Dynamics of water confined in single- and double-wall carbon nanotubes

Using high-resolution quasielastic neutron scattering, we investigated the temperature dependence of single-particle dynamics of water confined in single- and double-wall carbon nanotubes with the inner diameters of 14+/-1 and 16+/-3 A, respectively. The temperature dependence of the alpha relaxation time for water in the 14 A nanotubes measured on cooling down from 260 to 190 K exhibits a crossover at 218 K from a Vogel-Fulcher-Tammann law behavior to an Arrhenius law behavior, indicating a fragile-to-strong dynamic transition in the confined water. This transition may be associated with a structural transition from a high-temperature, low-density (<1.02 gcm(3)) liquid to a low-temperature, high-density (>1.14 gcm(3)) liquid found in molecular dynamics simulation at about 200 K. However, no such dynamic transition in the investigated temperature range of 240-195 K was detected for water in the 16 A nanotubes. In the latter case, the dynamics of water simply follows a Vogel-Fulcher-Tammann law. This suggests that the fragile-to-strong crossover for water in the 16 A nanotubes may be shifted to a lower temperature.     

Electrofreezing of confined water

We report results from molecular dynamics simulations of the freezing transition of TIP5P water molecules confined between two parallel plates under the influence of a homogeneous external electric field, with magnitude of 5 V/nm, along the lateral direction. For water confined to a thickness of a trilayer we find two different phases of ice at a temperature of T=280 K. The transformation between the two, proton-ordered, ice phases is found to be a strong first-order transition. The low-density ice phase is built from hexagonal rings parallel to the confining walls and corresponds to the structure of cubic ice. The high-density ice phase has an in-plane rhombic symmetry of the oxygen atoms and larger distortion of hydrogen bond angles. The short-range order of the two ice phases is the same as the local structure of the two bilayer phases of liquid water found recently in the absence of an electric field [J. Chem. Phys. 119, 1694 (2003)]. These high- and low-density phases of water differ in local ordering at the level of the second shell of nearest neighbors. The results reported in this paper, show a close similarity between the local structure of the liquid phase and the short-range order of the corresponding solid phase. This similarity might be enhanced in water due to the deep attractive well characterizing hydrogen bond interactions. We also investigate the low-density ice phase confined to a thickness of 4, 5, and 8 molecular layers under the influence of an electric field at T=300 K. In general, we find that the degree of ordering decreases as the distance between the two confining walls increases.     

An off-lattice Wang-Landau study of the coil-globule and melting transitions of a flexible homopolymer

The Wang-Landau Monte Carlo approach is applied to the coil-globule and melting transitions of off-lattice flexible homopolymers. The solid-liquid melting point and coil-globule transition temperatures are identified by their respective peaks in the heat capacity as a function of temperature. The melting and theta points are well separated, indicating that the coil-globule transition occurs separately from melting even in the thermodynamic limit. We also observe a feature in the heat capacity between the coil-globule and melting transitions which we attribute to a transformation from a low-density liquid globule to a high-density liquid globule.     

Differences in first neighbor orientation behind the anomalies in the low and high density trans-1,2-dichloroethene liquid

Trans-1,2-dichloroethene (HClC=CClH) has several structural and dynamic anomalies between its low- and high-density liquid, previously found through neutron scattering experiments. To explain the microscopic origin of the differences found in those experiments, a series of molecular dynamics simulations were performed. The analysis of molecular short-range order shows that the number of molecules in the first neighbor shell is 12 for the high-density liquid and 11 for the low-density one. It also shows that the angular position of the center of mass of the first neighbor is roughly the same although the molecular orientation is not. In both liquids the first neighbor and its reference molecule arrange mainly in two configurations, each being the most probable in one of the liquids. First neighbors in the configuration that predominates in the high-density liquid tend to locate themselves closer to the reference molecule, an evidence that they are more strongly bonded. This arrangement facilitates a better packing of the rest of molecules in the first neighbor shell so that on average an additional molecule can be included, and is proposed to be the key in the explanation of all the observed anomalies in the characteristics of both liquids.     

Comparative study of temperature dependent orientational relaxation in a model thermotropic liquid crystal and in a model supercooled liquid

Recent optical Kerr effect experiments have revealed a power law decay of the measured signal with a temperature independent exponent at short-to-intermediate times for a number of liquid crystals in the isotropic phase near the isotropic-nematic transition and supercooled molecular liquids above the mode coupling theory critical temperature. In this work, the authors investigate the temperature dependence of short-to-intermediate time orientational relaxation in a model thermotropic liquid crystal across the isotropic-nematic transition and in a binary mixture across the supercooled liquid regime in molecular dynamics simulations. The measure of the experimentally observable optical Kerr effect signal is found to follow a power law decay at short-to-intermediate times for both systems in agreement with recent experiments. In addition, the temperature dependence of the power law exponent is found to be rather weak. As the model liquid crystalline system settles into the nematic phase upon cooling, the decay of the single-particle second-rank orientational time correlation function exhibits a pattern that is similar to what has been observed for supercooled liquids.     

Wide-angle X-ray diffraction and molecular dynamics study of medium-range order in ambient and hot water

We have developed wide-angle X-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 °C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows for a reliable Fourier transform of the experimental data resolving shell structure out to ~12 ?, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell-structure in the range 4-12 ? although less agreement is seen for the first peak in the intermolecular pair-correlation function (PCF). The Shiratani-Sasai Local Structure Index [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the intermediate-range oscillations in the O-O PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water, even at high temperatures, can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water postulated in the liquid-liquid phase transition hypothesis.     

Nanophase segregation in supercooled aqueous solutions and their glasses driven by the polyamorphism of water

We use large-scale molecular dynamics simulations to investigate the phase transformation of aqueous solutions of electrolytes cooled at the critical rate to avoid the crystallization of ice. Homogeneous liquid solutions with up to 20% moles of ions demix on cooling producing nanophase segregated glasses with characteristic dimensions of phase segregation of about 5 nm. The immiscibility is driven by the transformation of water to form a four-coordinated low-density liquid (LDL) as it crosses the liquid-liquid transformation temperature T(LL) of the solution. The ions cannot be incorporated into the tetrahedral LDL network and are expelled to form a solute-rich water nanophase. The simulations quantitatively reproduce the relative amounts of low and high-density liquid water as a function of solute content in LiCl glasses [Suzuki and Mishima, Phys. Rev. Lett. 2000, 85, 1322-1325] and provide direct evidence of segregation in aqueous glasses and their dimensions of phase segregation.     

Role of liquid polymorphism during the crystallization of silicon

Using molecular simulation, we establish the pivotal role played by liquid polymorphs during the crystallization of silicon. When undercooled at a temperature 20% below the melting point, a silicon melt is under the form of the highly coordinated, high-density liquid (HDL) polymorph. We find that crystallization starts with the formation, within the HDL liquid, of a nanosized droplet of the least stable liquid polymorph, known as the almost tetracoordinated low-density liquid (LDL) polymorph. We then show that the crystalline embryo forms within the LDL droplet, close to the interface with the surrounding HDL liquid, thereby following a pathway associated with a much lower free energy barrier than the direct formation of the crystalline embryo from the HDL liquid would have required. This implies that, for substances exhibiting liquid polymorphs, theories, like the classical nucleation theory, and empirical rules, like Ostwald's rule, should be modified to account for the role of liquid polymorphs in the nucleation process.     

Communication: A dynamical theory of homogeneous nucleation for colloids and macromolecules

Homogeneous nucleation is formulated within the context of fluctuating hydrodynamics. It is shown that for a colloidal system in the strong damping limit the most likely path for nucleation can be determined by gradient descent in density space governed by a nontrivial metric. This is illustrated by application to low-density/high-density liquid transition of globular proteins in solution where it is shown that nucleation process involves two stages: the formation of an extended region with enhanced density followed by the formation of a cluster within this region.     

A one-dimensional model with water-like anomalies and two phase transitions

We investigate a one-dimensional model that shows several properties of water. The model combines the long-range attraction of the van der Waals model with the nearest-neighbor interaction potential by Ben-Naim, which is a step potential that includes a hard core and a potential well. Starting from the analytical expression for the partition function, we determine numerically the Gibbs energy and other thermodynamic quantities. The model shows two phase transitions, which can be interpreted as the liquid-gas transition and a transition between a high-density and a low-density liquid. At zero temperature, the low-density liquid goes into the crystalline phase. Furthermore, we find several anomalies that are considered characteristic for water. We explore a wide range of pressure and temperature values and the dependence of the results on the depth and width of the potential well.     

Correlation between Dynamic Heterogeneity and Local Structure in a Room‐Temperature Ionic Liquid: A Molecular Dynamics Study of [bmim][PF6]

The complex dynamics of a room‐temperature ionic liquid, 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate ([bmim][PF₆]), is studied using equilibrium classical molecular dynamics simulations in the temperature range of 250–450 K. The activation energies for the self‐diffusion of ions are around 30–34 kJ mol^?1, with that of the anion a little higher than that for the cation. The electrical conductivity of the liquid is calculated and good agreement with experiments is obtained. Structural relaxation is studied through the decay of coherent (total density–density correlation) and incoherent (self part of density–density correlation) intermediate scattering functions over a range of temperatures and wave vectors relevant to the system. The relaxation data are used to identify and characterize two processes, α and β. The dependence of the two relaxation times on temperature and wave vector is obtained. The dynamical heterogeneity of the ions determined through the non‐Gaussian parameter indicates the motion of the cation to be more heterogeneous than that of the anion. The faster ones among the cations are coordinated to faster anions, while slower cations are surrounded predominantly by slower anions. Thus, the dynamical heterogeneity in this ionic liquid is shown to have structural signatures.     

Evidence for a simple monatomic ideal glass former: the thermodynamic glass transition from a stable liquid phase

Under cooling, a liquid can undergo a transition to the glassy state either as a result of a continuous slowing down or by a first-order polyamorphous phase transition. The second scenario has so far always been observed in a metastable liquid domain below the melting point where crystalline nucleation interfered with the glass formation. We report the first observation of the liquid-glass transition by a first-order polyamorphous phase transition from the equilibrium stable liquid phase. The observation was made in a molecular dynamics simulation of a one-component system with a model metallic pair potential. In this way, the model, demonstrating the thermodynamic glass transition from a stable liquid phase, may be regarded as a candidate for a simple monatomic ideal glass former. This observation is of conceptual importance in the context of continuing attempts to resolve the long-standing Kauzmann paradox. The possibility of a thermodynamic glass transition from an equilibrium melt in a metallic system also indicates a new strategy for the development of bulk metallic glass-forming alloys.     

冷却速率对液态金属Zn快速凝固过程中微观结构的影响

用分子动力学模拟方法研究了六种不同冷却速率对液态金属Zn凝固过程微观结构的影响. 采用双体分布函数g(r)曲线、平均原子总能量、Honeycutt-Andersen(HA)键型指数法和原子团类型指数法(CTIM-2)对凝固过程中微观结构的变化进行了分析. 结果表明, 冷却速率对微观结构的转变有决定性影响, 当冷却速率为1×10¹⁴、5×10¹³、2×10¹³、1×10¹³、5×10¹² K·s-1时, 系统形成以1551、1541、1431键型为主体的非晶态结构; 当冷却速率为1×10¹² K·s-1时, 系统形成以1421、1422键型为主或以密排六方(hcp)基本原子团(12 0 0 0 6 6)和面心立方(fcc)基本原子团(12 0 0 0 1 2 0)共存的部分晶态结构. 同时发现, 在形成非晶的五个系统中,玻璃化转变温度Tg随着冷速的降低而降低.     

Molecular dynamics simulation of the glass transition temperature of fullerene filled cis-1,4-polybutadiene nanocomposites

t In this work,the effect of the fullerene (C60) weight fraction and PB-C60 interaction on the glass transition temperature (Tg) of polymer chains has been systemically investigated by adopting the united atom model of cis-1,4-poly(butadiene) (cis-PB).Various chain dynamics properties,such as atom translational mobility,bond/segment reorientation dynamics,torsional dynamics,conformational transition rate and dynamic heterogeneity of the cis-PB chains,are analyzed in detail.It is found that Tg could be affected by the C60 weight fraction due to its inhibition effect on the mobility of the cis-PB chains.However,Tg is different,which depends on different dynamics scales.Among the chain dynamics properties,Tg is the lowest from atom translational mobility,while it is the highest from the dynamic heterogeneity.In addition,Tg can be more clearly distinguished from the dynamic heterogeneity;however,the conformational transition rate seems to be not very sensitive to the C60 weight fraction compared with others.For pure cis-PB chains,Tg and the activation energy in this work can be compared with those of other polymers.In addition,the temperature dependence of the dynamic properties has different Arrhenius behaviors above and below Tg.The activation energy below Tg is lower than that above Tg.This work can help to understand the effect of the C60 on the dynamic properties and glass transition temperature of the cis-PB chains from different scales.     

冷却速率对液态Ni凝固过程中微观结构演变影响的模拟研究

用分子动力学方法和EAM模型势对液态金属Ni原子系统在不同冷却速率下凝固过程中微观结构的演变进行了模拟研究.结果表明, 冷却速率对微结构演变有决定性影响, 当冷速为1.0×10¹⁴和 4.0×10¹³ K•s^-1时, 系统将形成以1551、1541和1431三种键型为主的非晶态结构. 当冷速为2.0×10¹³和 1.0×10¹² K•s^-1时, 系统将形成不同的晶态结构；前者形成以1421、1422二种键型为主的 fcc 与hcp结构共存的晶态结构；后者形成以1421键型为主的fcc 结构占绝对优势的晶态结构, 其结晶起始温度Tc分别为1073 K和1173 K.同时发现, 原子的平均配位数（最近邻数）对温度和冷速的变化相当敏感, 且其突变点正好与结晶转变温度Tc相对应, 这将为液态金属结晶转变过程的研究提供一条新途径.     

The low-temperature dynamic crossover phenomenon in protein hydration water: simulations vs experiments

A super-Arrhenius-to-Arrhenius dynamic crossover phenomenon has been observed in the translational alpha-relaxation time and in the inverse of the self-diffusion constant both experimentally and by simulations for lysozyme hydration water in the temperature range of TL = 223 +/- 2 K. MD simulations are based on a realistic hydrated powder model, which uses the TIP4P-Ew rigid molecular model for the hydration water. The convergence of neutron scattering, nuclear magnetic resonance and molecular dynamics simulations supports the interpretation that this crossover is a result of the gradual evolution of the structure of hydration water from a high-density liquid to a low-density liquid form upon crossing of the Widom line above the possible liquid-liquid critical point of water.     

Anisotropy of viscoelastic transitions in oriented polyethylenes

Measurements have been made of the anisotropy of viscoelastic behavior in cold-drawn low-density and high-density polyethylene sheets. In the low-density polymer the β transition was shown to be highly anisotropic, maximum losses corresponding to shear on planes containing the axis of drawing and on planes perpendicular to this axis. In high-density polyethylene the α transition shows anisotropy.     

Atomic‐Level Mechanisms of Nucleation of Pure Liquid Metals during Rapid Cooling

To obtain a material with the desired performance, the atomic‐level mechanisms of nucleation from the liquid to solid phase must be understood. Although this transition has been investigated experimentally and theoretically, its atomic‐level mechanisms remain debatable. In this work, the nucleation mechanisms of pure Fe under rapid cooling conditions are investigated. The local atomic packing stability and liquid‐to‐solid transition‐energy pathways of Fe are studied using molecular dynamics simulations and first‐principle calculations. The results are expressed as functions of cluster size in units of amorphous clusters (ACs) and body‐centered cubic crystalline clusters (BCC‐CCs). We found the prototypes of ACs in supercooled liquids and successfully divided these ACs to three categories according to their transition‐energy pathways. The information obtained in this study could contribute to our current understanding of the crystallization of metallic melts during rapid cooling.     

Translational diffusion of cumene and 3-methylpentane on free surfaces and pore walls studied by time-of-flight secondary ion mass spectrometry

Mobility of molecules in confined geometry has been studied extensively, but the origins of finite size effects on reduction of the glass transition temperature, T(g), are controversial especially for supported thin films. We investigate uptake of probe molecules in vapor-deposited thin films of cumene, 3-methylpentane, and heavy water using secondary ion mass spectrometry and discuss roles of individual molecular motion during structural relaxation and glass-liquid transition. The surface mobility is found to be enhanced for low-density glasses in the sub-T(g) region because of the diffusion of molecules on pore walls, resulting in densification of a film via pore collapse. Even for high-density glasses without pores, self-diffusion commences prior to the film morphology change at T(g), which is thought to be related to decoupling between translational diffusivity and viscosity. The diffusivity of deeply supercooled liquid tends to be enhanced when it is confined in pores of amorphous solid water. The diffusivity of molecules is further enhanced at temperatures higher than 1.2-1.3 T(g) irrespective of the confinement.     

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations

The conformational dynamics in the flaps of HIV-1 protease plays a crucial role in the mechanism of substrate binding. We develop a kinetic network model, constructed from detailed atomistic simulations, to determine the kinetic mechanisms of the conformational transitions in HIV-1 PR. To overcome the time scale limitation of conventional molecular dynamics (MD) simulations, our method combines replica exchange MD with transition path theory (TPT) to study the diversity and temperature dependence of the pathways connecting functionally important states of the protease. At low temperatures the large-scale flap opening is dominated by a small number of paths; at elevated temperatures the transition occurs through many structurally heterogeneous routes. The expanded conformation in the crystal structure 1TW7 is found to closely mimic a key intermediate in the flap-opening pathways at low temperature. We investigated the different transition mechanisms between the semi-open and closed forms. The calculated relaxation times reveal fast semi-open ? closed transitions, and infrequently the flaps fully open. The ligand binding rate predicted from this kinetic model increases by 38-fold from 285 to 309 K, which is in general agreement with experiments. To our knowledge, this is the first application of a network model constructed from atomistic simulations together with TPT to analyze conformational changes between different functional states of a natively folded protein.