Statistics of a hydrophobic chain near a hydrophobic boundary

The European Physical Journal E - We study the behavior of a hydrophobic chain near a hydrophobic boundary in two dimensions, adapting the decorated lattice model of Berkema and Widom (G.T....     

微通道疏水表面滑移的耗散粒子动力学研究

了解疏水表面的滑移规律对其在流动减阻方面的应用至关重要.利用耗散粒子动力学(dissipative particle dynamics, DPD)方法研究了微通道疏水表面的滑移现象.采用固定住的粒子并配合修正的向前反弹机制,构建了DPD固体壁面边界模型,利用该边界模型模拟了平板间的Couette流动.研究结果表明,通过调整壁面与流体间排斥作用强度,壁面能实现从无滑移到滑移的转变,壁面与流体间排斥作用越强,即疏水性越强,壁面滑移越明显,并且滑移长度与接触角之间存在近似的二次函数关系.无滑移时壁面附近密度分布均匀,有滑移时壁面附近存在低密度区域,低密度区域阻碍了动量传递,致使壁面产生滑移.     

Liquid polyamorphism: Possible relation to the anomalous behaviour of water

We present evidence from experiments and computer simulations supporting the hypothesis that water displays polyamorphism, i.e., water separates into two distinct liquid phases. This concept of a new liquid-liquid phase transition is finding application to other liquids as well as water, such as silicon and silica. Specifically, we investigate, the relation between changes in dynamic and thermodynamic anomalies arising from the presence of the liquid-liquid critical point in (i) Two models of water, TIP5P and ST2, which display a first order liquid-liquid phase transition at low temperatures; (ii) the Jagla model, a spherically symmetric two-scale potential known to possess a liquid-liquid critical point, in which the competition between two liquid structures is generated by repulsive and attractive ramp interactions; and (iii) A Hamiltonian model of water where the idea of two length/energy scales is built in. This model also displays a first order liquid-liquid phase transition at low temperatures besides the first order liquid-gas phase transition at high temperatures. We find a correlation between the dynamic fragility crossover and the locus of specific heat maxima C_P^max (“Widom line”) emanating from the critical point. Our findings are consistent with a possible relation between the previously hypothesised liquid-liquid phase transition and the transition in the dynamics recently observed in neutron scattering experiments on confined water. More generally, we argue that this connection between C_P^max and the dynamic crossover is not limited to the case of water, a hydrogen bonded network liquid, but is a more general feature of crossing the Widom line, an extension of the first-order coexistence line in the supercritical region. Dedicated to Armin Bunde on the occasion of his 60th birthday.     

Collapse transitions of a periodic hydrophilic hydrophobic chain

We study a single self avoiding hydrophilic hydrophobic polymer chain, through Monte-Carlo lattice simulations. The affinity of monomer i for water is characterized by a (scalar) charge , and the monomer-water interaction is short-ranged. Assuming incompressibility yields an effective short ranged interaction between monomer pairs (i,j), proportional to . In this article, we take (resp. ()) for hydrophilic (resp. hydrophobic) monomers and consider a chain with (i) an equal number of hydro-philic and -phobic monomers (ii) a periodic distribution of the along the chain, with periodicity 2p. The simulations are done for various chain lengths N, in d=2 (square lattice) and d=3 (cubic lattice). There is a critical value p _c (d,N) of the periodicity, which distinguishes between different low temperature structures. For p >p _c , the ground state corresponds to a macroscopic phase separation between a dense hydrophobic core and hydrophilic loops. For p <p _c (but not too small), one gets a microscopic (finite scale) phase separation, and the ground state corresponds to a chain or network of hydrophobic droplets, coated by hydrophilic monomers. We restrict our study to two extreme cases, and to illustrate the physics of the various phase transitions. A tentative variational approach is also presented. Received: 10 March 1998 / Received in final form: 25 June 1998 / Accepted: 1st July 1998     

Ion specific protein assembly and hydrophobic surface forces

Large anions are attracted to hydrophobic surfaces while smaller, well solvated ions are repelled. Using a combination of explicit solvent and continuum model simulations we show that this leads to significant ion-specific protein-protein interactions due to hydrophobic patches on the protein surfaces. In solutions of NaI and NaCl we calculate the potentials of mean force and find that the resulting second virial coefficients for lysozyme correspond well with experiment. We argue that ionic interactions with nonpolar surface groups may play an important role for biomolecular assembly and Hofmeister-type effects.     

Monte Carlo simulations of an amphiphilic polymer at a hydrophobic/hydrophilic interface

Monte Carlo simulations have been carried out for an off-lattice model of an amphiphilic polymer at a hydrophobic/hydrophilic interface. The model system consists of a polynorbornene backbone with poly(ethylene oxide) (PEO) grafts modelled atomistically at an idealized interface between hydrophobic and hydrophilic regions, which are represented by external potentials. Results are presented for the distribution of PEO chain ends, and the density of PEO segments perpendicular to the surface. The latter is used to provide predictions for neutron reflectivity profiles normal to the surface as a function of the lateral confinement of the PEO grafts. At low surface coverage the simulation results are found to be in good agreement with experimental neutron scattering results from similar polymers studied at the water/air interface.     

Nanodroplets on rough hydrophilic and hydrophobic surfaces

We present results of Molecular Dynamics (MD) calculations on the behavior of liquid nanodroplets on rough hydrophobic and hydrophilic solid surfaces. On hydrophobic surfaces, the contact angle for nanodroplets depends strongly on the root-mean-square roughness amplitude, but it is nearly independent of the fractal dimension of the surface. Since increasing the fractal dimension increases the short-wavelength roughness, while the long-wavelength roughness is almost unchanged, we conclude that for hydrophobic interactions the short-wavelength (atomistic) roughness is not very important. We show that the nanodroplet is in a Cassie-like state. For rough hydrophobic surfaces, there is no contact angle hysteresis due to strong thermal fluctuations, which occur at the liquid-solid interface on the nanoscale. On hydrophilic surfaces, however, there is strong contact angle hysteresis due to higher energy barrier. These findings may be very important for the development of artificially biomimetic superhydrophobic surfaces.     

Dynamics of alpha helix formation in the CSAW model

We study the folding dynamics of polyalanine (Ala20), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain in Brownian motion, with interactions that include hydrophobic force and internal hydrogen bonding. We find that large-scale structures form before small-scale structures, and obtain the relevant relaxation times. We find that helix nucleation occurs at two separate points on the protein chain, one near each end. The evolution of small- and large-scale structures involves different mechanisms. While the former can be described by rate equations that govern the growth of helical content, the latter is akin to the relaxation of an elastic solid.     

Crystalline ice growth on PT(111): observation of a hydrophobic water monolayer

The growth of crystalline water films on Pt(111) is investigated using rare gas physisorption. The water monolayer wets Pt(111) at all temperatures investigated (20-155 K). At low temperatures (T< or =120 K), additional water layers kinetically wet the monolayer surface. However, crystalline ice films grown at higher temperatures (T > 135 K) do not wet the water monolayer. These results are consistent with recent theory and experiments suggesting that the molecules in the water monolayer form a surface with no dangling OH bonds or lone pair electrons, giving rise to a hydrophobic water monolayer on Pt(111).     

Intricate packing in the hydrophobic core of barstar through a CH–π interaction

Identification of specific packing interactions within in the hydrophobic core of proteins is important for understanding the integrity of protein structure. Finding such interactions is challenging because few tools allow monitoring of a specific interaction in the presence of several non‐specific forces that hold proteins together. It is important to understand how and when such interactions develop during protein folding. In this study, we have used the intrinsic tryptophan residue, Trp53, as an ultraviolet resonance Raman probe to elucidate the packing interactions in the hydrophobic core of the protein barstar. Barstar is extensively studied for its folding, unfolding and aggregation properties. The Trp53 residue is known to be completely buried in the hydrophobic core of the protein and is used extensively as an intrinsic probe to monitor the folding and unfolding reactions of barstar. A comparison of the resonance Raman cross sections of some bands of Trp53 with those observed for N‐acetyl‐tryptophanoamide in water suggests that Trp53 in barstar is indeed isolated from water. Intensity ratio of the Fermi doublet suggests that Trp53 is surrounded by several aliphatic amino acid residues in corroboration with the crystal structure of barstar. Importantly, we show that the side chain of Trp53 is involved in a unique CH–π interaction with CH groups of Phe56 as well as a steric interaction with the methyl group of Ile5. Copyright © 2014 John Wiley & Sons, Ltd.     

Large decrease of fluctuations for supercooled water in hydrophobic nanoconfinement

Using Monte Carlo simulations, we study a coarse-grained model of a water layer confined in a fixed disordered matrix of hydrophobic nanoparticles at different particle concentrations c. For c=0, we find a first-order liquid-liquid phase transition (LLPT) ending in one critical point at low pressure P. For c>0, our simulations are consistent with a LLPT line ending in two critical points at low and high P. For c=25%, at high P and low temperature, we find a dramatic decrease of compressibility, thermal expansion coefficient, and specific heat. Surprisingly, the effect is present also for c as low as 2.4%. We conclude that even a small presence of hydrophobic nanoparticles can drastically suppress thermodynamic fluctuations, making the detection of the LLPT more difficult.     

Steady Schrödinger cat state of a driven Ising chain

For short-range interacting systems, no Schrödinger cat state can be stable when their environment is in thermal equilibrium. We show, by studying a chain of two-level systems with nearest-neighbour Ising interactions, that this is possible when the surroundings consists of two heat reservoirs at different temperatures, or of a heat reservoir and a monochromatic field. The asymptotic state of the considered system can be a pure superposition of mesoscopically distinct states, the all-spin-up and all-spin-down states, at low temperatures. The main feature of our model leading to this result is the fact that the Hamiltonian of the chain and the dominant part of its coupling to the environment obey the same symmetry.     

Dewetting in associating lattice gas model confined by hydrophobic walls

The phase behavior of a two dimensional fluid confined within hydrophobic walls is obtained by Monte Carlo simulations. The fluid is described by the associating lattice gas model which reproduces the density and diffusion anomalous behavior of water.The confined fluid exhibits a liquid-liquid critical temperature which decreases with the decrease of the distance between the confining walls. In contact with the wall a dewetting is observed. The thickness of this interfacial layer is independent of the distance between the two walls. Even for very small distances between the two walls no total depletion is observed and consequently no drying transition is present.     

Surface studies of novel hydrophobic active carbons

The efficient adsorption of toxic organic species from humid airstreams by active carbons is impeded by the competitive adsorption of water vapour which, at low values of p/p^s, occurs at specific (polar) adsorption sites located at the edges of the carbon layer-planes and at in-plane defects. At higher pressures, adsorption in micropores and mesopores also occurs. The concentration of polar adsorption sites therefore determines the hydrophilicity of the carbon structure and their accelerated formation, by exposure to air and water vapour, is also responsible for the ‘ageing’ of active carbons. Overall, the adsorption of water reduces the volume of porosity available for the adsorption of target species and the hydrophilic nature of active carbons is recognized as a major barrier to their effective use in many applications.We present here results for the adsorption of nitrogen, organic and water vapours by a hydrophobic respirator granular active carbon produced by the thermal treatment of a base carbon, to desorb polar oxygen groups, followed by use of a plasma enhanced chemical vapour deposition (PECVD) treatment to apply a hydrophobic, fluorine containing, surface nanolayer. We show that at equivalent %RH values the treated carbon adsorbs significantly less water compared to an untreated (control) carbon and that the treatment does not reduce the levels of open porosity or impede the adsorption of a range of organic vapours at ambient temperatures. Preliminary evidence for the presence, after treatment, of constrictions at pore entrances which act as molecular gates is also presented. The treated carbon (after ageing for 6 weeks at 80%RH) is shown to have greater adsorptivity than an untreated base carbon toward hexane present in a humid (80%RH) airstream. This results in a 39% increase in break-through time. These hydrophobic properties persist one year after manufacture. The mechanism leading to the modified water adsorption properties is the partial desorption of polar oxygen sites followed by deposition at the external carbon surfaces of hydrophobic plasma polymer species. This reduces the polar surface free energy of the carbon and hence the amount of water adsorption occurring by the primary mechanism. This in turn retards the diffusion of water molecules into the micropores and leads to lower adsorption volumes at higher pressures.     

Measurement of chemical potentials of systems with strong excluded volume interactions by computing the density of states

At high densities and low temperatures, the conventional Widom test particle method to compute the chemical potential of a system of particles with excluded volume interactions fails owing to bad statistics. A way to circumvent this problem is the use of expanded ensemble simulation techniques or thermodynamic integration. In this article, we will describe an alternative method to compute the chemical potential which is conceptually much easier, by computing the density of states of systems of N and N + 1 particles directly; and by performing a test particle simulation at very high temperature. The advantage of our technique is that the densities of states of the N and N + 1 particle system are computed in an ensemble in which particles can pass each other, resulting in a more efficient sampling. We will demonstrate our method not only for single particles but also for chain molecules with intramolecular interactions. By using an infinite temperature expansion and an extension of the density of states to very high energies, we will show that it is also possible to compute the chemical potential without having to compute the density of states for the N + 1 particle system.     

Study of Low Temperature Magnetic Properties of a Single Chain Magnet with Alternate Isotropic and Non-collinear Anisotropic Units

Here we study thermodynamic properties of an important class of single-chain magnets (SCMs), where alternate units are isotropic and anisotropic with anisotropy axes being non-collinear. This class of SCMs shows slow relaxation at low temperatures which results from the interplay of two different relaxation mechanisms, namely dynamical and thermal. Here anisotropy is assumed to be large and negative, as a result, anisotropic units behave like canted spins at low temperatures; but even then simple Ising-type model does not capture the essential physics of the system due to quantum mechanical nature of the isotropic units. We here show how statistical behavior of this class of SCMs can be studied using a transfer matrix (TM) method. We also, for the first time, discuss in detail how weak inter-chain interactions can be treated by a TM method. The finite size effect is also discussed which becomes important for low temperature dynamics. At the end of this paper, we apply this technique to study a real helical chain magnet.     

Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins

Water and water-mediated interactions determine the thermodynamics and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we describe computer simulations of a few related model systems. The dynamics of collapse of eicosane shows that upon expulsion of water the linear hydrocarbon chain adopts an ordered helical hairpin structure with 1.5 turns. The structure of dimer of eicosane molecules has two well ordered helical hairpins that are stacked perpendicular to each other. As a prelude to studying folding in confined spaces we used simulations to understand changes in hydrophobic and ionic interactions in nano-sized water droplets. Solvation of hydrophobic and charged species change drastically in nano-scale water droplets. Hydrophobic species are localized at the boundary. The tendency of ions to be at the boundary where water density is low increases as the charge density decreases. The interactions between hydrophobic, polar, and charged residue are also profoundly altered in confined spaces. Using the results of computer simulations and accounting for loss of chain entropy upon confinement we argue and then demonstrate, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores.     

Structural and dynamical aspects of water in contact with a hydrophobic surface

By means of molecular dynamics simulations we study the structure and dynamics of water molecules in contact with a model hydrophobic surface: a planar graphene-like layer. The analysis of the distributions of a local structural index indicates that the water molecules proximal to the graphene layer are considerably more structured than the rest and, thus, than the bulk. This structuring effect is lost in a few angstroms and is basically independent of temperature for a range studied comprising parts of both the normal liquid and supercooled states (240K to 320K). In turn, such structured water molecules present a dynamics that is slower than the bulk, as a consequence of their improved interactions with their first neighbors.