Atomically detailed lipid bilayer models for the interpretation of small angle neutron and X-ray scattering data.

We present a new atom density profile (ADP) model and a statistical approach for extracting structural characteristics of lipid bilayers from X-ray and neutron scattering data. Models for five lipids with varying head and tail chemical composition in the fluid phase, 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), are optimized using a simplex based method to simultaneously reproduce both neutron and X-ray scattering data. Structural properties are determined using statistical analysis of multiple optimal model structures. The method and models presented make minimal assumptions regarding the atomic configuration, while taking into account the underlying physical properties of the system. The more general model and statistical approach yield data with well defined uncertainties, indicating the precision in determining density profiles, atomic locations, and bilayer structural characteristics. Resulting bilayer structures include regions exhibiting large conformational variation. Due to the increased detail in the model, the results demonstrate the possibility of a distinct hydration layer within the interfacial (backbone) region.

A reactive molecular dynamics simulation of the silica-water interface.

We report our study of a silica-water interface using reactive molecular dynamics. This first-of-its-kind simulation achieves length and time scales required to investigate the detailed chemistry of the system. Our molecular dynamics approach is based on the ReaxFF force field of van Duin et al. [J. Phys. Chem. A 107, 3803 (2003)]. The specific ReaxFF implementation (SERIALREAX) and force fields are first validated on structural properties of pure silica and water systems. Chemical reactions between reactive water and dangling bonds on a freshly cut silica surface are analyzed by studying changing chemical composition at the interface. In our simulations, reactions involving silanol groups reach chemical equilibrium in approximately 250 ps. It is observed that water molecules penetrate a silica film through a proton-transfer process we call "hydrogen hopping," which is similar to the Grotthuss mechanism. In this process, hydrogen atoms pass through the film by associating and dissociating with oxygen atoms within bulk silica, as opposed to diffusion of intact water molecules. The effective diffusion constant for this process, taken to be that of hydrogen atoms within silica, is calculated to be 1.68 x 10(-6) cm(2)/s. Polarization of water molecules in proximity of the silica surface is also observed. The subsequent alignment of dipoles leads to an electric potential difference of approximately 10.5 V between the silica slab and water.

Hyponatraemia in Hospitalised Adults: a Guide for the Junior Doctor.

Hyponatraemia is common and often a source of confusion for junior doctors. It is infrequently dangerous, but when it is, is a medical emergency and requires urgent treatment to avoid life-threatening cerebral oedema. Treatment of acute hyponatraemia is also potentially hazardous; it is therefore important to be able to recognise when urgent management is not indicated, and to investigate appropriately. This paper focuses on these issues, which are most likely to be the cause of consternation for the junior doctor. Recommendations are largely based on the 2014 joint European clinical practice guidance for management of hyponatraemia; the 2010 GAIN (N Ireland) guidance and 2013 American guidance are also referenced.

DCMS: A data analytics and management system for molecular simulation.

Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface (i.e., SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.

Automated optimization of water-water interaction parameters for a coarse-grained model.

We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.