Biomedical subjects

Athanassios Z Panagiotopoulos

Publications and source records attributed to Athanassios Z Panagiotopoulos.

At least 19 recordsLinked to original sources

PubMed2006

Tracing the critical loci of binary fluid mixtures using molecular simulation.

Monte Carlo simulations are used to trace the critical loci for a number of binary mixtures. In particular, we use grand canonical Monte Carlo (GCMC) simulations with histogram reweighting and mixed-field finite-size scaling to determine the mixture critical lines. Two different classes of criticality are investigated. A mixture of methane and ethane displays type I criticality, exhibiting continuous mixing between the two species across the entire composition range. A methane-water mixture shows type IIIb criticality, with a discontinuity in the critical locus. Quantitative agreement is found between simulation and experimental critical loci for the methane-ethane system using no adjustable parameters for interactions in the mixture. For the water-methane system, we investigate the effect of the combining rules for the intermolecular interaction between the two species on the mixture critical locus. We also investigate several potentials for methane: a nonpolar exponential-6, an octopolar fixed partial charge, and a polarizable fluctuating charge model. Qualitative agreement between simulations and experiments is found for all potentials, but none are able to quantitatively capture the abrupt increase in the critical temperature as methane is added to the system.

Journal Article↗

PubMed2006

Effect of stiffness on the micellization behavior of model H4T4 surfactant chains.

The micellization behavior of a series of model surfactants, all with four head and tail groups (H4T4) but with different degrees of chain stiffness, was studied using grand canonical Monte Carlo simulations on a cubic lattice. The critical micelle concentration, micellar size, and thermodynamics of micellization were examined. In all cases investigated, the critical micelle concentration was found to increase with increasing temperature as observed for nonionic surfactants in apolar or slightly polar solvents. At a fixed reduced temperature and increasing chain stiffness, in agreement with previous observations, it was found that the critical micelle concentration decreased and the average micelle size increased. This behavior is qualitatively consistent with that experimentally observed when comparing hydrogenated and homologous fluorinated surfactants. Thermodynamic considerations based on the analysis of the temperature dependence of the critical micelle concentration indicated that both effects could be interpreted as arising from an increased number of heterocontacts between hydrophobic portions of stiff surfactants and a lower entropic cost on packing rigid chains. Structural analysis that was also based on considering the inner micellar radial dependence of the surfactant head and tail site fraction distributions suggested that, on stiffening the molecular backbone, the resulting micellar aggregates grew, without appreciable deviations from spherical symmetry. Stiffer surfactants led to a slightly denser micellar core because of better packing.

Micelles↗

PubMed2006

Global phase diagram for the honeycomb potential.

We calculate the global phase diagram using classical statistical mechanics for an isotropic pair potential that has been previously [Rechtsman et al., Phys. Rev. Lett. 95, 228301 (2005)] shown to produce the low-coordinated two-dimensional honeycomb crystal as the ground-state structure. Low-coordinated crystals are of practical interest because they have desirable photonic band-gap properties. The phase diagram is obtained from Helmholtz free energies calculated using thermodynamic integration and Monte Carlo simulations. Our results show that the honeycomb crystal remains stable in the global phase diagram even after temperature effects are taken fully into account. Other stable phases in the phase diagram are high and low density triangular phases and a fluid phase. We find no evidence of gas-liquid or liquid-liquid phase coexistence.

Journal Article↗

PubMed2006

Phase behavior of the lattice restricted primitive model with nearest neighbor exclusion.

The global phase behavior of the lattice restricted primitive model with nearest neighbor exclusion has been studied by grand canonical Monte Carlo simulations. The phase diagram is dominated by a fluid (or charge-disordered solid) to charge-ordered solid transition that terminates at the maximum density rho*(max)= sqrt 2 and reduced temperature T* approximately equal to 0.29. At that point, there is a first-order phase transition between two phases of the same density, one charge-ordered, and the other charge-disordered. The liquid-vapor transition for the model is metastable, lying entirely within the fluid-solid phase envelope.

Journal Article↗

PubMed2006

Monte carlo simulations of micellization in model ionic surfactants: application to sodium dodecyl sulfate.

A lattice model for ionic surfactants with explicit counterions is proposed for which the micellization behavior can be accurately determined from grand canonical Monte Carlo simulations. The model is characterized by a few parameters that can be adjusted to represent various linear surfactants with ionic headgroups. The model parameters have a clear physical interpretation and can be obtained from experimental data unrelated to micellization, namely, geometric information and solubilities of tail segments. As a specific example, parameter values for sodium dodecyl sulfate were obtained by optimizing for the solubility of hydrocarbons in water and the structural properties of dodecane. The critical micelle concentration (cmc), average aggregation number, degree of counterion binding, and their dependence on temperature were determined from histogram reweighting grand canonical Monte Carlo simulations and were compared to experimental results. The model gives the correct trend and order of magnitude for all quantities but underpredicts the cmc and aggregation number. We suggest ways to modify the model that may improve agreement with experimental values.

Journal Article↗

PubMed2006

Computational characterization of the sequence landscape in simple protein alphabets.

We characterize the "sequence landscapes" in several simple, heteropolymer models of proteins by examining their mutation properties. Using an efficient flat-histogram Monte Carlo search method, our approach involves determining the distribution in energy of all sequences of a given length when threaded through a common backbone. These calculations are performed for a number of Protein Data Bank structures using two variants of the 20-letter contact potential developed by Miyazawa and Jernigan [Miyazawa S, Jernigan WL. Macromolecules 1985;18:534], and the 2-monomer HP model of Lau and Dill [Lau KF, Dill KA. Macromolecules 1989;22:3986]. Our results indicate significant differences among the energy functions in terms of the "smoothness" of their landscapes. In particular, one of the Miyazawa-Jernigan contact potentials reveals unusual cooperative behavior among its species' interactions, resulting in what is essentially a set of phase transitions in sequence space. Our calculations suggest that model-specific features can have a profound effect on protein design algorithms, and our methods offer a number of ways by which sequence landscapes can be quantified.

Amino Acid Sequence↗

PubMed2005

Shear ordering in thin films of spherical block copolymer.

We have investigated shear-induced alignment of a bilayer of spherical diblock copolymer micelles within thin films using molecular dynamics simulations at two different levels of coarse-graining. At the microscopic level, the copolymers are modeled as bead and spring chains with specific interaction potentials which produce strongly segregated spherical micelles. The simulations qualitatively reveal that long-range shear-induced ordering of hexagonally arranged micelles arises because of the tendency of micelles to pursue trajectories of minimum frictional resistance against micelles in the opposing layer. This influences their alignment in the direction of shear without them breaking apart and reforming within the time scale of the simulations. As observed in experiments, the ordering is shown to be very sensitive to the film thickness and shearing rates. To access larger lengths and longer time scales, we further coarse-grain our system to a mesoscopic level where an individual micelle is represented by a spherical particle, which interacts with other micelles through an effective potential obtained from the microscopic simulations. This approach enables us to follow the time evolution of global order from locally ordered domains. An exponentially fast growth of the orientational correlation length of the hexagonal pattern at early times, followed by a crossover to linear growth, is found in the presence of shear, in contrast to the much slower power-law scalings observed in experiments without shear.

Journal Article↗

PubMed2005

Universality of ionic criticality: size- and charge-asymmetric electrolytes.

Grand-canonical simulations designed to resolve critical universality classes are reported for z:1 hard-core electrolyte models with diameter ratios lambda=a+/a- less than or approximately equal 6. For z=1 Ising-type behavior prevails. Unbiased estimates of Tc(lambda) are within 1% of previous (biased) estimates but the critical densities are approximately 5% lower. Ising character is also established for the 2:1 and 3:1 equisized models, along with critical amplitudes and improved Tc estimates. For z=3, however, strong finite-size effects reduce the confidence level although classical and O (n>or=3) criticality are excluded.

Journal Article↗

PubMed2005

Log-rolling micelles in sheared amphiphilic thin films.

Using molecular dynamics simulations, we show that sheared solutions of cylindrical micelle-forming amphiphiles behave very differently under extreme confinement as compared to the bulk. When confined to ultrathin films, the self-assembled cylindrical micelles roll along the shearing direction and align parallel to each other with their axes along the vorticity direction, as opposed to aligning parallel to the shearing direction in the bulk. It is shown that this new "log-rolling" phase arises due to a strong coupling between the rotational degree of freedom of the micelles and the steady sliding motion of the confining surfaces. We examine the microscopic mechanism of the log-rolling phenomenon and also discuss its dependence on the segregation strength and length of the amphiphile, the shear rate, and the film thickness.

Colloids↗

PubMed2005

Critical point of electrolyte mixtures.

The critical behavior of electrolyte mixtures was studied using grand canonical Monte Carlo simulations. Mixtures consist of large multivalent macroions and small monovalent co- and counterions. The system can be viewed as a binary mixture of macroions (with their counterions) and salt (co- and counterion pair). The primitive model description was used, in which the ions are point charges with a hard core and the solvent is treated as a uniform dielectric continuum. The grand canonical simulations are based on insertions and removals of neutral molecules: macroion with its counterions or coions and a counterion. We propose a distance biasing method that enables direct grand canonical simulations up to charge asymmetry of 10:1. We calculated the critical loci that connect the salt-free state, which consists of only macroions and counterions, with the pure salt state using mixed-field finite-size scaling with no pressure mixing. The critical parameters are determined for macroion to counterion charge asymmetries of 2:1, 3:1, and 10:1. Our results suggest that binary electrolyte mixtures are type-I mixtures, where the two components mix continuously.

Journal Article↗

PubMed2005

Phase diagrams in the lattice restricted primitive model: from order-disorder to gas-liquid phase transition.

The phase behavior of the lattice restricted primitive model (RPM) for ionic systems with additional short-range nearest neighbor (NN) repulsive interactions has been studied by grand canonical Monte Carlo simulations. We obtain a rich phase behavior as the NN strength is varied. In particular, the phase diagram is very similar to that of the continuum RPM for high NN strength. Specifically, we have found both gas-liquid phase separation, with associated Ising critical point, and a first-order liquid-solid transition. We discuss how the line of continuous order-disorder transitions present for the low NN strength changes into continuum-space behavior as one increases the NN strength and compare our findings with recent theoretical results by Ciach and Stell [Phys. Rev. Lett. 91, 060601 (2003)].

Journal Article↗

PubMed2005

Coarse-grained computations for a micellar system.

We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms), and atomistic simulations of the Larson model of micelle formation. The procedure hinges on the (expected) evolution of a few slow, coarse-grained mesoscopic observables of the Monte Carlo simulation, and on (computational) time scale separation between these and the remaining "slaved," fast variables. Short bursts of appropriately initialized atomistic simulation are used to estimate the (coarse grained, deterministic) local dynamics of the evolution of the observables. These estimates are then in turn used to accelerate the evolution to computational stationarity through traditional continuum algorithms (forward Euler integration, Newton-Raphson fixed point computation). This "equation-free" framework, bypassing the derivation of explicit, closed equations for the observables (e.g., equations of state), may provide a computational bridge between direct atomistic/stochastic simulation and the analysis of its macroscopic, system-level consequences.

Journal Article↗

PubMed2005

Coarse-grained kinetic computations for rare events: application to micelle formation.

We discuss a coarse-grained approach to the computation of rare events in the context of grand canonical Monte Carlo (GCMC) simulations of self-assembly of surfactant molecules into micelles. The basic assumption is that the computational system dynamics can be decomposed into two parts-fast (noise) and slow (reaction coordinates) dynamics, so that the system can be described by an effective, coarse-grained Fokker-Planck (FP) equation. While such an assumption may be valid in many circumstances, an explicit form of FP equation is not always available. In our computations we bypass the analytic derivation of such an effective FP equation. The effective free energy gradient and the state-dependent magnitude of the random noise, which are necessary to formulate the effective Fokker-Planck equation, are obtained from ensembles of short bursts of microscopic simulations with judiciously chosen initial conditions. The reaction coordinate in our micelle formation problem is taken to be the size of a cluster of surfactant molecules. We test the validity of the effective FP description in this system and reconstruct a coarse-grained free energy surface in good agreement with full-scale GCMC simulations. We also show that, for very small clusters, the cluster size ceases to be a good reaction coordinate for a one-dimensional effective description. We discuss possible ways to improve the current model and to take higher-dimensional coarse-grained dynamics into account.

Journal Article↗

PubMed2004

Monte Carlo study of shear-induced alignment of cylindrical micelles in thin films.

The behavior of confined cylindrical micelle-forming surfactants under the influence of shear has been investigated using Monte Carlo simulations. The surfactants are modeled as coarse-grained lattice polymers, while the Monte Carlo shear flow is implemented with an externally imposed potential energy field which induces a linear drag velocity on the surfactants. It is shown that, in the absence of shear, cylindrical micelles confined within a monolayer coarsen gradually with Monte Carlo "time" t , the persistence length of the micelles scaling as t(0.24) , in agreement with the scaling obtained experimentally. Under the imposition of shear, the micelles within a monolayer align parallel to the direction of shear, as observed experimentally. Micelles confined within thicker films also align parallel to each other with a hexagonal packing under shear, but assume a finite tilt with respect to the velocity vector within the velocity-velocity gradient plane. We propose a mechanism for this shear-induced alignment of micelles based on breaking up of micelles aligned perpendicular to the shear and their reformation and subsequent growth in the shear direction. It is observed that there exists a "window" of shear rates within which such alignment occurs. A simple theory proposed to explain the above behavior is in good agreement with simulation results. A comparison of simulated and experimental self-diffusivities yields a physical time scale for Monte Carlo moves, which enables an assessment of the physical shear rates employed in our Monte Carlo simulations.

Journal Article↗

PubMed2004

Saddles in the energy landscape: extensivity and thermodynamic formalism.

We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system size, as well as several approximations for the properties of low-order saddles (i.e., those with only a few unstable directions). We then cast the canonical partition function in a saddle-explicit form and develop, for the first time, a rigorous energy landscape approach capable of reproducing trends observed in simulations, in particular, the temperature dependence of the energy and fractional order of sampled saddles.

Journal Article↗

PubMed2003

Thermodynamics of electrolytes on anisotropic lattices.

The phase behavior of ionic fluids on simple cubic and tetragonal (anisotropic) lattices has been studied by grand canonical Monte Carlo simulations. Systems with both the true lattice Coulombic potential and continuous-space 1/r electrostatic interactions have been investigated. At all degrees of anisotropy, only coexistence between a disordered low-density phase and an ordered high-density phase with the structure similar to ionic crystal was found, in contrast to recent theoretical predictions. Tricritical parameters were determined to be increasing functions of anisotropy parameters which is consistent with theoretical calculations based on the Debye-Hückel approach. At large anisotropies a two-dimensional-like behavior is observed, from which we estimated the dimensionless tricritical temperature and density for the two-dimensional square lattice electrolyte to be T*(tri)=0.14 and rho*(tri)=0.70.

Journal Article↗

PubMed2003

Monte carlo study of coulombic criticality in polyelectrolytes.

The role of charges in determining the water solubility of polyelectrolytes, a question of considerable relevance to biology, is currently unresolved. We use computer simulations to study the purely Coulombic phase separation of flexible polyelectrolytes with monovalent counterions in an athermal solvent. In agreement with recent theories we find that the critical temperature for this transition increases with chain length, but that the critical density remains unchanged. We therefore stress that the phase behavior of polyelectrolytes is qualitatively different from uncharged polymers, where the critical density decreases towards zero for long chains.

Computer Simulation↗

PubMed2002

Generalization of the Wang-Landau method for off-lattice simulations.

We present a rigorous derivation for off-lattice implementations of the so-called "random-walk" algorithm recently introduced by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)]. Originally developed for discrete systems, the algorithm samples configurations according to their inverse density of states using Monte Carlo moves; the estimate for the density of states is refined at each simulation step and is ultimately used to calculate thermodynamic properties. We present an implementation for atomic systems based on a rigorous separation of kinetic and configurational contributions to the density of states. By constructing a "uniform" ensemble for configurational degrees of freedom-in which all potential energies, volumes, and numbers of particles are equally probable-we establish a framework for the correct implementation of simulation acceptance criteria and calculation of thermodynamic averages in the continuum case. To demonstrate the generality of our approach, we perform sample calculations for the Lennard-Jones fluid using two implementation variants and in both cases find good agreement with established literature values for the vapor-liquid coexistence locus.

Journal Article↗