Ab initio van der Waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like

The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations using van der Waals (vdW) density-functional theory, i.e. using the new exchange-correlation functionals optPBE-vdW and vdW-DF2. Inclusion of the more isotropic vdW interactions counteracts highly directional hydrogen-bonds, which are enhanced by standard functionals. This brings about a softening of the microscopic structure of water, as seen from the broadening of angular distribution functions and, in particular, from the much lower and broader first peak in the oxygen-oxygen pair-correlation function (PCF), indicating loss of structure in the outer solvation shells. In combination with softer non-local correlation terms, as in the new parameterization of vdW-DF, inclusion of vdW interactions is shown to shift the balance of resulting structures from open tetrahedral to more close-packed. The resulting O-O PCF shows some resemblance with experiment for high-density water (A. K. Soper and M. A. Ricci, Phys. Rev. Lett., 84:2881, 2000), but not directly with experiment for ambient water. However, an O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from experiment on low-density liquid water reproduces near-quantitatively the experimental O-O PCF for ambient water, indicating consistency with a two-liquid model with fluctuations between high- and low-density regions

Disaccharide topology induces slow down in local water dynamics

Molecular level insight into water structure and structural dynamics near proteins, lipids and nucleic acids is critical to the quantitative understanding of many biophysical processes. Un- fortunately, understanding hydration and hydration dynamics around such large molecules is challenging because of the necessity of deconvoluting the effects of topography and chemical heterogeneity. Here we study, via classical all atom simulation, water structure and structural dynamics around two biologically relevant solutes large enough to have significant chemical and topological heterogeneity but small enough to be computationally tractable: the disaccharides Kojibiose and Trehalose. We find both molecules to be strongly amphiphilic (as quantified from normalized local density fluctuations) and to induce nonuniform local slowdown in water translational and rotational motion. Detailed analysis of the rotational slowdown shows that while the rotational mechanism is similar to that previously identified in other aqueous systems by Laage, Hynes and coworkers, two novel characteristics are observed: broadening of the transition state during hydrogen bond exchange (water rotation) and a subpopulation of water for which rotation is slowed because of hindered access of the new accepting water molecule to the transition state. Both of these characteristics are expected to be generic features of water rotation around larger biomolecules and, taken together, emphasize the difficulty in transferring insight into water rotation around small molecules to much larger amphiphilic solutes.This work is part of the research program of the “Stichting voor Fundamenteel Onderzoek der Materie (FOM)” which is financially supported by the “Nederlandse organisatie voor Wetenschap- pelijk Onderzoek (NWO)”. Further financial support was provided by a Marie Curie Incoming International Fellowship (RKC). We gratefully acknowledge SARA, the Dutch center for high- performance computing, for computational time and Huib Bakker and Daan Frenkel for useful critical reviews on an earlier version of this work. We thank two anonymous reviewers for their excellent work, especially for bringing to our attention calculations done on the transition state geometry of dimers and the overstructuring of the O-O radial distribution function of SPC/E water

Subsurface circulation in the Somali Current

Direct velocity measurements were made at intermediate depths along the East African coast from March to July 1979. Strong time-dependent flows with multiple reversals in direction were found in the upper 1000 meters between 3°N and 4°S. At 700 meters, there may be a connection between the southwestward coastal current and an equatorial jet observed at 49°E, the latter turning south near the coast. North of 3°N little spatial organization of the flow can be recognized. Copyright © 1980 AAAS

A perspective on the future of physical oceanography

The ocean flows because it is forced by winds, tides and exchanges of heat and freshwater with the overlying atmosphere and cryosphere. To achieve a state where the defining properties of the ocean (such as its energy and momentum) do not continuously increase, some form of dissipation or damping is required to balance the forcing. The ocean circulation is thought to be forced primarily at the large scales characteristic of ocean basins, yet to be damped at much smaller scales down to those of centimetre-sized turbulence. For decades, physical oceanographers have sought to comprehend the fundamentals of this fractal puzzle: how the ocean circulation is driven, how it is damped and how ocean dynamics connects the very different scales of forcing and dissipation. While in the last two decades significant advances have taken place on all these three fronts, the thrust of progress has been in understanding the driving mechanisms of ocean circulation and the ocean's ensuing dynamical response, with issues surrounding dissipation receiving comparatively little attention. This choice of research priorities stems not only from logistical and technological difficulties in observing and modelling the physical processes responsible for damping the circulation, but also from the untested assumption that the evolution of the ocean's state over time scales of concern to humankind is largely independent of dissipative processes. In this article, I illustrate some of the key advances in our understanding of ocean circulation that have been achieved in the last 20 years and, based on a range of evidence, contend that the field will soon reach a stage in which uncertainties surrounding the arrest of ocean circulation will pose the main challenge to further progress. It is argued that the role of the circulation in the coupled climate system will stand as a further focal point of major advances in understanding within the next two decades, supported by the drive of physical oceanography towards a more operational enterprise by contextual factors. The basic elements that a strategy for the future must have to foster progress in these two areas are discussed, with an overarching emphasis on the promotion of curiosity-driven fundamental research against opposing external pressures and on the importance of upholding fundamental research as the apex of education in the field