Transitions between Inherent Structures in Water

The energy landscape approach has been useful to help understand the dynamic properties of supercooled liquids and the connection between these properties and thermodynamics. The analysis in numerical models of the inherent structure (IS) trajectories -- the set of local minima visited by the liquid -- offers the possibility of filtering out the vibrational component of the motion of the system on the potential energy surface and thereby resolving the slow structural component more efficiently. Here we report an analysis of an IS trajectory for a widely-studied water model, focusing on the changes in hydrogen bond connectivity that give rise to many IS separated by relatively small energy barriers. We find that while the system \emph{travels} through these IS, the structure of the bond network continuously modifies, exchanging linear bonds for bifurcated bonds and usually reversing the exchange to return to nearly the same initial configuration. For the 216 molecule system we investigate, the time scale of these transitions is as small as the simulation time scale ($\approx 1$ fs). Hence for water, the transitions between each of these IS is relatively small and eventual relaxation of the system occurs only by many of these transitions. We find that during IS changes, the molecules with the greatest displacements move in small ``clusters'' of 1-10 molecules with displacements of $\approx 0.02-0.2$ nm, not unlike simpler liquids. However, for water these clusters appear to be somewhat more branched than the linear ``string-like'' clusters formed in a supercooled Lennar d-Jones system found by Glotzer and her collaborators.Comment: accepted in PR

Organization of atomic bond tensions in model glasses

In order to understand whether internal stresses in glasses are correlated or randomly distributed, we study the organization of atomic bond tensions (normal forces between pairs of atoms). Measurements of the invariants of the atomic bond tension tensor in simulated 2D and 3D binary Lennard-Jones glasses, reveal new and unexpected correlations and provide support for Alexander's conjecture about the non-random character of internal stresses in amorphous solids

Water-like anomalies for core-softened models of fluids: One dimension

We use a one-dimensional (1d) core-softened potential to develop a physical picture for some of the anomalies present in liquid water. The core-softened potential mimics the effect of hydrogen bonding. The interest in the 1d system stems from the facts that closed-form results are possible and that the qualitative behavior in 1d is reproduced in the liquid phase for higher dimensions. We discuss the relation between the shape of the potential and the density anomaly, and we study the entropy anomaly resulting from the density anomaly. We find that certain forms of the two-step square well potential lead to the existence at T=0 of a low-density phase favored at low pressures and of a high-density phase favored at high pressures, and to the appearance of a point $C'$ at a positive pressure, which is the analog of the T=0 ``critical point'' in the $1d$ Ising model. The existence of point $C'$ leads to anomalous behavior of the isothermal compressibility $K_T$ and the isobaric specific heat $C_P$.Comment: 22 pages, 7 figure

Landscape equivalent of the shoving model

It is shown that the shoving model expression for the average relaxation time of viscous liquids follows largely from a classical "landscape" estimation of barrier heights from curvature at energy minima. The activation energy involves both instantaneous bulk and shear moduli, but the bulk modulus contributes less than 8% to the temperature dependence of the activation energy. This reflects the fact that the physics of the two models are closely related.Comment: 4 page

Equilibration times in numerical simulation of structural glasses: Comparing parallel tempering and conventional molecular dynamics

Generation of equilibrium configurations is the major obstacle for numerical investigation of the slow dynamics in supercooled liquid states. The parallel tempering (PT) technique, originally proposed for the numerical equilibration of discrete spin-glass model configurations, has recently been applied in the study of supercooled structural glasses. We present an investigation of the ability of parallel tempering to properly sample the liquid configuration space at different temperatures, by mapping the PT dynamics into the dynamics of the closest local potential energy minima (inherent structures). Comparing the PT equilibration process with the standard molecular dynamics equilibration process we find that the PT does not increase the speed of equilibration of the (slow) configurational degrees of freedom.Comment: 5 pages, 3 figure

Simulation study of Non-ergodicity Transitions: Gelation in Colloidal Systems with Short Range Attractions

Computer simulations were used to study the gel transition occurring in colloidal systems with short range attractions. A colloid-polymer mixture was modelled and the results were compared with mode coupling theory expectations and with the results for other systems (hard spheres and Lennard Jones). The self-intermediate scattering function and the mean squared displacement were used as the main dynamical quantities. Two different colloid packing fractions have been studied. For the lower packing fraction, $\alpha$-scaling holds and the wave-vector analysis of the correlation function shows that gelation is a regular non-ergodicity transition within MCT. The leading mechanism for this novel non-ergodicity transition is identified as bond formation caused by the short range attraction. The time scale and diffusion coefficient also show qualitatively the expected behaviour, although different exponents are found for the power-law divergences of these two quantities. The non-Gaussian parameter was also studied and very large correction to Gaussian behaviour found. The system with higher colloid packing fraction shows indications of a nearby high-order singularity, causing $\alpha$-scaling to fail, but the general expectations for non-ergodicity transitions still hold.Comment: 13 pages, 15 figure

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10-11 to 5.0 × 10-21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10-6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation

Associations of autozygosity with a broad range of human phenotypes

In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (F-ROH) for >1.4 million individuals, we show that F-ROH is significantly associated (p <0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: F-ROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of F-ROH are confirmed within full-sibling pairs, where the variation in F-ROH is independent of all environmental confounding.Peer reviewe

New Blood Pressure-Associated Loci Identified in Meta-Analyses of 475,000 Individuals

Background - Genome-wide association studies have recently identified &gt;400 loci that harbor DNA sequence variants that influence blood pressure (BP). Our earlier studies identified and validated 56 single nucleotide variants (SNVs) associated with BP from meta-analyses of exome chip genotype data. An additional 100 variants yielded suggestive evidence of association. Methods and Results - Here, we augment the sample with 140 886 European individuals from the UK Biobank, in whom 77 of the 100 suggestive SNVs were available for association analysis with systolic BP or diastolic BP or pulse pressure. We performed 2 meta-analyses, one in individuals of European, South Asian, African, and Hispanic descent (pan-ancestry, ≈475 000), and the other in the subset of individuals of European descent (≈423 000). Twenty-one SNVs were genome-wide significant (P&lt;5×10-8) for BP, of which 4 are new BP loci: rs9678851 (missense, SLC4A1AP), rs7437940 (AFAP1), rs13303 (missense, STAB1), and rs1055144 (7p15.2). In addition, we identified a potentially independent novel BP-associated SNV, rs3416322 (missense, SYNPO2L) at a known locus, uncorrelated with the previously reported SNVs. Two SNVs are associated with expression levels of nearby genes, and SNVs at 3 loci are associated with other traits. One SNV with a minor allele frequency &lt;0.01, (rs3025380 at DBH) was genome-wide significant. Conclusions - We report 4 novel loci associated with BP regulation, and 1 independent variant at an established BP locus. This analysis highlights several candidate genes with variation that alter protein function or gene expression for potential follow-up