Dmitri Rozmanov

Crystal growth simulations of methane hydrates in the presence of silica surfaces

We present a molecular dynamics simulation study of the crystal growth of methane hydrates in the presence of model silica (SiO(2)) surfaces. The crystal growth under apparent steady-state conditions shows a clear preference for bulk solution. We observe rather disordered water arrangements very close to the silica surface within about 5 Å in both liquid and crystalline regions of the system. These disordered structures have dynamic and structural properties intermediate between those exhibited by molecules in bulk liquid and crystalline phases. The presence of methane molecules appears to help stabilize these structures. We observe that under appropriate conditions, the hydroxylated silica surfaces can serve as a source of methane molecules which can help promote hydrate growth near the surfaces.

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.

Anisotropy in the crystal growth of hexagonal ice, Ih

Growth of ice crystals has attracted attention because ice and water are ubiquitous in the environment and play critical roles in natural processes. Hexagonal ice, I(h), is the most common form of ice among 15 known crystalline phases of ice. In this work we report the results of an extensive and systematic molecular dynamics study of the temperature dependence of the crystal growth on the three primary crystal faces of hexagonal ice, the basal {0001} face, the prism {1010} face, and the secondary prism {1120} face, utilizing the TIP4P-2005 water model. New insights into the nature of its anisotropic growth are uncovered. It is demonstrated that the ice growth is indeed anisotropic; the growth and melting of the basal face are the slowest of the three faces, its maximum growth rates being 31% and 43% slower, respectively, than those of the prism and the secondary prism faces. It is also shown that application of periodic boundary conditions can lead to varying size effect for different orientations of an ice crystal caused by the anisotropic physical properties of the crystal, and results in measurably different thermodynamic melting temperatures in three systems of similar, yet moderate, size. Evidence obtained here provides the grounds on which to clarify the current understanding of ice growth on the secondary prism face of ice. We also revisit the effect of the integration time step on the crystal growth of ice in a more thorough and systematic way. Careful evaluation demonstrates that increasing the integration time step size measurably affects the free energy of the bulk phases and shifts the temperature dependence of the growth rate curve to lower temperatures by approximately 1 K when the step is changed from 1 fs to 2 fs, and by 3 K when 3 fs steps are used. A thorough investigation of the numerical aspects of the simulations exposes important consequences of the simulation parameter choices upon the delicate dynamic balance that is involved in ice crystal growth.

Composition Fluctuations in Lipid Bilayers

Cell membranes contain multiple lipid and protein components having heterogeneous in-plane (lateral) distribution. Nanoscale rafts are believed to play an important functional role, but their phase state—domains of coexisting phases or composition fluctuations—is unknown. As a step toward understanding lateral organization of cell membranes, we investigate the difference between nanoscale domains of coexisting phases and composition fluctuations in lipid bilayers. We simulate model lipid bilayers with the MARTINI coarse-grained force field on length scales of tens of nanometers and timescales of tens of microseconds. We use a binary and a ternary mixture: a saturated and an unsaturated lipid, or a saturated lipid, an unsaturated lipid, and cholesterol, respectively. In these mixtures, the phase behavior can be tuned from a mixed state to a coexistence of a liquid-crystalline and a gel, or a liquid-ordered and a liquid-disordered phase. Transition from a two-phase to a one-phase state is achieved by raising the temperature and adding a hybrid lipid (with a saturated and an unsaturated chain). We analyze the evolution of bilayer properties along this transition: domains of two phases transform to fluctuations with local ordering and compositional demixing. Nanoscale domains and fluctuations differ in several properties, including interleaflet overlap and boundary length. Hybrid lipids show no enrichment at the boundary, but decrease the difference between the coexisting phases by ordering the disordered phase, which could explain their role in cell membranes.