The effects of shape and flexibility on bio-engineered fd-virus suspensions

We present a theoretical model to describe binary mixtures of semi-flexible rods, applied here to fd-virus suspensions. We investigate the effects of rod stiffness on both monodisperse and binary systems, studying thick-thin and long-short mixtures. For monodisperse systems, we find that fd-virus particles have to be made extremely stiff to even approach the behavior of rigid rods. For thick-thin mixtures, we find increasingly rich phase behavior as the rods are either made more flexible or if their diameter ratio is increased. For long-short rod mixtures we find that the phase behavior is controlled by the relative stiffness of the rods, with increasing the stiffness of the long rods or decreasing that of the short rods resulting in richer phase behavior. We also calculate the state point dependent effective shape of the rods. The flexible rods studied here always behave as shorter, thicker rigid rods, but with an effective shape that varies widely throughout the phase diagrams, and plays a key role in determining phase behavior.     

An efficient ring polymer contraction scheme for imaginary time path integral simulations

A quantum simulation of an imaginary time path integral typically requires around n times more computational effort than the corresponding classical simulation, where n is the number of ring polymer beads (or imaginary time slices) used in the calculation. However, this estimate neglects the fact that the potential energies of many systems can be decomposed into a sum of rapidly varying short-range and slowly varying long-range contributions. For such systems, the computational effort of the path integral simulation can be reduced considerably by evaluating the long-range forces on a contracted ring polymer with fewer beads than are needed to evaluate the short-range forces. This idea is developed and then illustrated with an application to a flexible model of liquid water in which the intramolecular forces are evaluated with 32 beads, the oxygen-oxygen Lennard-Jones forces with seven, and the intermolecular electrostatic forces with just five. The resulting static and dynamic properties are within a few percent of those of a full 32-bead calculation, and yet they are obtained with a computational effort less than six times (rather than 32 times) that of a classical simulation. We hope that this development will encourage future studies of quantum mechanical fluctuations in liquid water and aqueous solutions and in many other systems with similar interaction potentials.     

Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations.

A comparison of different treatments of bond-stretching interactions in molecular dynamics simulation is presented. Relative free energies from simulations using rigid bonds maintained with the SHAKE algorithm, using partially rigid bonds maintained with a recently introduced flexible constraints algorithm, and using fully flexible bonds are compared in a multi-configurational thermodynamic integration calculation of changing liquid water into liquid methanol. The formula for the free energy change due to a changing flexible constraint in a flexible constraint simulation is derived. To allow for a more direct comparison between these three methods, three different pairs of models for water and methanol were used: a flexible model (simulated without constraints and with flexible constraints), a rigid model (simulated with standard hard constraints), and an alternative flexible model (simulated with flexible constraints and standard hard constraints) in which the ideal or constrained bond lengths correspond to the average bond lengths obtained from a short simulation of the unconstrained flexible model. The particular treatment of the bonds induces differences of up to 2 % in the liquid densities, whereas (excess) free energy differences of up to 5.7 (4.3) kJ mol(-1) are observed. These values are smaller than the differences observed between the three different pairs of methanol/water models: up to 5 % in density and up to 8.5 kJ mol(-1) in (excess) free energy.     

Explicit ions condensation around strongly charged polyelectrolytes and spherical macroions: the influence of salt concentration and chain linear charge density. Monte Carlo simulations

The condensation of monovalent counterions and trivalent salt particles around strong rigid and flexible polyelectrolyte chains as well as spherical macroions is investigated by Monte Carlo simulations. The results are compared with the condensation theory proposed by Manning. Considering flexible polyelectrolyte chains, the presence of trivalent salt is found to play an important role by promoting chain collapse. The attraction of counterions and salt particles near the polyelectrolyte chains is found to be strongly dependent on the chain linear charge density with a more important condensation at high values. When trivalent salt is added in a solution containing monovalent salt, the trivalent cations progressively replace the monovalent counterions. Ion condensation around flexible chains is also found to be more efficient compared with rigid rods due to monomer rearrangement around counterions and salt cations. In the case of spherical macroions, it is found that a fraction of their bare charge is neutralized by counterions and salt cations. The decrease of the Debye length, and thus the increase of salt concentration, promotes the attraction of counterions and salt particles at the macroion surface. Excluded volume effects are also found to significantly influence the condensation process, which is found to be more important by decreasing the ion size.     

Phase behavior of lyotropic rigid-chain polymer liquid crystal studied by dissipative particle dynamics

The phase behavior of lyotropic rigid-chain liquid crystal polymer was studied by dissipative particle dynamics (DPD) with variations of the solution concentration and temperature. A chain of fused DPD particles was used to represent each mesogenic polymer backbone surrounded with the strongly interacted solvent molecules. The free solvent molecules were modeled as independent DPD particles, where each particle includes a lump of solvent molecules with the volume roughly equal to the solvated polymer segment. The simulation shows that smectic-B (S(B)), smectic-A (S(A)), nematic (N), and isotropic (I) phases exist within certain regions in the temperature and concentration parameter space. The temperature-dependent S(B)∕S(A), S(A)∕N, and N∕I phase transitions occur in the high concentration range. In the intermediate concentration range, the simulation shows coexistence of the anisotropic phases and isotropic phase, where the anisotropic phases can be the S(B), S(A), or N phases. Mole fraction and compositions of the coexisted phases are determined from the simulation, which indicates that concentration of rigid rods in isotropic phase increases as the temperature increases. By fitting the orientational distribution function of the systems, the biphasic coexistence is further confirmed. From the parameter α obtained for the simulation, the distribution of the rigid rods in the two coexistence phases is quantitatively evaluated. By using model and simulation methods developed in this work, the phase diagrams of the lyotropic rigid-chain polymer liquid crystal are obtained. Incorporating the solvent particles in the DPD simulation is critical to predict the phase coexistence and obtain the phase diagrams.     

Strong effect of hydrodynamic coupling on the electric dichroism of bent rods

The effect of hydrodynamic coupling on the spatial orientation of rigid bent rods in electric fields has been analyzed by Brownian dynamics simulations. Bead models for smoothly bent rods were constructed with dimensions of DNA double helices, and established simulation procedures were used to calculate their diffusion tensor, including the translational-rotational coupling tensor. The electric and optical parameters were assigned on the basis of known properties of double helices. Brownian dynamics simulations of the orientation of these models in electric fields showed that both transients and amplitudes of the calculated dichroism are very strongly dependent on translational-rotational coupling over a wide range of electric field strengths. For example, the stationary dichroism of a smoothly bent 179 bp DNA fragment calculated at low field strengths is positive in the presence and negative in the absence of hydrodynamic coupling. The transients are converted from a biphasic to a monophasic shape, when hydrodynamic coupling is turned off. The large changes resulting from hydrodynamic coupling were controlled by calculations based on analytical expressions derived for electrooptical response curves in the limit of low electric field strengths; the results obtained by this independent approach are in very satisfactory agreement with our Brownian dynamics simulations. The effect is strongly dependent on the electric dipole and on its direction. In the absence of any dipole the coupling effect was not observed. The coupling effect increases with the size of the bent rods. Because most macromolecular structures are known to have induced and/or permanent dipole moments, large effects of hydrodynamic coupling on both the amplitudes and the transients of the electric dichroism/birefringence must be expected in general for structures with nonsymmetric shape.     

A comparison of field-based similarity searching methods: CatShape, FBSS, and ROCS

Three field-based similarity methods are compared in retrospective virtual screening experiments. The methods are the CatShape module of CATALYST, ROCS, and an in-house program developed at the University of Sheffield called FBSS. The programs are used in both rigid and flexible searches carried out in the MDL Drug Data Report. UNITY 2D fingerprints are also used to provide a comparison with a more traditional approach to similarity searching, and similarity based on simple whole-molecule properties is used to provide a baseline for the more sophisticated searches. Overall, UNITY 2D fingerprints and ROCS with the chemical force field option gave comparable performance and were superior to the shape-only 3D methods. When the flexible methods were compared with the rigid methods, it was generally found that the flexible methods gave slightly better results than their respective rigid methods; however, the increased performance did not justify the additional computational cost required.     

The quest for the best nonpolarizable water model from the adaptive force matching method

The recently introduced adaptive force matching (AFM) method is used to develop a significantly improved pair‐wise nonpolarizable potential for water. A rigid version of the potential is also presented to enable larger time steps for biological simulations. In this work, it is demonstrated that the AFM method can be used to systematically assess the importance of each functional term during the construction of a force field. For a water potential, it is established that a single off‐atom charge center (M) in the plane of water outperforms two out‐of‐plane charge sites for reproducing intermolecular forces. The four‐site pair‐wise nonpolarizable force field developed in this work rivals some of the most sophisticated polarizable models in terms of reproducing accurate ab initio forces. The force fields are parameterized to perform best in the temperature range from 0 to 40°C. Equilibrium and dynamical properties calculated with the flexible and rigid force fields are in good agreement with experimental results. For the flexible model, the agreement improves when path integral simulation is performed. These force fields provide high‐quality results at a very low computational cost and are thus well suited to atomistic scale biological simulations. The AFM method provides a mechanism for selecting important terms in force field expressions and is a very promising tool for producing accurate force fields in condensed phases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Polymer blends containing liquid crystal polymers

Polymer blends can be either composed of mixtures of flexible components, of a stiff chain and a flexible macromolecule, or of two stiff-chain polymers. All three cases may be dealt with in terms of the Flory lattice model. Special attention is paid to the influence of liquid crystalline order on the miscibility of the two polymers. For isotropic mixtures all three cases may be described in terms of the usual Flory–Huggins approximation. If a nematic phase is formed the miscibility of blends of rigid rods with flexible macromolecules (molecular composites) is strongly reduced because of entropic reasons. Highly ordered mixture of two stiff-chain polymers in melt can be described in terms of the regular solution theory leading to the same miscibility criterion as is valid for two flexible polymers. All deductions are compared to recent experimental work.     

Comparison of rigid and flexible simple point charge water models at supercritical conditions

This study investigates the differences between the predictions of various properties of rigid and flexible simple point charge water models at supercritical conditions. Molecular dynamics simulations were conducted for supercritical water in a temperature range of 773–1073 K and densities in the range 115–659 kg/m³. We present thermodynamic data, pair correlation functions, self-diffusivity, power spectra, dielectric constants, and variaous measures of hydrogen bonding at different state conditions. The flexible water model performs better in predicting the pressures along the supercritical isotherms simulated. Agreement between experimental and calculated dielectric constants is superior for the flexible water model, particularly at high densities. The flexible model exhibits a greater degree of hydrogen bonding and more persistent hydrogen bonds than does the rigid model. The structural features of supercritical water at high densities are identical for the two water models. At low densities, however, the flexible potential exhibits pair correlation functions with enhanced peaks. Inclusion of flexibility in the potential model does not result in a significant shift in the position of the rotational/librational peak in the power spectrum. The self-diffusivities obtained from the simulations are within the accuracy of the experimental values for both the rigid and flexible models. On balance the inclusion of flexibility improves agreement with the properties of real supercritical water while incurring little or no additional computational burden. © 1996 by John Wiley & Sons, Inc.     

Are large micelles rigid or flexible? A reinterpretation of viscosity data for micellar solutions

Surfactant solutions in which large cylindrical micelles form are characterized by two essential features, namely, they are polydisperse and the average micelle size is proportional to the square root of the micelle concentration. These features of the cylindrical micelles imply that the intrinsic viscosities of these micellar solutions should also depend on the concentration of micelles. This fact has been ignored in all past treatments of micellar viscosity data. Here, viscosity data available in literature were reexamined in terms of concentration-dependent intrinsic viscosity so as to evaluate the rigidity or the flexibility of the large micelles. It is found that the interpretation of viscosity data assuming that the large micelles are rigid rods is in very good agreement with the theoretically anticipated essential features of large micelles. It is concluded that large micelles can be satisfactorily represented by rigid rods rather than by flexible rods or coils.     

The role of attractive interactions in rod-sphere mixtures

We present a computer simulation study of binary mixtures of prolate Gay-Berne particles and Lennard-Jones spheres. Results are presented for three such rod-sphere systems which differ from each other only in the interaction between unlike particles. Both the mixing-demixing behavior and the transitions between the isotropic and any liquid crystalline phases are studied for each system, as a function of temperature and concentration ratio. For systems which show macroscopic demixing, the rod-sphere interaction is shown to give direct control over interfacial anchoring properties, giving rise to the possibility of micellar phase formation in the case of homeotropic anchoring. Additionally, it is shown that on incorporating high concentrations of spheres into a system of rods with weak demixing properties, microphase-separated structures can be induced, including bicontinuous and lamellar arrangements.     

Depletion potentials in colloidal mixtures of hard spheres and rods

The depletion potential between a hard sphere and a planar hard wall, or two hard spheres, imposed by suspended rigid spherocylindrical rods is computed by the acceptance ratio method through the application of Monte Carlo simulation. The accurate results and ideal-gas approximation results of the depletion potential are determined with the acceptance ratio method in our simulations. For comparison, the depletion potentials are also studied by using both the density functional theory and Derjaguin approximations. The density profile as a function of positions and orientations of rods, used in the density functional theory, is calculated by Monte Carlo simulation. The potential obtained by the acceptance ratio method is in good agreement with that of density functional theory under the ideal-gas approximation. The comparison between our results and those of other theories suggests that the acceptance ratio method is the only efficient method used to compute the depletion potential induced by nonspherical colloids with the volume fraction beyond the ideal-gas approximation.     

Microstructure and self-assembly of inhomogeneous rigid rodlike chains between two neutral surfaces: A hybrid density functional approach

We use a hybrid density functional approach to investigate the microstructure and self-assembly of inhomogeneous rigid rodlike chains between two neutral surfaces, i.e., two hard walls. In the calculation, the rodlike molecule is modeled as a rigid rod linearly connected by the tangent sphere beads. The hybrid method combines a single-chain Monte Carlo (MC) simulation for the ideal-gas part of Helmholtz energy and a DFT approach for the excess Helmholtz energy. The DFT approach includes a modified fundamental measure theory for the excluded-volume effect, the first order thermodynamics perturbation theory for chain connectivity, and the mean field approximation for the van der Waals attraction. We investigate the effect of the chain length (i.e., aspect ratio) of the rodlike molecule and the separation between two surfaces on the microstructure and self-assembly of inhomogeneous rigid rodlike chains. For the athermal systems, the rodlike chain fluids present a smaller partitioning coefficient compared to the flexible chain fluids. For the thermal systems, lamellar thin films formed by the rigid rodlike molecules perpendicular to the neutral surface are observed. The effects of the head-head interaction and the separation on the self-assembly of the rodlike chain fluids in the slit are investigated.     

Simulation of the rheological properties of liquid media containing solid anisometric particles

Theoretical simulation of the rheological properties of liquid media containing solid anisometric particles is performed. Procedures for the calculation of the degree of ordering in the nematic systems under equilibrium conditions and their rheological characteristics are proposed. Earlier developed notions of the calculation procedures for the properties of systems considered are analyzed and corrections to the theory are substantiated. Based on developed model notions, equilibrium and transport equations are derived and a program for their numerical solution is proposed. Model calculations of the lines of phase transition and the ordering of systems containing isotropic and nematic phases, as well as anisotropic (in orienting field) and effective dynamic viscosities under the conditions of free flow of such systems, are carried out at various concentrations and geometry of anisometric particles. A comparison of calculated and experimental data for the solutions of polymer-salt compositions with induced chain rigidity demonstrates the adequacy of the model proposed.     

Computer simulation studies of anisotropic systems. XXII. An equimolar mixture of rods and discs: A biaxial nematic?

In principle, binary mixtures of rod-like and disc-like particles should exhibit a biaxial nematic phase, but in practice phase separation into two uniaxial nematic phases prevents this. Here, we report the results of a computer simulation study of an equimolar mixture of rods and discs in which phase separation is not allowed. The particles are confined to the sites of a simple cubic lattice in which each rod is surrounded by six discs and vice versa. Neighbouring particles interact such that they prefer to align with their respective symmetry axes orthogonal to each other. In contrast, the interaction between next nearest neighbours, which are either rods or discs, is such that their symmetry axes tend to be parallel. Monte Carlo simulations of this model mixture show that an orientationally ordered phase exists at low temperatures. This nematic phase has overall uniaxial symmetry and the particles have a negative second rank orientational order parameter, indicating that they tend to align at right angles to the director. The two interpenetrating sub-lattices containing either rods or discs, however, exhibit a biaxial nematic phase. The results of the simulation are found to be in reasonable agreement with the predictions of a molecular field theory for this model mixture. We have also investigated the behaviour of this mixture when the rods and discs are allowed to exchange between their lattice sites. The mixture is found to separate into two uniaxial nematic phases composed essentially of either rods or discs, as expected.     

Dilute solution properties,chain stiffness,and liquid crystalline properties of cellulose propionate

The solution properties of cellulose derivatives are of interest from both technological and purely scientific aspects. At high concentrations these solutions form liquid crystalline structures. In dilute solution cellulosic chains can be described as semiflexible or wormlike with properties intermediate between random coils and rigid rods. A series of fractions of cellulose propionate have been examined by dilute solution viscometry, static and dynamic light scattering, and polarizing microscopy. Power law exponents are considerably larger than those observed for flexible chains and analysis of the intrinsic viscosity and hydrodynamic radii has yielded chain diameters and Kuhn statistical segment lengths. Corresponding aspect ratios from the hydrodynamic measurements are in good agreement with those obtained from polarizing microscopy, as analyzed in light of Flory's theory. Some aggregation and specific solvent effects have been observed, however separation of these effects has proven to be difficult. Results of these studies are compared to previous work for other cellulose derivatives. ©1995 John Wiley & Sons, Inc.     

Percolation of randomly centered rods and spheres

The percolation properties of randomly centered rods and spheres are studied. The approach is based on the detailed study of frequencies of cluster occurrences. For random rods, the analytic expressions are derived for all cluster frequencies. It is then shown that one-dimensional systems of random rods exhibit critical behaviour with? _c = ∞,γ = 1. For randomly centered spheres, we designed a numerical method for calculating the cluster frequencies. The approach is based on the principles of the Monte Carlo method. It can cope with clusters containing up to seven particles, which should suffice for the evaluation of accurate values of critical density and critical exponents.     

The short-time self-diffusion coefficient of a sphere in a suspension of rigid rods

The short-time self-diffusion coefficient of a sphere in a suspension of rigid rods is calculated in first order in the rod volume fraction phi. For low rod concentrations, the correction to the Einstein diffusion constant of the sphere due to the presence of rods is a linear function of phi with the slope alpha proportional to the equilibrium averaged mobility diminution trace of the sphere interacting with a single freely translating and rotating rod. The two-body hydrodynamic interactions are calculated using the so-called bead model in which the rod of aspect ratio p is replaced by a stiff linear chain of touching spheres. The interactions between spheres are calculated using the multipole method with the accuracy controlled by a multipole truncation order and limited only by the computational power. A remarkable accuracy is obtained already for the lowest truncation order, which enables calculations for very long rods, up to p=1000. Additionally, the bead model is checked by filling the rod with smaller spheres. This procedure shows that for longer rods the basic model provides reasonable results varying less than 5% from the model with filling. An analytical expression for alpha as a function of p is derived in the limit of very long rods. The higher order corrections depending on the applied model are computed numerically. An approximate expression is provided, valid for a wide range of aspect ratios.     

Diffusion of chain molecules and mixtures in carbon nanotubes: the effect of host lattice flexibility and theory of diffusion in the Knudsen regime

A novel algorithm for modeling the influence of the host lattice flexibility in molecular dynamics simulations is extended to chain-like molecules and mixtures. This technique, based on a Lowe-Andersen thermostat, maintains the advantages of both simplicity and efficiency. The same diffusivities and other properties of the flexible framework system are reproduced. Advantageously, the computationally demanding flexible host lattice simulations can be avoided. Using this methodology we study the influence of flexibility on diffusion of n-alkanes inside single-walled carbon nanotubes. Furthermore, results are shown for diffusion of two mixtures (methane-helium and ethane-butane). Using these results we investigate the accuracy of theories describing diffusion in the Knudsen regime. For the dynamics in carbon nanotubes the Knudsen diffusivities are much too low. The Smoluchowski model gives better results. Interestingly, the extended Smoluchowski model can reproduce our simulation results obtained with a rigid host lattice. We modify this model to also treat collisions with a flexible interface correctly. As the tangential momentum accommodation coefficient is needed for the theoretical models, we introduce a simple concept to calculate it.