Entropy-driven phase transitions and the Kauzmann entropy crisis

R. Hołyst

Physica A: Statistical Mechanics and its Applications 2001, 292, 1–4, 255-258

We briefly present the Kauzmann entropy crisis and show that it may have a simple explanation in terms of the entropy-driven phase transitions. We discuss in a pedagogical manner why the enthalpy change at the freezing transition is positive even for a hard sphere fluid, despite the fact that the transition is driven by the increase of the entropy. We use this observation to explain qualitatively the Kauzmann entropy crisis.

Intermediate Scaling Regime in the Phase Ordering Kinetics

M. Fialkowski and R. Holyst

ACTA PHYSICA POLONICA B. 2001, 32, 1579-1588

We have investigated the intermediate scaling regime in the phase ordering/separating kinetics of the three-dimensional system of the non-conserved scalar order parameter. It is demonstrated that the observed scaling behavior can be described in terms of two length scales LH(t) ∼ t2/5 and LK(t) ∼ t3/10. The quantity LH(t) is related to the geometrical properties of the phase interface and describes time evolution of the characteristic domain size, surface area, and the mean curvature. The second length scale, L)K(t), determining the Gaussian curvature and the Euler characteristic, can be regarded as the topological measure of the phase interface. Also, we have shown that the existence of the two length scales has a simple physical interpretation and is related to the domains-necks decoupling process observed in the intermediate regime.

Approach to equilibrium of particles diffusing on curved surfaces

D. Plewczyński and R. Hołyst

Physica A: Statistical Mechanics and its Applications 2001, 295, 3–4, 371-378

We present a simple numerical analysis of the diffusion on a curved surface given by the equation φ(r)=0 in a finite domain D⊂R3. The first non-vanishing eigenvalue of the Beltrami–Laplace operator with the reflecting boundary conditions is determined in our simulations for the P, D, G, S, S1 and I-WP, nodal periodic surfaces, where D is their respective cubic unit cell. We observe that the first eigenvalue for the surfaces of simple topology (P,D,G,I-WP) is smaller than for the surfaces of complex topology (S,S1).

Mechanisms for facilitated target location and the optimal number of molecules in the diffusion search process

K. Burdzy and R. Hołyst

Phys. Rev. E 2001, 64, 011914

We investigate the number N of molecules needed to perform independent diffusion in order to achieve bonding of a single molecule to a specific site in time t0. For a certain range of values of t0, an increase from N to kN molecules (k>1) results in the decrease of search time from t0 to t0/k. In this regime, increasing the number of molecules is an effective way of speeding up the search process. However when N>~N0 (optimal number of N) the reduction of time from t0 to t0/k can be achieved only by an exponentially large increase in the number of molecules [from N to Nexp(ck) for some c>0].

Scattering patterns of self-assembled gyroid cubic phases in amphiphilic systems

P. Garstecki and R. Hołyst

J. Chem. Phys. 2001, 115, 1095-1099

We present scattering patterns (with surface contrast) for five triply periodic minimal surfaces of the Ia3̄dIa3̄d cubic symmetry. We obtain a very good agreement between the numerically obtained spectrum and experimental patterns for the simple gyroid G structure. We show the scattering patterns for four gyroid GX1, GX2, GX3, and GX5 structures of a complex topology. We show how the scattering patterns change with increasing complexity of the unit cell of the structure. The spectra of the complex structures can give wrong estimates about the cubic cell parameter and even wrong establishment of the space symmetry group. Thus the correct recognition of the structure present in the system requires the analysis of the intensities of the peaks and comparison with numerically obtained spectra.

Periodic surfaces of simple and complex topology: Comparison of scattering patterns

P. Garstecki and R. Hołyst

Phys. Rev. E 2001, 64, 021501

We compute scattering patterns for six triply periodic minimal surfaces formed in oil/surfactant/water solutions: Three surfaces of a simple topology, Schwarz P (Im3¯m), Schwarz D–diamond (Pn3¯m), and Schoen G–gyroid (Ia3¯d), and three surfaces of a complex topology, SCN1 (Im3¯m), CD (Pn3¯m), and GX6 (Ia3¯d). We show that in the case of the complex structures, scattering intensity is shifted towards the higher hkl peaks. This might cause their misidentification and wrong estimates about the cell size of the structure.

Spinodal Decomposition of Homopolymer Blends: Geometrical Properties of the Interface

A. Aksimentiev, K. Moorthi and R. Hołyst

Progress of Theoretical Physics Supplement, 2000, 138, 398–399

The spinodal decomposition (SD) of the homopolymer blends has been studied by the numerical integration of the Cahn-Hilliard-Cook equation with the Flory-Huggins-de Gennes free energy functional. The scaling dependences for the surface area density, Euler characteristics density, average Gaussian and mean curvatures of the blend interface have been found. In the shallow and asymmetric quenches the topological transformation from the bicontinuous to droplet morphology has been observed. The influence of the thermal fluctuations on the curvature distribution has been investigated.

Reduction of dimensionality in a diffusion search process and kinetics of gene expression

R. Hołyst, M. Błażejczyk, K. Burdzy, G. Góralski and L. Bocquet

Physica A: Statistical Mechanics and its Applications 2000, 277, 1–2, 71-82

In order to activate a gene in a DNA molecule a specific protein (transcription factor) has to bind to the promoter of the gene. We formulate and partially answer the following question: how much time does a transcription factor, which activates a given gene, need in order to find this gene inside the nucleus of a cell? The estimate based on the simplest model of diffusion gives a very long time of days. We discuss various mechanisms by which the time can be reduced to seconds, in particular, the reduction of dimensionality, in which diffusion takes place, from three-dimensional space to two-dimensional space. The potential needed to keep the diffusing particle in 2D (i.e, at the surface of size L2 in a volume of size L3) should scale as U∼kBTlnL. For aL=1μm and a target size a=10 Å we find U=8kBT, i.e., it is a potential strength of the order of the strength of ionic interactions in water.

Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends

A. Aksimentiev and K. Moorthi

J. Chem. Phys. 2000, 112, 6049

The spinodal decomposition of the homopolymer blends has been studied by the numerical integration of the Cahn–Hilliard–Cook equation. We have investigated the time evolution of the morphological measures that characterize quantitatively the interface in the system. For symmetric blends we have found that the Euler characteristic of the interface is negative and increases with time as τ0.75 (connectivity of the domains decreases) regardless of the final quench temperature. The homogeneity index of the interface is constant in this case. This suggests that at the level of the integral geometry quantities (Minkowski functionals), the dynamic scaling hypothesis holds for the evolution of the interface morphology in quenched critical systems. The nonuniversal morphological evolution of the asymmetric blends have been studied. Also, we have shown that the thermal fluctuations can modify significantly the curvature distribution.

Topological Lifshitz Line, Off-Specular Scattering, and Mesoporous Materials

R. Hołyst and B. Przybylski

Phys. Rev. Lett. 2000, 85, 130

Ordered phases formed by surfactants in water solutions, and used in technological processes as templates for the synthesis of mesoporous materials, exhibit topological fluctuations. From the results of the Monte Carlo simulations of the lamellar phase we have established a relation between topological fluctuations and the behavior of the off-specular scattering intensity. We have defined the topological Lifshitz line. At this line the peak position in the off-specular scattering intensity moves from the zero (lamellar phase with fixed topology) to the nonzero value of the scattering wave vector (lamellar phase with fluctuating topology).

Scattering on triply periodic minimal surfaces—the effect of the topology, Debye–Waller, and molecular form factors

P. Garstecki and R.Hołyst

J. Chem. Phys. 2000, 113, 3772

We compute scattering patterns for four triply periodic surfaces (TPS). Three minimal—Schwarz P (Im3̄m), Schwarz D—diamond (Pn3̄m), Schoen G—gyroid (Ia3̄d), and one nodal S1 (Ia3̄d). Simple approximations are adopted to examine the influence of the molecular form factor, and the Debye–Waller factor on the scattering pattern. We find that the Debye–Waller factor has a much smaller influence on the scattering intensities of TPS than on the intensities of the lamellar structure consisting of parallel surfaces. This is caused by an almost spherelike distribution of normal vectors for TPS. We give a simple formula that allows a comparison of the experimental scattering data with the data for the P, D, G mathematical surfaces. Finally, the spectra of the two surfaces G and S1 of the same space group symmetry and different topologies are compared. It is found that in the case of the more complex S1 structure the intensities of the first two peaks are very small.

Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends

A. Aksimentiev and R. Hołyst

Phys. Rev. E 2000, 62, 6821

The spinodal decomposition of a binary mixture has been studied within several mesoscopic models. It has been found that the form of the equilibrium free energy has a crucial effect on the morphological development in asymmetric blends. We have shown that the principal quantity that determines the topology of the interface (and type of morphology) is the equilibrium minority phase volume fraction, while the transition from bicontinuous to droplet morphology can be treated as a percolation. The concentration dependence of the square gradient coefficient attributed for the Flory-Huggins–de Gennes free energy has no significant influences on the average domain growth, but can be distinguished experimentally from its constant-coefficient alternative by measuring the maximum wave vector of the scattering intensity as a function of the minority phase volume fraction for spinodally decomposing asymmetric blends. The concentration dependence of the Onsager coefficient has the weak, systematic effect of slowing down the morphological development. The local shape of the interface is not affected considerably by the concentration dependence of the square gradient and Onsager coefficient.

A Fleming–Viot Particle Representation of the Dirichlet Laplacian

K. Burdzy, R. Hołyst and P. March

Communications in Mathematical Physics 2000, 214, 679–703

We consider a model with a large number N of particles which move according to independent Brownian motions. A particle which leaves a domain D is killed; at the same time, a different particle splits into two particles. For large N, the particle distribution density converges to the normalized heat equation solution in D with Dirichlet boundary conditions. The stationary distributions converge as N→∞ to the first eigenfunction of the Laplacian in D with the same boundary conditions.

Kinetics of the droplet formation at the early and intermediate stages of the spinodal decomposition in homopolymer blends

A. Aksimentiev, R. Hołyst and K. Moorthi

Macromolecular Theory and Simulations 2000, 9, 8, 661-674

The kinetics of the droplet formation during the spinodal decomposition (SD) of the homopolymer blends has been studied by numerical integration of the Cahn‐Hilliard‐Cook equation. We have found that the droplet formation and growth occurs when the minority phase volume fraction, fm , approaches the percolation threshold value, fthr = 0.3 ± 0.01. The time for the formation of the disperse droplet morphology (coarsening time) depends only on the equilibrium minority phase volume fraction, fm . fm approaches its equilibrium value logarithmically at the late SD stages, and, therefore, the coarsening time decreases exponentially as the average volume fraction or the quench depth decrease. Since the temporal evolution of the total interfacial area does not depend on the quench conditions and blend morphology, the average droplet size and the droplet number density is determined by the coarsening time. Within the time scale studied, the droplet number density decreases with time as t –0.63±0.03; the average mean curvature decreases as t –0.35±0.05; the average Gaussian curvature decreases as t –0.42±0.03, and the average droplet compactness ˜V/S3/2 where S is the surface area and V is the volume) approaches a spherical limit logarithmically with time. The droplets with larger area have lower compactness and in the low compactness limit their area is a parabolic function of compactness. The size and shape distribution functions have been also investigated.

Reorientational angle distribution and diffusion coefficient for nodal and cylindrical surfaces

D. Plewczyński and R. Hołyst

J. Chem. Phys. 2000, 113, 9920

We present a catalogue of diffusion coefficients and reorientational angle distribution (RAD) for various periodic surfaces, such as I-WP, F-RD, S, and S1 nodal surfaces; cylindrical structures like simple, undulated, and spiral cylinders, and a three-dimensional interconnected-rod structures. The results are obtained on the basis of a simulation algorithm for a diffusion on a surface given by the general equation φ(r)=0φ(r)=0 [Hołyst et al., Phys Rev. E 60, 302 (1999)]. I-WP, S, and S1 surfaces have a spherelike RAD, while F-RD has a cubelike RAD. The average of the second Legendre polynomial with RAD function for all nodal surfaces, except the F-RD nodal surface, decays exponentially with time for short times. The decay time is related to the Euler characteristic and the area per unit cell of a surface. This analytical formula, first proposed by B. Halle, S. Ljunggren, and S. Lidin in J. Chem. Phys. 97, 1401 (1992), is checked here on nodal surfaces, and its range of validity is determined. RAD function approaches its stationary limit exponentially with time. We determine the time to reach stationary state for all surfaces. In the case of the value of the effective diffusion coefficient the mean curvature and a connectivity between parts of surfaces have the main influence on it. The surfaces with low mean curvature at every point of the surface are characterized by high-diffusion coefficient. However if a surface has globally low mean curvature with large regions of nonzero mean curvature (negative and positive) the effective diffusion coefficient is low, as for example, in the case of undulated cylinders. Increasing the connectivity, at fixed curvatures, increases the diffusion coefficient.

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