Phase Coexistence of a Stockmayer Fluid in an Applied Field

We examine two aspects of Stockmayer fluids which consists of point dipoles that additionally interact via an attractive Lennard-Jones potential. We perform Monte Carlo simulations to examine the effect of an applied field on the liquid-gas phase coexistence and show that a magnetic fluid phase does exist in the absence of an applied field. As part of the search for the magnetic fluid phase, we perform Gibbs ensemble simulations to determine phase coexistence curves at large dipole moments, $\mu$. The critical temperature is found to depend linearly on $\mu^2$ for intermediate values of $\mu$ beyond the initial nonlinear behavior near $\mu=0$ and less than the $\mu$ where no liquid-gas phase coexistence has been found. For phase coexistence in an applied field, the critical temperatures as a function of the applied field for two different $\mu$ are mapped onto a single curve. The critical densities hardly change as a function of applied field. We also verify that in an applied field the liquid droplets within the two phase coexistence region become elongated in the direction of the field.Comment: 23 pages, ReVTeX, 7 figure

The Non-Commutative Cycle Lemma

We present a non-commutative version of the cycle lemma of Dvoretsky and Motzkin that applies to free groups and use this result to solve a number of problems involving cyclic reduction in the free group. We also describe an application to random matrices, in particular the fluctuations of Kesten's Law.Comment: 13 pages, minor corrections and improvement

Orientational Ordering in Spatially Disordered Dipolar Systems

This letter addresses basic questions concerning ferroelectric order in positionally disordered dipolar materials. Three models distinguished by dipole vectors which have one, two or three components are studied by computer simulation. Randomly frozen and dynamically disordered media are considered. It is shown that ferroelectric order is possible in spatially random systems, but that its existence is very sensitive to the dipole vector dimensionality and the motion of the medium. A physical analysis of our results provides significant insight into the nature of ferroelectric transitions.Comment: 4 pages twocolumn LATEX style. 4 POSTSCRIPT figures available from [email protected]

Functional limit theorems for random regular graphs

Consider d uniformly random permutation matrices on n labels. Consider the sum of these matrices along with their transposes. The total can be interpreted as the adjacency matrix of a random regular graph of degree 2d on n vertices. We consider limit theorems for various combinatorial and analytical properties of this graph (or the matrix) as n grows to infinity, either when d is kept fixed or grows slowly with n. In a suitable weak convergence framework, we prove that the (finite but growing in length) sequences of the number of short cycles and of cyclically non-backtracking walks converge to distributional limits. We estimate the total variation distance from the limit using Stein's method. As an application of these results we derive limits of linear functionals of the eigenvalues of the adjacency matrix. A key step in this latter derivation is an extension of the Kahn-Szemer\'edi argument for estimating the second largest eigenvalue for all values of d and n.Comment: Added Remark 27. 39 pages. To appear in Probability Theory and Related Field

Ferroelectric and Dipolar Glass Phases of Non-Crystalline Systems

In a recent letter [Phys. Rev. Lett. {\bf 75}, 2360 (1996)] we briefly discussed the existence and nature of ferroelectric order in positionally disordered dipolar materials. Here we report further results and give a complete description of our work. Simulations of randomly frozen and dynamically disordered dipolar soft spheres are used to study ferroelectric ordering in non-crystalline systems. We also give a physical interpretation of the simulation results in terms of short- and long-range interactions. Cases where the dipole moment has 1, 2, and 3 components (Ising, XY and XYZ models, respectively) are considered. It is found that the Ising model displays ferroelectric phases in frozen amorphous systems, while the XY and XYZ models form dipolar glass phases at low temperatures. In the dynamically disordered model the equations of motion are decoupled such that particle translation is completely independent of the dipolar forces. These systems spontaneously develop long-range ferroelectric order at nonzero temperature despite the absence of any fined-tuned short-range spatial correlations favoring dipolar order. Furthermore, since this is a nonequilibrium model we find that the paraelectric to ferroelectric transition depends on the particle mass. For the XY and XYZ models, the critical temperatures extrapolate to zero as the mass of the particle becomes infinite, whereas, for the Ising model the critical temperature is almost independent of mass and coincides with the ferroelectric transition found for the randomly frozen system at the same density. Thus in the infinite mass limit the results of the frozen amorphous systems are recovered.Comment: 25 pages (LATEX, no macros). 11 POSTSCRIPT figures enclosed. Submitted to Phisical Review E. Contact: [email protected]

Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges

Nuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water's properties. These have been combined with theoretical developments such as the introduction of the principle of competing quantum effects that allows the subtle interplay of water's quantum effects and their manifestation in experimental observables to be explained. We discuss how this principle has recently been used to explain the apparent dichotomy in water's isotope effects, which can range from very large to almost nonexistent depending on the property and conditions. We then review the latest major developments in simulation algorithms and theory that have enabled the efficient inclusion of nuclear quantum effects in molecular simulations, permitting their combination with on-the-fly evaluation of the potential energy surface using electronic structure theory. Finally, we identify current challenges and future opportunities in this area of research

Genes responsive to rapamycin and serum deprivation are clustered on chromosomes and undergo re-organization within local chromatin environments.

Supplementary materials are available at University of Toronto: https://tspace.library.utoronto.ca/handle/1807/9982

Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure

Structural Anisotropy in Polar Fluids Subjected to Periodic Boundary Conditions

A heuristic model based on dielectric continuum theory for the long-range solvation free energy of a dipolar system possessing periodic boundary conditions (PBCs) is presented. The predictions of the model are compared to simulation results for Stockmayer fluids simulated using three different cell geometries. The boundary effects induced by the PBCs are shown to lead to anisotropies in the apparent dielectric constant and the long-range solvation free energy of as much as 50%. However, the sum of all of the anisotropic energy contributions yields a value that is very close to the isotropic one derived from dielectric continuum theory, leading to a total system energy close to the dielectric value. It is finally shown that the leading-order contribution to the energetic and structural anisotropy is significantly smaller in the noncubic simulation cell geometries compared to when using a cubic simulation cell