Implicit-solvent mesoscale model based on soft-core potentials for self-assembled lipid membranes

An efficient implicit-solvent model for self-assembled lipid bilayers is presented and analyzed using Langevin molecular dynamics simulations. The model is based on soft interactions between particles and short-range attractive interaction between lipid tails, leading for the self-assembly of a lipid bilayer without an explicit solvent. This allows for efficient simulations of large membranes over long times. The model exhibits a fluid phase at high temperatures and a gel phase at low temperatures, identified with the Lbeta-phase. The melting transition is investigated via analysis of the diffusivity of the lipid molecules, the chain-orientational order parameter, the sixfold bond-orientational order parameter, and the positional and bond-orientational correlation functions. The analysis suggests the existence of a hexatic phase over a narrow range of temperatures around the melting transition. The elastic properties of the membrane in the fluid phase are also investigated.     

Orientational melting and reorientational motion in a cubane molecular crystal: a molecular simulation study

Detailed molecular simulations are carried out to investigate the effect of temperature on orientational order in cubane molecular crystal. We report a transition from an orientationally ordered to an orientationally disordered plastic crystalline phase in the temperature range 425-450 K. This is similar to the experimentally reported transition at 395 K. The nature of this transition is first order and is associated with a 4.8% increase in unit cell volume that is comparable to the experimentally reported unit cell volume change of 5.4% (Phys. Rev. Lett. 1997, 78, 4938). An orientational order parameter, eta(T), has been defined in terms of average angle of libration of a molecular 3-fold axis and the orientational melting has been characterized by using eta(T). The orientational melting is associated with an anomaly in specific heat at constant pressure (C(P)) and compressibility (kappa). The enthalpy of transition and entropy of transition associated with this orientational melting are 20.8 J mol(-1) and 0.046 J mol(-1) K(-1), respectively. The structure of crystalline as well as plastic crystalline phases is characterized by using various radial distribution functions and orientational distribution functions. The coefficient of thermal expansion of the plastic crystalline phase is more than twice that of the crystalline phase.     

Lindemann measures for the solid-liquid phase transition

A set of Lindemann measures, based on positional deviations or return distances, defined with respect to mechanically stable inherent structure configurations, is applied to understand the solid-liquid phase transition in a Lennard-Jones-type system. The key quantity is shown to be the single-particle return distance-squared distribution. The first moment of this distribution is related to the Lindemann parameter which is widely used to predict the melting temperature of a variety of solids. The correlation of the single-particle return distance and local bond orientational order parameter in the liquid phase provides insights into mechanisms for melting. These generalized Lindemann measures, especially the lower order moments of the single-particle return distance distribution, show clear signatures of the transition of the liquid from the stable to the metastable, supercooled regime and serve as landscape-based indicators of the thermodynamic freezing transition for the Lennard-Jones-type system investigated.     

Molecular dynamics simulations of the melting mechanisms of perfect and imperfect crystals of dimethylnitramine

The melting mechanisms of perfect and imperfect crystalline dimethylnitramine have been studied using molecular dynamics simulations. The imperfect crystal was created by removing approximately 10% of the molecules from the center of the simulation cell. The density, diffusion coefficient, translational and orientational order parameters, and void size were calculated as functions of temperature and simulation time. Upon melting, the volume of the imperfect crystal slowly decreases with time due to the shrinkage of the void then suddenly decreases to a minimum value due to collapse of the structure around the void with concomitant diffusion of molecules into the void. The simulation cell volume then increases as the liquid nucleus formed at the void expands. The melting of perfect crystals must occur by a different mechanism. As the temperature of the perfect crystal reaches the maximum superheating temperature, there is an increase in the thermal motions of the molecules that result in the formation of liquid centers (characterized by translational order parameter consistent with the liquid phase) at random locations. The liquid centers rapidly grow, resulting in a complete transition to the liquid phase. The increases in orientational and translational freedom occur simultaneously in the imperfect crystal, and in the perfect crystal, orientational freedom significantly precedes translational freedom.     

Predicting the phase diagram of two-dimensional colloidal systems with long-range interactions

The phase diagram of a two-dimensional model system for colloidal particles at the air-water interface was determined using Monte Carlo computer simulations in the isothermic-isobaric ensemble. The micrometer-range binary colloidal interaction has been modeled by hard disklike particles interacting via a secondary minimum followed by a weaker longer-range repulsive maximum, both of the order of kBT. The repulsive part of the potential drives the clustering of particles at low densities and low temperatures. Pinned voids are formed at higher densities and intermediate values of the surface pressure. The analysis of isotherms, translational and orientational correlation functions as well as structure factor gives clear evidence of the presence of a melting first-order transition. However, the melting process can be also followed by a metastable route through a hexatic phase at low surface pressures and low temperatures, before crystalization occurs at higher surface pressure.     

一个新的液晶相转变动力学理论

本文以保留系统的宏观特性为基本原则,从用动力学方法处理非稳态相转变入手,在物理化学基础上,建立了描述液晶相转变的动力学方程,提出了动力学意义上的相转变级数参数,推导出相转变级数的理论公式及参数的变化范围,丹卉将其应用于一新的聚合物体系,获得了该体系各聚合物加热过程中所经历相态的动力学相转变级数。     

一个新的液晶相转变动力学理论

 本文以保留系统的宏观特性为基本原则,从用动力学方法处理非稳态相转变入手,在物理化学基础上,建立了描述液晶相转变的动力学方程,提出了动力学意义上的相转变级数参数,推导出相转变级数的理论公式及参数的变化范围,丹卉将其应用于一新的聚合物体系,获得了该体系各聚合物加热过程中所经历相态的动力学相转变级数。     

Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced "1/f noise characteristics" between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R(g)) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape.     

Low-dimensionality effects in the melting of a Langmuir-Blodgett multilayer

Low-dimensionality effects in the melting behavior of a cadmium arachidate Langmuir-Blodgett multilayer have been studied. Depth resolved information about structural changes occurring with temperature is obtained using in-plane X-ray diffraction under standing wave conditions. The surface region exhibits a distinctly different melting behavior as compared to the bulk of the film. While in the bulk of a 13-monolayer cadmium arachidate multilayer, the crystalline phase directly transforms to a tilted hexaticlike phase at 360 K, in the near surface region transformation occurs via an intermediate smectic phase. This behavior of the surface region is similar to that observed in two-dimensional crystals. Thus even in a thick Langmuir-Blodgett multilayer, the surface region exhibits low-dimensionality effects.     

Systematic study of pretransitional orientational order at the free surface of nCB liquid crystals (n=5-12) in the isotropic phase

A high precision rotating ellipsometer was used to perform a systematic study of the pretransitional orientational order induced by the free surface of n-alkylcyanobiphenyl liquid crystals (n=5-12) in the isotropic phase. All the compounds of this series show a complete wetting behaviour at the free surface. The temperature dependence of the surface order parameter was determined via calculations based on the Landau-de Gennes theory and the results show an even-odd behaviour. Moreover, we used a neural network recognition algorithm to reconstruct the order parameter profile S ( z ) near the surface. The results of this model-independent analysis are compared with the model based calculations.     

Phase transitions in two-dimensional colloidal particles at oil/water interfaces

Enhanced digital video microscopy is applied to study the equilibrium structure of a two-dimensional charged sulfate-polystyrene particle (2 mum in diameter) monolayer at decane/water interfaces. When the surface density is decreased, a sequential phase transition, pure solid phase-->pure hexatic phase-->liquid-hexatic-coexisting phase-->pure liquid phase, is observed. In addition, the transition between liquid and hexatic phases is first order, while the solid-hexatic phase transition is second order. The temperature effect on this two-dimensional melting transition is discussed by performing the experiments at three different temperatures. The Voronoi [J. Reine Angew. Math. 134, 198 (1908)] construction is applied to analyze the defect structure in the two-dimensional particle monolayer. The pair interaction potential of the two-dimensional colloidal particles is found to be a very long range repulsion and to decay with distance to the power of -3.     

Multiple structural transformations in Lennard-Jones clusters: generic versus size-specific behavior

The size-temperature "phase diagram" for Lennard-Jones clusters LJn with sizes up to n=147 is constructed based on the analysis of the heat capacities and orientational bond order parameter distributions computed by the exchange Monte Carlo method. Two distinct types of "phase transitions" accompanied by peaks in the heat capacities are proven to be generic. Clusters with Mackay atom packing in the overlayer undergo a lower-temperature melting (or Mackay-anti-Mackay) transition that occurs within the overlayer. All clusters undergo a higher-temperature transition, which for the three-layer clusters is proven to be the 55-atom-core-melting transition. For the two-layer clusters, the core/overlayer subdivision is ambiguous, so the higher-temperature transition is better characterized as the breaking of the local icosahedral coordination symmetry. A pronounced size-specific behavior can typically be observed at low temperatures and often occurs in clusters with highly symmetric global minima. An example of such behavior is LJ135, which undergoes a low-temperature solid-solid transition, besides the two generic transitions, i.e., the overlayer reconstruction and the core melting.     

First order melting transitions of highly ordered dipalmitoyl phosphatidylcholine gel phase membranes in molecular dynamics simulations with atomistic detail

Molecular dynamics simulations with atomistic detail of the gel phase and melting transitions of dipalmitoyl phosphatidylcholine bilayers in water reveal the dependency of many thermodynamic and structural parameters on the initial system ordering. We quantitatively compare different methods to create a gel phase system and we observe that a very high ordering of the gel phase starting system is necessary to observe behavior which reproduces experimental data. We performed heating scans with speeds down to 0.5 K/ns and could observe sharp first order phase transitions. Also, we investigated the transition enthalpy as the natural intrinsic parameter of first order phase transitions, and obtained a quantitative match with experimental values. Furthermore, we performed systematic investigations of the statistical distribution and heating rate dependency of the microscopic phase transition temperature.     

Recent advances in nematic and smectic A anchoring on amorphous solid surfaces [1]

New anchoring properties of liquid crystals on amorphous solid surfaces are presented. In nematics (N), angular anchoring is usually described in terms of the Rapini-Papoular form, assuming constant surface order parameter. We generalize this expression, predicting a decrease of surface order for strong surface disorientation. Recent experiments on anchorings of varying strength confirm these predictions. Conjectures for the angular anchoring of smectic A on a solid amorphous surface explain the two easy layer orientations, normal to the surface or parallel, faceting inside a small critical angle. Roughness-induced surface transitions are discussed. For antagonistic nematic and smectic anchorings, we expect, below the N-S_A transition, a bent nematic surface boundary layer, recently observed by smectization under an electric field. Finally, the positional anchoring strength of smectics is introduced in terms of shear induced surface melting, and confirmed by a recent observation of oscillating shear stresses at the layer period.     

自由表面的Ni原子团簇的熔化

采用分子动力学模拟技术研究了不同尺寸的Ni原子团簇的熔化过程.团簇的最初构型为FCC结构.研究结果表明,原子团簇的熔化温度与原子团簇中原子的个数有关,团簇的熔化首先从表面开始,当外层原子成为液态后,整个团簇的熔化从液态层开始,直至核心区域.该熔化过程可以被称为非均质熔化,自由表面充当非均质形核位置.作为对比,对无自由表面的大块固态Ni的熔化过程也进行了模拟,其熔化温度高于实验温度约400 K.表明对无自由表面的大块固态的熔化过程,液相形成无非均质形核位置,熔化的本质过程受均质形核机理控制.     

Smectic order induced at homeotropically aligned nematic surfaces: a neutron reflection study

Neutron reflection was used to measure the buildup of layers at a solid surface as the smectic phase is approached from higher temperatures in a nematic liquid crystal. The liquid crystal was 4-octyl-4'-cyanobiphenyl (8CB), and the solid was silicon with one of five different surface treatments that induce homeotropic alignment: (i) silicon oxide; (ii) a cetyltrimethylammonium bromide coating; (iii) an octadecyltrichlorosilane monolayer; (iv) an n-n-dimethyl-n-octadecyl-3- aminopropyltrimethyloxysilyl chloride monolayer; and (v) a lecithin coating. The development of surface smectic layers in the nematic phase of 8CB was followed by measuring specular reflectivity and monitoring the pseudo-Bragg peak from the layers. The scattering data were processed to remove the scattering from short-ranged smecticlike fluctuations in the bulk nematic phase from the specular reflection. The pseudo-Bragg peak at scattering vector Q approximately 0.2 A(-1) therefore corresponded to the formation of long-range smectic layers at the surface. The amplitude of the smectic density wave decayed with increasing distance from the surface, and the characteristic thickness of this smectic region diverged as the transition temperature was approached. It was found that the characteristic thickness for some of the surface treatments was greater than the correlation length in the bulk nematic. The different surfaces gave different values of the smectic order parameter at the surface. This suggests that the interaction with the surface is significantly different from a "hard wall" which would give the same values of the smectic order parameter and penetration depths similar to the bulk correlation length. Comparison of the different surfaces also suggested that the strength and range of the surface smectic ordering may be varied independently.     

Surface modification of polyethylene with multi-end-functional polyethylene additives

We have prepared and characterized a series of multifluorocarbon end-functional polyethylene additives, which when blended with polyethylene matrices increase surface hydrophobicity and lipophobicity. Water contact angles of >112° were observed on spin-cast blended film surfaces containing less than 1% fluorocarbon in the bulk, compared to ~98° in the absence of any additive. Crystallinity in these films gives rise to surface roughness that is an order of magnitude greater than is typical for amorphous spin-cast films but is too little to give rise to superhydrophobicity. X-ray photoelectron spectroscopy (XPS) confirms the enrichment of the multifluorocarbon additives at the air surface by up to 80 times the bulk concentration. Ion beam analysis was used to quantify the surface excess of the additives as a function of composition, functionality, and molecular weight of either blend component. In some cases, an excess of the additives was also found at the substrate interface, indicating phase separation into self-stratified layers. The combination of neutron reflectometry and ion beam analysis allowed the surface excess to be quantified above and below the melting point of the blended films. In these films, where the melting temperatures of the additive and matrix components are relatively similar (within 15 °C), the surface excess is almost independent of whether the blended film is semicrystalline or molten, suggesting that the additive undergoes cocrystallization with the matrix when the blended films are allowed to cool below the melting point.     

A novel method for evaluating the critical nucleus and the surface tension in systems with first order phase transition

We introduce a novel method for calculating the size of the critical nucleus and the value of the surface tension in systems with first order phase transition. The method is based on classical nucleation theory, and it consists in studying the thermodynamics of a sphere of given radius embedded in a frozen metastable surrounding. The frozen configuration creates a pinning field on the surface of the free sphere. The pinning field forces the sphere to stay in the metastable phase as long as its size is smaller than the critical nucleus. We test our method in two first order systems, both on a two-dimensional lattice: a system where the parameter tuning the transition is the magnetic field, and a second system where the tuning parameter is the temperature. In both cases the results are satisfying. Unlike previous techniques, our method does not require an infinite volume limit to compute the surface tension, and it therefore gives reliable estimates even by using relatively small systems. However, our method cannot be used at, or close to, the critical point, i.e., at coexistence, where the critical nucleus becomes infinitely large.