H3+ energy levels of Neale and Tennyson (Astrophys. J., 1995, 454, L169) may underestimate just how much energy this ion is radiating to space. So we present a new fit to the calculated values of Q(T) that is accurate to within 2% for the range 100 K to 10 000 K, a very significant improvement on the fit originally provided by Neale and Tennyson themselves. We also present a fit to Q(T) calculated from only those values Neale and Tennyson computed from first principles, which may be more appropriate for planetary scientists wishing to calculate the amount of atmospheric cooling from the H3+ ion.

Formation of NH3 and CH2NH in Titan's upper atmosphere

Abstract: The large abundance of NH3 in Titan's upper atmosphere is a consequence of coupled ion and neutral chemistry. The density of NH3 is inferred from the measured abundance of NH4+. NH3 is produced primarily through reaction of NH2 with H2CN, a process neglected in previous models. NH2 is produced by several reactions including electron recombination of CH2NH2+. The density of CH2NH2+ is closely linked to the density of CH2NH through proton exchange reactions and recombination. CH2NH is produced by reaction of N(2D) and NH with ambient hydrocarbons. Thus, production of NH3 is the result of a chain of reactions involving non-nitrile functional groups and the large density of NH3 implies large densities for these associated molecules. This suggests that amine and imine functional groups may be incorporated as well in other, more complex organic molecules.

The influence of molecular-scale roughness on the surface spreading of an aqueous nanodrop

Abstract: We examine the effect of nanoscale roughness on spreading and surface mobility of water nanodroplets. Using molecular dynamics, we consider model surfaces with sub-nanoscale asperities at varied surface coverage and with different distribution patterns. We test materials that are hydrophobic, and those that are hydrophilic in the absence of surface corrugations. Interestingly, on both types of surfaces, the introduction of surface asperities gives rise to a sharp increase in the apparent contact angle. The Cassie–Baxter equation is obeyed approximately on hydrophobic substrates, however, the increase in the contact angle on a hydrophilic surface differs qualitatively from the behavior on macroscopically rough surfaces described by the Wenzel equation. On the hydrophobic substrate, the superhydrophobic state with the maximal contact angle of 180 degrees is reached when the asperity coverage falls below 25%, suggesting that superhydrophobicity can also be achieved by the nanoscale roughness of a macroscopically smooth material. We further examine the effect of surface roughness on droplet mobility on the substrate. The apparent diffusion constant shows a dramatic slow down of the nanodroplet translation even for asperity coverage in the range of 1% for a hydrophilic surface, while droplets on corrugated hydrophobic surfaces retain the ability to flow around the asperities. In contrast, for smooth surfaces we find that the drop mobility on the hydrophilic surface exceeds that on the hydrophobic one.

Formation of nitriles and imines in the atmosphere of Titan: combined crossed-beam and theoretical studies on the reaction dynamics of excited nitrogen atoms N(2D) with ethane

Abstract: The dynamics of the H-displacement channels in the reaction N(2D) + C2H6 have been investigated by the crossed molecular beam technique with mass spectrometric detection and time-of-flight analysis at two different collision energies (18.0 and 31.4 kJ mol−1). From the derived center-of-mass product angular and translational energy distributions the reaction micromechanisms and the product energy partitioning have been obtained. The interpretation of the scattering results is assisted by new ab initio electronic structure calculations of stationary points and product energetics for the C2H6N ground state doublet potential energy surface. C–C bond breaking and NH production channels have been theoretically characterized and the statistical branching ratio derived at the temperatures relevant for the atmosphere of Titan. Methanimine plus CH3 and ethanimine plus H are the main reaction channels. Implications for the atmospheric chemistry of Titan are discussed.

Volatile inventories in clathrate hydrates formed in the primordial nebula

Abstract: The examination of ambient thermodynamic conditions suggests that clathrate hydrates could exist in the Martian permafrost, on the surface and in the interior of Titan, as well as in other icy satellites. Clathrate hydrates are probably formed in a significant fraction of planetesimals in the solar system. Thus, these crystalline solids may have been accreted in comets, in the forming giant planets and in their surrounding satellite systems. In this work, we use a statistical thermodynamic model to investigate the composition of clathrate hydrates that may have formed in the primordial nebula. In our approach, we consider the formation sequence of the different ices occurring during the cooling of the nebula, a reasonable idealization of the process by which volatiles are trapped in planetesimals. We then determine the fractional occupancies of guests in each clathrate hydrate formed at a given temperature. The major ingredient of our model is the description of the guest–clathrate hydrate interaction by a spherically averaged Kihara potential with a nominal set of parameters, most of which are fitted to experimental equilibrium data. Our model allows us to find that Kr, Ar and N2 can be efficiently encaged in clathrate hydrates formed at temperatures higher than ∼48.5 K in the primitive nebula, instead of forming pure condensates below 30 K. However, we find at the same time that the determination of the relative abundances of guest species incorporated in these clathrate hydrates strongly depends on the choice of the parameters of the Kihara potential and also on the adopted size of cages. Indeed, by testing different potential parameters, we have noted that even minor dispersions between the different existing sets can lead to non-negligible variations in the determination of the volatiles trapped in clathrate hydrates formed in the primordial nebula. However, these variations are not found to be strong enough to reverse the relative abundances between the different volatiles in the clathrate hydrates themselves. On the other hand, if contraction or expansion of the cages due to temperature variations are imposed in our model, the Ar and Kr mole fractions can be modified up to several orders of magnitude in clathrate hydrates. Moreover, mole fractions of other molecules such as N2 or CO are also subject to strong changes with the variation of the size of the cages. Our results may affect the predictions of the composition of the planetesimals formed in the outer solar system. In particular, the volatile abundances calculated in the giant planets’ atmospheres should be altered because these quantities are proportional to the mass of accreted and vaporized icy planetesimals. For similar reasons, the estimates of the volatile budgets accreted by icy satellites and comets may also be altered by our calculations. For instance, under some conditions, our calculations predict that the abundance of argon in the atmosphere of Titan should be higher than the value measured by Huygens. Moreover, the Ar abundance in comets could be higher than the value predicted by models invoking the incorporation of volatiles in the form of clathrate hydrates in these bodies.

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

Abstract: An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a heterogeneous elastic network, while the lipids are modeled using the hybrid analytic-systematic (HAS) methodology, where in both cases atomistic level information obtained from molecular dynamics simulation is used to parameterize the model. A feature of this approach is that from the outset liposome length scales are employed in the simulation (i.e., on the order of 1/2 a million lipids plus protein). A route to develop highly coarse-grained models from molecular-scale information is proposed and results for N-BAR domain protein remodeling of a liposome are presented.

Transparent superhydrophobic and highly oleophobic coatings.

Abstract: We report a facile process for fabrication of transparent superhydrophobic and highly oleophobic surfaces through assembly of silica nanoparticles and sacrificial polystyrene nanoparticles. The silica and polystyrene nanoparticles are first deposited by a layer-by-layer assembly technique. The polystyrene nanoparticles are then removed by calcination, which leaves a porous network of silica nanoparticles. The cavities created by the sacrificial polystyrene particles form overhang structures on the surfaces. Modified with a fluorocarbon molecule, such surfaces are superhydrophobic and transparent. They also repel liquids with low surface tensions, such as hexadecane, due to the overhang structures that prevent liquids from getting into the air pockets even though the intrinsic contact angles of these liquids are less than 90°.

Drop dynamics on hydrophobic and superhydrophobic surfaces

Abstract: We investigate the dynamics of micron-scale drops pushed across a hydrophobic or superhydrophobic surface. The velocity profile across the drop varies from quadratic to linear with increasing height, indicating a crossover from a sliding to a rolling motion. We identify a mesoscopic slip capillary number which depends only on the motion of the contact line and the shape of the drop, and show that the angular velocity of the rolling increases with increasing viscosity. For drops on superhydrophobic surfaces we argue that a tank treading advance from post to post replaces the diffusive relaxation that allows the contact line to move on smooth surfaces. Hence drops move on superhydrophobic surfaces more quickly than on smooth geometries.

Meteoric ion layers in the Martian atmosphere

Abstract: Low-lying plasma layers have been observed sporadically in the Martian atmosphere by radio occultation measurements from spacecraft such as the Mars Express Orbiter and the Mars Global Surveyor. These layers are just a few km wide, and tend to occur around 90 km. It has been proposed that the layers consist of metallic ions, for two reasons: they occur in the aerobraking region of the planet where meteoroids ablate; and they resemble sporadic E layers in the terrestrial atmosphere which are known to be composed principally of Fe+ and Mg+ ions. This paper addresses the problem of how metallic ions can persist in a CO2-rich atmosphere, where the ions should be neutralized rapidly by formation of metal–CO2 cluster ions followed by dissociative electron recombination. Laboratory studies using the pulsed laser photolysis/laser induced fluorescence and flow tube/mass spectrometer techniques were used to measure the following rate coefficients: k (Mg+ + CO2 (+ CO2) → Mg+.CO2, 190–403 K) = (5.3 ± 0.7) × 10−29 (T/300 K)(−1.86±0.03) cm6 molecule−2 s−1; k(Mg+.CO2 + O2 → MgO2+ + CO2, 297 K) = (2.2 ± 0.8) × 10−11 cm3 molecule−1 s−1; k(MgO2+ + O → MgO+ + O2, 297 K) = (6.5 ± 1.8) × 10−10 cm3 molecule−1 s−1; and k(MgO+ + O → Mg+ + O2, 297 K) = (5.9 ± 2.4) × 10−10 cm3 molecule−1 s−1. A model of magnesium and iron chemistry in the Martian atmosphere was then constructed, which includes meteoric differential ablation rates calculated with the Leeds CABMOD model, photo-ionization, and gas-phase ion–molecule and neutral chemistry. The model shows that nearly all the metallic ions between 70 and 110 km should be Mg+, because the reactions of MgO2+ and MgO+ with atomic O are fast enough to prevent these molecular ions undergoing dissociative electron recombination (unlike the analogous Fe species). There are enough Mg+ ions to form sporadic layers of the observed plasma density, and the layers can have a lifetime against neutralization in excess of 20 h.

Coarse-grained simulations of charge, current and flow in heterogeneous media

Abstract: We present a coarse-grained simulation method for complex charged systems. This mesoscopic model couples a hydrodynamic description to a free energy functional accounting for the interactions between solvent(s) and charged solutes. It is implemented in a hybrid lattice-based algorithm, whereby the evolution of the overall mass and momentum is taken care of via a Lattice Boltzmann scheme, whereas the composition and ionic concentrations are updated using the link-flux method. Several applications illustrate the power of this coarse-grained model for charged heterogeneous media: the transport of charged tracers in charged porous media, the deformation of an oil droplet in water under the effect of an applied electric field, and the distribution of ions at an oil–water interface as a function of their affinity for both solvents.

Simulations of theoretically informed coarse grain models of polymeric systems

Abstract: Simulations of theoretically informed coarse grain models, where the interaction energy is given by a functional of the local density, are discussed in the context of polymeric melts. Two different implementations are presented by addressing two examples. The first relies on a grid-based representation of non-bonded interactions and focuses on the concept of density multiplication in block copolymer lithography. Monte Carlo simulations are used in a high-throughput manner to explore the parameter space, and to identify morphologies amenable to lithographic fabrication. In the second example, which focuses on the order–disorder transition of block copolymers, the constraints imposed by a grid are removed, thereby enabling simulations in arbitrary ensembles and direct calculation of local stresses and free energies.

Spiers Memorial Lecture: Interplay of theory and computation in chemistry—examples from on-water organic catalysis, enzyme catalysis, and single-molecule fluctuations

Abstract: In this lecture, several examples are considered that illustrate the interplay of experiment, theory, and computations. The examples include on-water catalysis of organic reactions, enzymatic catalysis, single molecule fluctuations, and some much earlier work on electron transfer and atom or group transfer reactions. Computations have made a major impact on our understanding and in the comparisons with experiments. There are also major advantages of analytical theories that may capture in a single equation an entire field and relate experiments of one type to those of another. Such a theory has a generic quality. These topics are explored in the present lecture.

Negative ions at Titan and Enceladus: recent results

Abstract: The detection of heavy negative ions (up to 13 800 amu) in Titan's ionosphere is one of the tantalizing new results from the Cassini mission. These heavy ions indicate for the first time the existence of heavy hydrocarbon and nitrile molecules in this primitive Earth-like atmosphere. These ions were suggested to be precursors of aerosols in Titan's atmosphere and may precipitate to the surface as tholins. We present the evidence for and the analysis of these heavy negative ions at Titan. In addition we examine the variation of the maximum mass of the Titan negative ions with altitude and latitude for the relevant encounters so far, and we discuss the implications for the negative ion formation process. We present data from a recent set of encounters where the latitude was varied between encounters, with other parameters fixed. Models are beginning to explain the low mass negative ions, but the formation process for the higher mass ions is still not understood. It is possible that the structures may be chains, rings or even fullerenes. Negative ions, mainly water clusters in this case, were seen during Cassini's recent close flybys of Enceladus. We present mass spectra from the Enceladus plume, showing water clusters and additional species. As at Titan, the negative ions indicate chemical complexities which were unknown before the Cassini encounters, and are indicative of a complex balance between neutrals and positively and negatively charged ions.

Lateral pressure profiles in lipid monolayers

Abstract: We have used molecular dynamics simulations with coarse-grained and atomistic models to study the lateral pressure profiles in lipid monolayers. We first consider simple oil/air and oil/water interfaces, and then proceed to lipid monolayers at air/water and oil/water interfaces. The results are qualitatively similar in both atomistic and coarse-grained models. The lateral pressure profile in a monolayer is characterized by a headgroup/water pressure-interfacial tension-chain pressure pattern. In contrast to lipid bilayers, the pressure decreases towards the chain free ends. An additional chain/air tension peak is present in monolayers at the air/water interface. Lateral pressure profiles are calculated for monolayers of different lipid composition under varying surface tension. Increasing the surface tension suppresses both pressure peaks and widens the interfacial tension in monolayers at the oil/water interface, and mainly suppresses the chain pressure in monolayers at the air/water interface. In monolayers in the liquid-condensed phase, the pressure peaks split due to ordering. Variation of lipid composition leads to noticeable changes in all regions of the pressure profile at a fixed surface tension.