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How Water's Properties Are Encoded in Its Molecular Structure and Energies.
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties
Carbon superatom thin films
Assembling clusters on surfaces has emerged as a novel way to grow thin films
with targeted properties. In particular, it has been proposed from experimental
findings that fullerenes deposited on surfaces could give rise to thin films
retaining the bonding properties of the incident clusters. However the
microscopic structure of such films is still unclear. By performing quantum
molecular dynamics simulations, we show that C_28 fullerenes can be deposited
on a surface to form a thin film of nearly defect free molecules, which act as
carbon superatoms. Our findings help clarify the structure of disordered small
fullerene films and also support the recently proposed hyperdiamond model for
solid C_28.Comment: 13 pages, RevTeX, 2 figures available as black and white PostScript
files; color PostScript and/or gif files available upon reques
Two-dimensional structure in a generic model of triangular proteins and protein trimers
Motivated by the diversity and complexity of two-dimensional crystals formed
by triangular proteins and protein trimers, we have investigated the structures
and phase behavior of hard-disk trimers. In order to mimic specific binding
interactions, each trimer possesses on `attractive' disk which can interact
with similar disks on other trimers via an attractive square-well potential. At
low density and low temperature, the fluid phase mainly consists of tetramers,
pentamers, or hexamers. Hexamers provide the structural motif for a
high-density, low-temperature periodic solid phase, but we also identify a
metastable periodic structure based on a tetramer motif. At high density there
is a transition between orientationally ordered and disordered solid phases.
The connections between simulated structures and those of 2D protein crystals
-- as seen in electron microscopy -- are briefly discussed.Comment: 7 pages, 6 figure
Structure and Dynamics of amorphous Silica Surfaces
We use molecular dynamics computer simulations to study the equilibrium
properties of the surface of amorphous silica. Two types of geometries are
investigated: i) clusters with different diameters (13.5\AA, 19\AA, and
26.5\AA) and ii) a thin film with thickness 29\AA. We find that the shape of
the clusters is independent of temperature and that it becomes more spherical
with increasing size. The surface energy is in qualitative agreement with the
experimental value for the surface tension. The density distribution function
shows a small peak just below the surface, the origin of which is traced back
to a local chemical ordering at the surface. Close to the surface the partial
radial distribution functions as well as the distributions of the bond-bond
angles show features which are not observed in the interior of the systems. By
calculating the distribution of the length of the Si-O rings we can show that
these additional features are related to the presence of two-membered rings at
the surface. The surface density of these structures is around 0.6/nm^2 in good
agreement with experimental estimates. From the behavior of the mean-squared
displacement at low temperatures we conclude that at the surface the cage of
the particles is larger than the one in the bulk. Close to the surface the
diffusion constant is somewhat larger than the one in the bulk and with
decreasing temperature the relative difference grows. The total vibrational
density of states at the surface is similar to the one in the bulk. However, if
only the one for the silicon atoms is considered, significant differences are
found.Comment: 30 pages of Latex, 16 figure
Computers and Liquid State Statistical Mechanics
The advent of electronic computers has revolutionised the application of
statistical mechanics to the liquid state. Computers have permitted, for
example, the calculation of the phase diagram of water and ice and the folding
of proteins. The behaviour of alkanes adsorbed in zeolites, the formation of
liquid crystal phases and the process of nucleation. Computer simulations
provide, on one hand, new insights into the physical processes in action, and
on the other, quantitative results of greater and greater precision. Insights
into physical processes facilitate the reductionist agenda of physics, whilst
large scale simulations bring out emergent features that are inherent (although
far from obvious) in complex systems consisting of many bodies. It is safe to
say that computer simulations are now an indispensable tool for both the
theorist and the experimentalist, and in the future their usefulness will only
increase.
This chapter presents a selective review of some of the incredible advances
in condensed matter physics that could only have been achieved with the use of
computers.Comment: 22 pages, 2 figures. Chapter for a boo
The role of local structure in dynamical arrest
Amorphous solids, or glasses, are distinguished from crystalline solids by
their lack of long-range structural order. At the level of two-body structural
correlations, glassformers show no qualitative change upon vitrifying from a
supercooled liquid. Nonetheless the dynamical properties of a glass are so much
slower that it appears to take on the properties of a solid. While many
theories of the glass transition focus on dynamical quantities, a solid's
resistance to flow is often viewed as a consequence of its structure. Here we
address the viewpoint that this remains the case for a glass. Recent
developments using higher-order measures show a clear emergence of structure
upon dynamical arrest in a variety of glass formers and offer the tantalising
hope of a structural mechanism for arrest. However a rigorous fundamental
identification of such a causal link between structure and arrest remains
elusive. We undertake a critical survey of this work in experiments, computer
simulation and theory and discuss what might strengthen the link between
structure and dynamical arrest. We move on to highlight the relationship
between crystallisation and glass-forming ability made possible by this deeper
understanding of the structure of the liquid state, and emphasize the potential
to design materials with optimal glassforming and crystallisation ability, for
applications such as phase-change memory. We then consider aspects of the
phenomenology of glassy systems where structural measures have yet to make a
large impact, such as polyamorphism (the existence of multiple liquid states),
aging (the time-evolution of non-equilibrium materials below their glass
transition) and the response of glassy materials to external fields such as
shear.Comment: 70 page
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