Subdiffusive dynamics of a liquid crystal in the isotropic phase

The isotropic phase dynamics of a system of 4-n-hexyl-4'-cyano-biphenyl (6CB) molecules has been studied by molecular dynamics computer simulations. We have explored the range of 275-330 K keeping the system isotropic, although supercooled under its nematic transition temperature. The weak rototranslational coupling allowed us to separately evaluate translational (TDOF) and orientational degrees of freedom (ODOF). Evidences of subdiffusive dynamics, more apparent at the lowest temperatures, are found in translational and orientational dynamics. Mean square displacement as well as self-intermediate center of mass and rotational scattering functions show a plateau, also visible in the orientational correlation function. According to the mode coupling theory (MCT), this plateau is the signature of the beta-relaxation regime. Three-time intermediate scattering functions reveal that the plateau is related to a homogeneous dynamics, more extended in time for the orientational degrees of freedom (up to 1 ns). The time-temperature superposition principle and the factorization property predicted by the idealized version of MCT hold, again for both kinds of dynamics. The temperature dependence of diffusion coefficient and orientational relaxation time is well described by a power law. Critical temperatures Tc are 244+/-6 and 258+/-6 K, respectively, the latter is some 10 K below the corresponding experimental values. The different values of Tc we obtained indicate that ODOF freezes earlier than TDOF. This appears due to the strongly anisotropic environment that surrounds a 6CB molecule, even in the isotropic phase. The lifetime of these "cages," estimated by time dependent conditional probability functions, is strongly temperature dependent, ranging from some hundreds of picoseconds at 320 K to a few nanoseconds at 275 K.     

Computational probes of molecular motion in the Lewis-Wahnstrom model for ortho-terphenyl

We use molecular dynamics simulations to investigate translational and rotational diffusion in a rigid three-site model of the fragile glass former ortho-terphenyl, at 260 K< or =T< or =346 K and ambient pressure. An Einstein formulation of rotational motion is presented, which supplements the commonly used Debye model. The latter is shown to break down at supercooled temperatures as the mechanism of molecular reorientation changes from small random steps to large infrequent orientational jumps. We find that the model system exhibits non-Gaussian behavior in translational and rotational motion, which strengthens upon supercooling. Examination of particle mobility reveals spatially heterogeneous dynamics in translation and rotation, with a strong spatial correlation between translationally and rotationally mobile particles. Application of the Einstein formalism to the analysis of translation-rotation decoupling results in a trend opposite to that seen in conventional approaches based on the Debye formalism, namely, an enhancement in the effective rate of rotational motion relative to translation upon supercooling.     

Glass formation in the Gay-Berne nematic liquid crystal

We present the results of molecular dynamics simulations of the Gay-Berne model of liquid crystals, supercooled from the nematic phase at constant pressure. We find a glass transition to a metastable phase with nematic order and frozen translational and orientational degrees of freedom. For fast quench rates the local structure is nematic-like, while for slower quench rates smectic order is present as well.     

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.     

Structural relaxation and glass transition behavior of binary hard-ellipse mixtures

Structural relaxation and glass transition in binary hard-spherical particle mixtures have been reported to exhibit unusual features depending on the size disparity and composition. However, the mechanism by which the mixing effects lead to these features and whether these features are universal for particles with anisotropic geometries remains unclear. Here, we employ event-driven molecular dynamics simulation to investigate the dynamical and structural properties of binary two-dimensional hard-ellipse mixtures. We find that the relaxation dynamics for translational degrees of freedom exhibit equivalent trends as those observed in binary hard-spherical mixtures. However, the glass transition densities for translational and rotational degrees of freedom present different dependencies on size disparity and composition. Furthermore, we propose a mechanism based on structural properties that explain the observed mixing effects and decoupling behavior between translational and rotational motions in binary hard-ellipse systems.     

Aging in a free-energy landscape model for glassy relaxation

The aging properties of a simple free-energy landscape model for the primary relaxation in supercooled liquids are investigated. The intermediate scattering function and the rotational correlation functions are calculated for the generic situation of a quench from a high temperature to below the glass transition temperature. It is found that the reequilibration of molecular orientations takes longer than for translational degrees of freedom. The time scale for reequilibration is determined by that of the primary relaxation as an intrinsic property of the model.     

Translational to rotational energy transfer in molecule-surface collisions

A theoretical approach that combines classical mechanics for treating translational and rotational degrees of freedom and quantum mechanics for describing the excitation of internal molecular modes is applied to the scattering of diatomic molecules from metal surfaces. Calculations are carried out for determining the extent of energy transfer to the rotational degrees of freedom of the projectile molecule. For the case of observed spectra of intensity versus final rotational energy, quantitative agreement with available experimental data for the scattering of NO and N(2) from close packed metal surfaces is obtained. It is shown that such measurements can be used to determine the average rotational energy of the incident molecular beam. Measurements of the exchange of energy between translational and rotational degrees of freedom upon collision are also described by calculations for these same systems.     

Dynamic light scattering by optically anisotropic colloidal particles in polyacrylamide gels

The translational and rotational motions of optically anisotropic spherical particles embedded in cross-linked polyacrylamide gels is studied by dynamic light scattering. The particles are liquid crystal droplets solidified in the nematic phase. The amount of cross linkers is varied to cross the sol-gel transition where the system becomes nonergodic for both translational and rotational diffusion modes of the probes. The translational and rotational dynamic correlation functions are obtained by measuring the intensity correlation function between crossed polarizers in the parallel and perpendicular geometries. Data from nonergodic systems is analyzed using an extension, to include rotations, of the method of Pusey and van Megen [Physica A 157, 705 (1989)]. Both diffusion modes are observed to be arrested as the rigidity of the gel increases.     

Transport coefficients of the TIP4P-2005 water model

A detailed understanding of the dynamics of liquid water at molecular level is of fundamental importance as well as have applications in many branches of science and technology. In this work, the diffusion of the TIP4P-2005 model of water is systematically investigated in liquid phase in the temperature range 210-310 K. The translational and rotational diffusions, as well as correlations between them, are examined. The effects of system size and shape are also probed in this study. The results suggest the presence of a temperature of dynamical arrest of molecular translations in the range of 150-180 K and of molecular rotations in the range of 80-130 K, depending on specific direction. A substantial change in the preferred directions of translations and rotations relative to the molecular coordinate system is observed slightly below (≈15 K) the melting temperature of the model. It is shown that there is a correlation between translational and rotational molecular motions essential for diffusion in the liquid. The presence of hydrodynamic size effects is confirmed and quantified; it is also shown that using a non-cubic simulation box for a liquid system leads to an anisotropic splitting in the diffusion tensor. The findings of this study enhance our general understanding of models of water, specifically the TIP4P-2005 model, as well as provide evidences of the direct connection between thermodynamics of liquid water and dynamics of its molecules.     

Conformational and Orientational Order of Molecules in Nematic Liquid Crystals

The statistical properties of the conformational and orientational distribution of molecules with internal rotation in the isotropic and nematic phases of liquid crystal (LC) are investigated in terms of molecular statistical theory. The paper discusses the effect of mutual correlation between the molecular conformational and orientational degrees of freedom on the conformational, orientational, and mixed order parameters of molecules in LC and on the nematic–isotropic liquid transition temperature. For these order parameters, the recurrent relation method is suggested and used to derive the partial functions of the conformational and orientational distributions of molecules in LC.     

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method's sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.     

Aerodynamical acceleration and rotational-vibrational temperatures in seeded supersonic molecular beams

The time-of-flight (TOF) technique was used to study the aerodynamical acceleration in seeded supersonic molecular beams of heavy molecules and light seeding gas. We also studied the correlation between the degree of aerodynamic acceleration achieved, and rotational-vibrational temperatures as measured using the laser-induced fluorescence (LIF) technique. The velocity slip (difference) between helium and hydrogen carrier gases and iodine and aniline heavy molecules was determined in free-jet expansion by TOF measurements and compared with rotational temperatures measured by LIF. The helium translational temperature was found to be abnormally high and dependent on teh heavy-molecule concentration, even at concentration as low as 400 ppm. In the case of iodine it was found that the rotational degrees of freedom were equilibrated with the helium or hydrogen seeding gas translational and slip temperatures, although this temperature was more than an order of magnitude higher than theoretical predictions obtained for the pure-gas expansion. In aniline, the rotational temperature is found to be higher than the gas-dynamic temperature and rotational relaxation is incomplete. The heavy-molecule kinetic energy increases linearly with the light-gas pressure up to = 50% of its maximum available kinetic energy. The possibility of making accurate heavy-molecule kinetic-energy measurements using the LIF technique is discussed. It is claimed that the existence of velocity slip can largely effect theoretical calculations concerning vibrational and rotational relaxation in seeded supersonic beams.     

Molecular dynamics simulations of melting of perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine

The melting mechanism of superheated perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (alpha-RDX) has been investigated using molecular dynamics simulations with the fully flexible force field developed by Smith and Bharadwaj [J. Phys. Chem. B 103, 3570 (1999)]. Sequential 50 ps equilibration simulations of the constant stress-constant temperature ensemble were performed at 10 K intervals over the range of 300-650 K, corresponding to a heating rate of 2.0 x 10(11) Ks. A solid-solid phase transition is observed between 480 and 490 K, followed by melting, which occurs between 500 and 510 K. The solid-solid phase transition, both displacive and rotational, is characterized by an abrupt decrease in the lengths of the unit cell edges a and b and an increase of the length of edge c. The molecular conformation in the new phase is AAE, although the axial nitro groups have different changes: one shift is more axial and the other is more equatorial. Phases other than alpha-RDX have been observed experimentally, however, there are insufficient data for comparisons to ascertain that the new phase observed here corresponds to a real phase. At the high heating rate (2.0 x 10(11) Ks) used in the simulations, the melted RDX reaches full orientational disorder at about 540 K and translational freedom at around 580 K. If the simulation at the melting temperature (510 K) is run sufficiently long complete rotational freedom is achieved in a few hundreds of picoseconds, while complete translational freedom requires much longer. These results show that given a sufficiently high heating rate, the system can exist for significant periods of time in a near-liquid state in which the molecules are not as free to rotate and diffuse as in the true liquid state. The bond lengths and bond angles undergo little change upon melting, while there are significant changes in the dihedral angles. The molecular conformation of RDX changes from AAE to EEE upon melting. The ramification of this for formulating force fields that accurately describe melting is that it is important that the torsional motions are accurately described.     

Temperature dependence of dimerization and dewetting of large-scale hydrophobes: a molecular dynamics study

We studied by molecular dynamics simulations the temperature dependence of hydrophobic association and drying transition of large-scale solutes. Similar to the behavior of small solutes, we found the association process to be characterized by a large negative heat capacity change. The origin of this large change in heat capacity is the high fragility of hydrogen bonds between water molecules at the interface with hydrophobic solutes; an increase in temperature breaks more hydrogen bonds at the interface than in the bulk. With increasing temperature, both entropy and enthalpy changes for association strongly decrease, while the change in free energy weakly varies, exhibiting a small minimum at high temperatures. At around T=Ts=360 K, the change in entropy is zero, a behavior similar to the solvation of small nonpolar solutes. Unexpectedly, we find that at Ts, there is still a substantial orientational ordering of the interfacial water molecules relative to the bulk. Nevertheless, at this point, the change in entropy vanishes due to a compensating contribution of translational entropy. Thus, at Ts, there is rotational order and translational disorder of the interfacial water relative to bulk water. In addition, we studied the temperature dependence of the drying-wetting transition. By calculating the contact angle of water on the hydrophobic surface at different temperatures, we compared the critical distance observed in the simulations with the critical distance predicted by macroscopic theory. Although the deviations of the predicted from the observed values are very small (8-23%), there seems to be an increase in the deviations with an increase in temperature. We suggest that these deviations emerge due to increased fluctuations, characterizing finite systems, as the temperature increases.     

Rotational correlation and dynamic heterogeneity in a kinetically constrained lattice gas

We study the dynamical heterogeneity and glassy dynamics in a kinetically constrained lattice-gas model which has both translational and rotational degrees of freedom. We find that the rotational relaxation time tracks the structural relaxation time as density is increased whereas the translational diffusion constant exhibits a strong decoupling. We investigate distributions of exchange and persistence times for both the rotational and translational degrees of freedom and compare our results on the distributions of rotational exchange times to recent single molecule studies.     

Characteristic behavior of short-term dynamics in reorientation for Gay-Berne particles near the nematic-isotropic phase transition temperature

A specific transition behavior was found in the tumbling motion near the nematic-isotropic phase boundary using molecular dynamics simulations of the Gay-Berne mesogenic model under isobaric conditions at a reduced pressure P* of 2.0. The relaxation time for the motion obtained from the second-rank orientational time correlation function and the rotational diffusion coefficient showed a clear jump at the nematic-isotropic phase transition temperature. Regardless of the temperature dependence of the relaxation time, the change in the rotational diffusion coefficient evaluated from the orientational order parameters and the relaxation time agreed qualitatively with that of real mesogens. The rotational viscosity coefficients gamma(1) and gamma(2) were obtained from the simulation data for the relaxation time for the short-term dynamics and for the rotational diffusion coefficients. gamma(1) was proportional to (2), where is the second-rank orientational parameter. Furthermore, the rotational behavior of the model was compared with that of the Debye approximation in the isotropic phase.     

Diffusion of hydrocarbons in confined media: Translational and rotational motion

Diffusion of monatomic guest species within confined media has been understood to a good degree due to investigations carried out during the past decade and a half. Most guest species that are of industrial relevance are actually polyatomics such as, for example, hydrocarbons in zeolites. We attempt to investigate the influence of non-spherical nature of guest species on diffusion. Recent molecular dynamics (MD) simulations of motion of methane in NaCaA and NaY, benzene in NaY and one-dimensional channels AlPO₄−5, VPI−5 and carbon nanotube indicate interesting insights into the influence of the host on rotational degrees of freedom and orientational properties. It is shown that benzene in one-dimensional channels where the levitation parameter is near unity exhibits translational motion opposite to what is expected on the basis of molecular anisotropy. Rotational motion of benzene also possesses rotational diffusivities aroundC ₆ and C₂axes opposite to what is expected on the basis of molecular geometry. Methane shows orientational preference for 2+ 2 or 1 + 3 depending on the magnitude of the levitation parameter.     

Advanced gradient-like methods for rigid-body molecular dynamics

A novel approach is developed to integrate the equations of motion in many-body systems of interacting rigid polyatomic molecules. It is based on an advanced gradient-like decomposition technique in the presence of translational and orientational degrees of freedom. As a result, a new class of reversible phase-space volume preserving fourth-order algorithms for rotational motion is introduced. Contrary to standard nongradient decomposition integrators, the algorithms derived take into account additional analytically integrable terms in the exponential propagators, while the arising gradients are expressed in terms of forces and torques. This allows one to increase significantly the precision of the integration and, at the same time, reduce the increased computational costs. The optimized second-order integrator is also presented. The gradient-like and optimized algorithms are tested in molecular dynamics simulations of water versus well-established integrators known previously. It is shown that the new algorithms lead to the best efficiency in the rigid-body integration.     

Frequency shift in smectic multiple relaxations and the effect of a flexible end chain

The low frequency (LF) dielectric constant was studied as a function of temperature in the Schiff 's base liquid crystalline compounds of N ( p - n -alkoxybenzylidene)- p - n -alkylanilines with the applied field parallel to the director to determine the phase transition temperatures and the underlying dipolar association. The low frequency (1 kHz to 10 MHz) complex dielectric spectrum systematically studied in the smectic polymorphs of these compounds implied multiple relaxations. The rotational degrees of freedom were found to be squeezed with the decrease of temperature as the low temperature smectic phases were approached. The ColeDavidson method was used to differentiate the fast dynamics of the rigid core-associated dipole from the slow component of the flexible end chain. A comparative study of the orientational dynamics of the rigid core dipole (type I) was carried out by designing a normalized scale in smectic phases. Arrehenius dependence was used in the estimation of smectic relaxation frequency at a common normalized smectic temperature scale point. The results imply the downward shift of frequency with increase in length of the flexible end chain. The distinct loss of rotational degrees of freedom of the rigid core dipole with increasing chain length suggests its solute particle behaviour in the solvent concentration.     

Molecular dynamics with quantum transitions study of the vibrational relaxation of the HOD bend fundamental in liquid D2O

The molecular dynamics with quantum transitions method is used to study the vibrational relaxation of the HOD bend fundamental in liquid D(2)O. All of the vibrational bending degrees of freedom of the HOD and D(2)O molecules are described by quantum mechanics, while the remaining translational and rotational degrees of freedom are described classically. The effect of the coupling between the rotational and vibrational degrees of freedom of the deuterated water molecules is analyzed. A kinetic mechanism based on three steps is proposed in order to interpret the dynamics of the system. It is shown that intermolecular vibrational energy transfer plays an important role in the relaxation process and also that the transfer of energy into the rotational degrees of freedom is favored over the transfer of energy into the translational motions. The thermalization of the system after the relaxation is reached in a shorter time scale than that of the recovery of the hydrogen bond network. The relaxation and equilibration times obtained compare well with experimental and previous theoretical results.