Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized molecular dynamics simulations.

We present an accurate and efficient method to obtain Kirkwood-Buff (KB) integrals in the thermodynamic limit from small-sized molecular dynamics simulations. By introducing finite size effects into integral equations of statistical mechanics, we derive an analytical expression connecting the KB integrals of the bulk system with the fluctuations of the number of molecules in the corresponding closed system. We validate the method by calculating the activity coefficients of aqueous urea mixtures and the KB integrals of Lennard-Jones fluids. Moreover, our results demonstrate how to identify simulation conditions under which computer simulations reach the thermodynamic limit.

The glass transition and the distribution of voids in room-temperature ionic liquids: a molecular dynamics study.

The glass transition in prototypical room temperature ionic liquids has been investigated by molecular dynamics simulations based on an Amber-like empirical force field. Samples of [C(4)mim][PF(6)], [C(4)mim][Tf(2)N], and [C(3)mim][Tf(2)N] have been quenched from the liquid phase at T = 500 to a glassy state at T ∼ 0 K in discontinuous steps of 20 K every 1.2 ns. The glass temperature estimated by simulation (T(g) = 209 K for [C(4)mim][PF(6)], T(g) = 204 K for [C(4)mim][Tf(2)N], and T(g) = 196 K for [C(3)mim][Tf(2)N]) agrees semi-quantitatively with the experimental values (T(g) = 193÷196 K for [C(4)mim][PF(6)], T(g) = 186÷189 K for [C(4)mim][Tf(2)N], and T(g) = 183 K for [C(3)mim][Tf(2)N]). A model electron density is introduced to identify voids in the system. The temperature dependence of the size distribution of voids provided by simulation reproduce well the experimental results of positron annihilation lifetime spectroscopy reported in G. Dlubek, Y. Yu, R. Krause-Rehberg, W. Beichel, S. Bulut, N. Pogodina, I. Krossing, and Ch. Friedrich, J. Chem. Phys. 133, 124502 (2010), with only one free parameter needed to fit the experimental data.

Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method.

In the Hamiltonian adaptive resolution simulation method (H-AdResS) it is possible to simulate coexisting atomistic (AT) and ideal gas representations of a physical system that belong to different subdomains within the simulation box. The Hamiltonian includes a field that bridges both models by smoothly switching on (off) the intermolecular potential as particles enter (leave) the AT region. In practice, external one-body forces are calculated and applied to enforce a reference density throughout the simulation box, and the resulting external potential adds up to the Hamiltonian. This procedure suggests an apparent dependence of the final Hamiltonian on the system's thermodynamic state that challenges the method's statistical mechanics consistency. In this paper, we explicitly include an external potential that depends on the switching function. Hence, we build a grand canonical potential for this inhomogeneous system to find the equivalence between H-AdResS and density functional theory (DFT). We thus verify that the external potential inducing a constant density profile is equal to the system's excess chemical potential. Given DFT's one-to-one correspondence between external potential and equilibrium density, we find that a Hamiltonian description of the system is compatible with the numerical implementation based on enforcing the reference density across the simulation box. In the second part of the manuscript, we focus on assessing our approach's convergence and computing efficiency concerning various model parameters, including sample size and solute concentrations. To this aim, we compute the excess chemical potential of water, aqueous urea solutions and Lennard-Jones (LJ) mixtures. The results' convergence and accuracy are convincing in all cases, thus emphasising the method's robustness and capabilities.

Identification and validation of endogenous control miRNAs in plasma samples for normalization of qPCR data for Alzheimer's disease.

BACKGROUND: MicroRNAs (miRNAs) are noncoding RNAs that are highly relevant as disease biomarkers. Several studies that explored the role of miRNAs in Alzheimer's disease (AD) demonstrated their usefulness in clinical identification. Nevertheless, miRNAs that may act as endogenous controls (ECs) have not yet been established. The identification of ECs would contribute to the standardization of these biomarkers in AD. The objective of the study was to identify miRNAs that can be used as ECs in AD. METHODS: We evaluated 145 patients divided into two different cohorts. One was a discovery cohort of 19 women diagnosed with mild to moderate AD (Mini-Mental State Examination (MMSE) score ≥ 20) and with confirmed pathologic levels of Aß42 in CSF. The stability assessment cohort consisted of 126 individuals: 24 subjects without AD or any kind of dementia and negative for all core CSF biomarkers of AD, 25 subjects with MCI and negative for CSF biomarkers (MCI -), 22 subjects with MCI and positive for CSF biomarkers (MCI +), and 55 subjects with AD and positive for CSF biomarkers. In the discovery cohort, a profile of 384 miRNAs was determined in the plasma by TaqMan low-density array. The best EC candidates were identified by mean-centering and concordance correlation restricted normalization methods. The stability of the EC candidates was assessed using the GeNorm, BestKeeper, and NormFinder algorithms. RESULTS: Nine miRNAs (hsa-miR-324-5p, hsa-miR-22-5p, hsa-miR-103a-2-5p, hsa-miR-362-5p, hsa-miR-425-3p, hsa-miR-423-5p, hsa-let-7i-3p, hsa-miR-532-5p, and hsa-miR-1301-3p) were identified as EC candidates in the discovery cohort. The validation results indicated that hsa-miR-103a-2-5p was the best EC, followed by hsa-miR-22-5p, hsa-miR-1301-3p, and hsa-miR-425-3p, which had similar stability values in all three algorithms. CONCLUSIONS: We identified a profile of four miRNAs as potential plasma ECs to be used for normalization of miRNA expression data in studies of subjects with cognitive impairment.

Surface of Half-Neutralized Diamine Triflate Ionic Liquids. A Molecular Dynamics Study of Structure, Thermodynamics, and Kinetics of Water Absorption and Evaporation.

Surface properties of room temperature ionic liquids (RTILs) consisting of half neutralized diamine cations (H2N-(CH2)n-NH3+, n = 2, 4) and triflate anions have been investigated by molecular dynamics simulations, based on an empirical atomistic force field. Planar slabs periodically repeated in 2D have been considered, and the temperature range 260 ≤ T ≤ 360 K has been covered, extending from below the melting and glass point to the equilibrium liquid range of the diamine compounds under investigation. Addition of water at 1% weight concentration allowed us to investigate the kinetics of water absorption through the RTIL surface, and to characterize the structural and dynamical properties of subsurface water. Animations of the simulation trajectory highlight the quick absorption of water molecules, progressing downhill in free energy and taking place without apparent intermediate kinetic stages. To verify and quantify these observations, a variant of the umbrella sampling algorithm has been applied to compute the variation of excess free energy upon displacing a water molecule along the normal to the surface, from the center of the slab to the vapor phase. The results provide a comprehensive picture of the thermodynamic properties underlying the kinetics of water absorption and evaporation through the surface, and they also provide the ratio of the equilibrium density of water in the vapor and liquid phase at the average concentration considered by simulations. A variety of properties such as the surface energy, the 90-10% width of the profile, the layering of different species at the interface, and the electrostatic double layer at the surface are computed and discussed, focusing on the effect of water contamination on all of them.

Beamline Performance Simulations for the Fundamental Neutron Physics Beamline at the Spallation Neutron Source.

Monte Carlo simulations are being performed to design and characterize the neutron optics components for the two fundamental neutron physics beamlines at the Spallation Neutron Source. Optimization of the cold beamline includes characterization of the guides and benders, the neutron transmission through the 0.89 nm monochromator, and the expected performance of the four time-of-flight choppers. The locations and opening angles of the choppers have been studied using a simple spreadsheet-based analysis that was developed for other SNS chopper instruments. The spreadsheet parameters are then optimized using Monte Carlo techniques to obtain the results presented in this paper. Optimization of the 0.89 nm beamline includes characterizing the double crystal monochromator and the downstream guides. The simulations continue to be refined as components are ordered and their exact size and performance specifications are determined.

Trifluoperazine inhibition of insulin-induced increase in skeletal muscle glucose uptake.

The ability of trifluoperazine, a calmodulin blocker, to prevent increases in skeletal muscle glucose uptake induced by insulin was tested. Insulin significantly increased glucose uptake by the rat hindlimb and trifluoperazine (10(-6) M) completely inhibited this increase. We conclude that calmodulin is a factor involved in the regulation of insulin-mediated glucose transport in muscle cells.

Different mechanism for insulin induced and contraction induced increases in skeletal muscle glucose uptake.

Glucose facilitated diffusion into cells depends on concentration gradients between intracellular and extracellular spaces and can be modified by several factors such as insulin and contractions. Calmodulin participates in the insulin induced recruitment of vesicles containing glucose transporter molecules and its inhibition by trifluoperazine blocks insulin increases in glucose uptake. In the present study we tested if calmodulin inhibition with trifluoperazine blocks hindlimb muscle glucose uptake increase induced by contractions. Trifluoperazine does not inhibit exercise induced increases in glucose uptake; therefore, the mechanisms by which insulin and functional activity increase glucose uptake are different.

Molecular dynamics simulations of the formation of 1D spin-valves from stretched Au-Co and Pt-Co nanowires.

We have performed molecular dynamics (MD) simulations of stretched Aux-Co1 - x and Ptx-Co1 - x nanowires to investigate the formation of bimetallic monoatomic wires between two electrodes. We have considered nanowires with two concentrations x = 0.2 and 0.8, aspect ratio of 13, a cross section of 1 nm(2) and a wide range of temperatures (from 10 to 400 K). For the MD simulations we have used a semi-empirical interatomic potential based on the second moment approximation (SMA) of the density of states to the tight-binding Hamiltonian.For Au-Co alloys, Au atoms tends to migrate towards the narrowed region to form almost pure Au wires. In the PtCo case the formed chains usually consist of Pt enriched alternating structures. The most striking result is probably the Au(0.2)-Co(0.8) alloy where pure monoatomic Au chains form between two Co electrodes constituting a potential 1D spin valve. Despite the known ease with which the 5d metals (Pt, Ir, and Au) form monoatomic chains (MACS), our results show that in the presence of Co (x = 0.2), the percentage of chain formation is higher than in the Pt and Au rich cases (x = 0.8).

Spontaneous spin polarization and charge localization in metal nanowires: the role of a geometric constriction.

An idealized jellium model of conducting nanowires with a geometric constriction is investigated by density functional theory (DFT) in the local spin density (LSD) approximation. The results reveal a fascinating variety of spin and charge patterns arising in wires of sufficiently low (r(s) ≥ 15) average electron density, pinned at the indentation by an apparent attractive interaction with the constriction. The spin-resolved frequency-dependent conductivity shows a marked asymmetry in the two spin channels, reflecting the spontaneous spin polarization around the wire neck. The relevance of the computational results is discussed in relation to the so-called 0.7 anomaly found by experiments in the low-frequency conductivity of nanowires at near-breaking conditions (see 2008 J. Phys.: Condens Matter 20, special issue on the 0.7 anomaly). Although our mean-field approach cannot account for the intrinsic many-body effects underlying the 0.7 anomaly, it still provides a diagnostic tool to predict impending transitions in the electronic structure.

Regulation by glucose availability of tension development and electrical activity in fetal and neonatal rat hearts.

The aim of the present article was to study if changes in glucose availability modify the functional activity of the glucose-dependent developing heart. Our data indicate that a decrease in glucose availability increases tension development and action potential duration at early fetal stages. This fact could probably be explained by the enhancement of Ca2+ movements that regulate the number and turnover rate of membrane glucose transporters in muscle cells. The sensitivity to glucose availability decreases postnatally as the heart becomes fatty acid-dependent.