Molecular hydrodynamic theory of the velocity autocorrelation function

The velocity autocorrelation function (VACF) encapsulates extensive information about a fluid's molecular-structural and hydrodynamic properties. We address the following fundamental question: How well can a purely hydrodynamic description recover the molecular features of a fluid as exhibited by the VACF? To this end, we formulate a bona fide hydrodynamic theory of the tagged-particle VACF for simple fluids. Our approach is distinguished from previous efforts in two key ways: collective hydrodynamic modes are modeled by \emph{linear} hydrodynamic equations; the fluid's static kinetic energy spectrum is identified as a necessary initial condition for the momentum current correlation. Our formulation leads to a natural physical interpretation of the hydrodynamic VACF as a superposition of quasinormal hydrodynamic modes weighted commensurately with the static kinetic energy spectrum, which appears to be essential to bridging continuum hydrodynamical behavior and discrete-particle kinetics. Our methodology yields VACF calculations quantitatively on par with existing approaches for liquid noble gases and alkali metals; moreover, our hydrodynamic model for the self-intermediate scattering function extends the applicable domain to low densities where the Schmidt number is of order unity, enabling calculations for gases and supercritical fluids.Comment: 14 pages, 3 figures; 5 appendices, 2 appendix figures; improved method/results for Fig. 3 w/ appendix 4; added new results w/ procedure in appendix 5. (v2: 11 pages, 3 figures, 3 appendices

Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site

Liquid-Drop Model and Quantum Resistance Against Noncompact Nuclear Geometries

The importance of quantum effects for exotic nuclear shapes is demonstrated. Based on the example of a sheet of nuclear matter of infinite lateral dimensions but finite thickness, it is shown that the quantization of states in momentum space, resulting from the confinement of the nucleonic motion in the conjugate geometrical space, generates a strong resistance against such a confinement and generates restoring forces driving the system towards compact geometries. In the liquid-drop model, these quantum effects are implicitly included in the surface energy term, via a choice of interaction parameters, an approximation that has been found valid for compact shapes, but has not yet been scrutinized for exotic shapes.Comment: 9 pages with 3 figure

Functional changes in the major United States Great Lakes ports since the opening of the new St. Lawrence Seaway

Call number: LD2668 .R4 1967 S51

Discerning autotrophy, mixotrophy and heterotrophyin marine TACK archaea from the North Atlantic

DNA stable isotope probing (SIP) was used to track the uptake of organic and inorganic carbon sources for TACK archaea(Thaumarchaeota/Aigarchaeota/Crenarchaeota/Korarchaeota) on a cruise of opportunity in the North Atlantic. Due to water limitations, duplicate samples from the deep photic (60–115 m), the mesopelagic zones (local oxygen minimum; 215–835 m)and the bathypelagic zone (2085–2835 m) were amended with various combinations of12C- or13C-acetate/urea/bicarbonate to assess cellular carbon acquisition. The SIP results indicated the majority of TACK archaeal operational taxonomic units(OTUs) incorporated13C from acetate and/or urea into newly synthesized DNA within 48 h. A small fraction (16%) of the OTUs, often representing the most dominant members of the archaeal community, were able to incorporate bicarbonate in addition to organic substrates. Only two TACK archaeal OTUs were found to incorporate bicarbonate but not urea or acetate.These results further demonstrate the utility of SIP to elucidate the metabolic capability of mesothermal archaea in distinct oceanic settings and suggest that TACK archaea play a role in organic carbon recycling in the mid-depth to deep ocea

Measles resurges in Italy: preliminary data from September 2007 to May 2008.

Following an incidence rate of 1/100,000 inhabitants in 2006 [1], Italy has been facing an upsurge of measles cases since September 2007, with outbreaks being reported in various regions. In Italy, measles vaccination is currently offered free of charge as combined measles-mumps-rubella (MMR) vaccine. The current national vaccination schedule recommends two doses of MMR vaccine, given respectively at 11-12 months and 5-6 years of age. Although childhood vaccination coverage has increased in recent years, reaching the national average of 88% in 2006 (source: Ministry of Health), with some regional variability (Figure 1), it is still below the target of 95% set by the National Measles Elimination Plan (MEP) launched in 2003 [2], and outbreaks continue to occur