Cooling rate, heating rate and aging effects in glassy water

We report a molecular dynamics simulation study of the properties of the potential energy landscape sampled by a system of water molecules during the process of generating a glass by cooling, and during the process of regenerating the equilibrium liquid by heating the glass. We study the dependence of these processes on the cooling/heating rates as well as on the role of aging (the time elapsed in the glass state). We compare the properties of the potential energy landscape sampled during these processes with the corresponding properties sampled in the liquid equilibrium state to elucidate under which conditions glass configurations can be associated with equilibrium liquid configurations.Comment: to be published in Phys. Rev. E (rapid comunication

A Potential Energy Landscape Study of the Amorphous-Amorphous Transformation in H2_2O

We study the potential energy landscape explored during a compression-decompression cycle for the SPC/E (extended simple point charge) model of water. During the cycle, the system changes from low density amorphous ice (LDA) to high density amorphous ice (HDA). After the cycle, the system does not return to the same region of the landscape, supporting the interesting possibility that more than one significantly different configuration corresponds to LDA. We find that the regions of the landscape explored during this transition have properties remarkably different from those explored in thermal equilibrium in the liquid phase

The Glass Transition Temperature of Water: A Simulation Study

We report a computer simulation study of the glass transition for water. To mimic the difference between standard and hyperquenched glass, we generate glassy configurations with different cooling rates and calculate the $T$ dependence of the specific heat on heating. The absence of crystallization phenomena allows us, for properly annealed samples, to detect in the specific heat the simultaneous presence of a weak pre-peak (``shadow transition''), and an intense glass transition peak at higher temperature. We discuss the implications for the currently debated value of the glass transition temperature of water. We also compare our simulation results with the Tool-Narayanaswamy-Moynihan phenomenological model.Comment: submitted to Phys. Re

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

Glass polymorphism in glycerol–water mixtures: I. A computer simulation study

We perform out-of-equilibrium molecular dynamics (MD) simulations of water–glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA–HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/ decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration wg = 0–13% and find that, for the present mixture models and rates, the LDA–HDA transformation is detectable up to wg E 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately wg r 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately wg 4 5%. We present an analysis of the molecular-level changes underlying the LDA–HDA transformation. As observed in pure glassy water, during the LDA-to- HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA–HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA–HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA–HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol–water mixtures prepared by isobaric cooling at 1 ba

Development time mediates the effect of larval diet on ageing and mating success of male antler flies in the wild

International audienceHigh-quality developmental environments often improve individual performance into adulthood, but allocating toward early-life traits, such as growth, development rate, and reproduction, may lead to trade-offs with late life performance. It is therefore uncertain how a rich developmental environment will affect the ageing process (senescence), particularly in wild insects. To investigate the effects of early-life environmental quality on insect life-history traits, including senescence, we reared larval antler flies (Protopiophila litigata) on four diets of varying nutrient concentration, then recorded survival and mating success of adult males released in the wild. Declining diet quality was associated with slower development, but had no effect on other life-history traits once development time was accounted for. Fast developing males were larger and lived longer, but experienced more rapid senescence in survival and lower average mating rate compared to slow developers. Ultimately, larval diet, development time, and body size did not predict lifetime mating success. Thus, a rich environmentled to a mixture of apparent benefits and costs, mediated by development time. Our results indicate that“silver spoon” effects can be complex and that development time mediates the response of adult life-history traits to early-life environmental quality

Phosphoprotein Isotope-Coded Affinity Tag Approach for Isolating and Quantitating Phosphopeptides in Proteome-Wide Analyses

A method has been developed that utilizes phosphoprotein isotope-coded affinity tags (PhIAT) that combines stable isotope and biotin labeling to enrich and quantitatively measure differences in the O-phosphorylation states of proteins. The PhIAT labeling approach involves hydroxide ion-mediated beta-elimination of the O-phosphate moiety and the addition of 1,2-ethanedithiol containing either four alkyl hydrogens (EDT-D0) or four alkyl deuteriums (EDT-D4) followed by biotinylation of the EDT-D0/D4 moiety using (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine. The PhIAT reagent, which contains the nucleophilic sulfhydryl and isotopic label covalently linked to a biotin moiety, was synthesized and has the potential utility to reduce the O-phosphorylation derivatization into a one-step process. The PhIAT labeling approach was initially demonstrated using the model phosphoprotein beta-casein. After proteolytic digestion, the PhIAT-labeled peptides were affinity isolated using immobilized avidin and analyzed using capillary reversed-phase liquid chromatography-mass spectrometry. PhIAT-labeled beta-casein peptides corresponding to peptides containing known sites of O-phosphorylation were isolated and identified. The PhIAT labeling method was also applied to a yeast protein extract. The PhIAT labeling technique provides a reliable method for making quantitative measurements of differences in the O-phosphorylation state of proteins

Phosphoprotein Isotope-Coded Affinity Tags: Application to the Enrichment and Identification of Low-Abundance Phosphoproteins

The use of a phosphoprotein isotope-coded affinity tag (PhIAT), which employs differential isotopic labeling and biotinylation, has been shown capable of enriching and identifying mixtures of low-abundance phosphopeptides. A denatured solution of beta-casein was labeled using the PhIAT method, and after proteolytic digestion, the labeled peptides were isolated using immobilized avidin. The recovered peptides were separated by capillary reversed-phase liquid chromatography and identified by tandem mass spectrometry. PhIAT-labeled peptides corresponding to known O-phosphorylated peptides from beta-casein were identified along with the phosphorylated peptides from alphas1-casein and alphas2-casein, known low-level (\u3c5%) contaminants of commercially available beta-casein. All of the casein-phosphorylated residues identified by the present PhIAT approach correspond to previously documented sites of phosphorylation. The results illustrate the efficacy of the PhIAT-labeling strategy to not only enrich mixtures for phosphopeptides but also, more importantly, permit the detection and identification of low-level phosphopeptides. In addition, the differences in the phosphorylation state could be determined between phosphopeptides in comparative samples by stoichiometric conversion using the light and heavy isotopic versions of the PhIAT reagents. Overall, our results exemplify the application of the PhIAT approach and demonstrate its utility for proteome-wide phosphoprotein identification and quantitation