Liquid-liquid critical point in supercooled silicon

A novel liquid-liquid phase transition has been proposed and investigated in a wide variety of pure substances recently, including water, silica and silicon. From computer simulations using the Stillinger-Weber classical empirical potential, Sastry and Angell [1] demonstrated a first order liquid-liquid transition in supercooled silicon, subsequently supported by experimental and simulation studies. Here, we report evidence for a liquid-liquid critical end point at negative pressures, from computer simulations using the SW potential. Compressibilities exhibit a growing maximum upon lowering temperature below 1500 K and isotherms exhibit density discontinuities below 1120 K, at negative pressure. Below 1120 K, isotherms obtained from constant volume-temperature simulations exhibit non-monotonic, van der Waals-like behavior signaling a first order transition. We identify Tc ~ 1120 +/- 12 K, Pc -0.60 +/- 0.15 GPa as the critical temperature and pressure for the liquid-liquid critical point. The structure of the liquid changes dramatically upon decreasing the temperature and pressure. Diffusivities vary over 4 orders of magnitude, and exhibit anomalous pressure dependence near the critical point. A strong relationship between local geometry quantified by the coordination number, and diffusivity, is seen, suggesting that atomic mobility in both low and high density liquids can usefully be analyzed in terms of defects in the tetrahedral network structure. We have constructed the phase diagram of supercooled silicon. We identify the lines of compressibility, density extrema (maxima and minima) and the spinodal which reveal the interconnection between thermodynamic anomalies and the phase behaviour of the system as suggested in previous works [2-9]Comment: (to be published in revised form); small corrections to previous version; Nature Physics 201

Irreversible reorganization in a supercooled liquid originates from localised soft modes

The transition of a fluid to a rigid glass upon cooling is a common route of transformation from liquid to solid that embodies the most poorly understood features of both phases1,2,3. From the liquid perspective, the puzzle is to understand stress relaxation in the disordered state. From the perspective of solids, the challenge is to extend our description of structure and its mechanical consequences to materials without long range order. Using computer simulations, we show that the localized low frequency normal modes of a configuration in a supercooled liquid are causally correlated to the irreversible structural reorganization of the particles within that configuration. We also demonstrate that the spatial distribution of these soft local modes can persist in spite of significant particle reorganization. The consequence of these two results is that it is now feasible to construct a theory of relaxation length scales in glass-forming liquids without recourse to dynamics and to explicitly relate molecular properties to their collective relaxation.Comment: Published online: 20 July 2008 | doi:10.1038/nphys1025 Available from http://www.nature.com/nphys/journal/v4/n9/abs/nphys1025.htm

A thermodynamic unification of jamming

Fragile materials ranging from sand to fire-retardant to toothpaste are able to exhibit both solid and fluid-like properties across the jamming transition. Unlike ordinary fusion, systems of grains, foams and colloids jam and cease to flow under conditions that still remain unknown. Here we quantify jamming via a thermodynamic approach by accounting for the structural ageing and the shear-induced compressibility of dry sand. Specifically, the jamming threshold is defined using a non-thermal temperature that measures the 'fluffiness' of a granular mixture. The thermodynamic model, casted in terms of pressure, temperature and free-volume, also successfully predicts the entropic data of five molecular glasses. Notably, the predicted configurational entropy avoids the Kauzmann paradox entirely. Without any free parameters, the proposed equation-of-state also governs the mechanism of shear-banding and the associated features of shear-softening and thickness-invariance.Comment: 16 pgs double spaced. 4 figure

Configurational Entropy and Diffusivity of Supercooled Water

We calculate the configurational entropy S_conf for the SPC/E model of water for state points covering a large region of the (T,rho) plane. We find that (i) the (T,rho) dependence of S_conf correlates with the diffusion constant and (ii) that the line of maxima in S_conf tracks the line of density maxima. Our simulation data indicate that the dynamics are strongly influenced by S_conf even above the mode-coupling temperature T_MCT(rho).Comment: Significant update of reference

Cellular Bases of Barbiturate and Phenytoin Anticonvulsant Drug Action

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65509/1/j.1528-1157.1982.tb06093.x.pd

Detection of hidden structures for arbitrary scales in complex physical systems

Recent decades have experienced the discovery of numerous complex materials. At the root of the complexity underlying many of these materials lies a large number of contending atomic- and largerscale configurations. In order to obtain a more detailed understanding of such systems, we need tools that enable the detection of pertinent structures on all spatial and temporal scales. Towards this end, we suggest a new method that applies to both static and dynamic systems which invokes ideas from network analysis and information theory. Our approach efficiently identifies basic unit cells, topological defects, and candidate natural structures. The method is particularly useful where a clear definition of order is lacking, and the identified features may constitute a natural point of departure for further analysis

Phosphorylation of p130Cas initiates Rac activation and membrane ruffling

<p>Abstract</p> <p>Background</p> <p>Non-receptor tyrosine kinases (NTKs) regulate physiological processes such as cell migration, differentiation, proliferation, and survival by interacting with and phosphorylating a large number of substrates simultaneously. This makes it difficult to attribute a particular biological effect to the phosphorylation of a particular substrate. We developed the Functional Interaction Trap (FIT) method to phosphorylate specifically a single substrate of choice in living cells, thereby allowing the biological effect(s) of that phosphorylation to be assessed. In this study we have used FIT to investigate the effects of specific phosphorylation of p130Cas, a protein implicated in cell migration. We have also used this approach to address a controversy regarding whether it is Src family kinases or focal adhesion kinase (FAK) that phosphorylates p130Cas in the trimolecular Src-FAK-p130Cas complex.</p> <p>Results</p> <p>We show here that SYF cells (mouse fibroblasts lacking the NTKs Src, Yes and Fyn) exhibit a low level of basal tyrosine phosphorylation at focal adhesions. FIT-mediated tyrosine phosphorylation of NTK substrates p130Cas, paxillin and FAK and cortactin was observed at focal adhesions, while FIT-mediated phosphorylation of cortactin was also seen at the cell periphery. Phosphorylation of p130Cas in SYF cells led to activation of Rac1 and increased membrane ruffling and lamellipodium formation, events associated with cell migration. We also found that the kinase activity of Src and not FAK is essential for phosphorylation of p130Cas when the three proteins exist as a complex in focal adhesions.</p> <p>Conclusion</p> <p>These results demonstrate that tyrosine phosphorylation of p130Cas is sufficient for its localization to focal adhesions and for activation of downstream signaling events associated with cell migration. FIT provides a valuable tool to evaluate the contribution of individual components of the response to signals with multiple outputs, such as activation of NTKs.</p

Excess-entropy scaling in supercooled binary mixtures

Supercooled liquids near the glass transition show remarkable non-Arrhenius transport phenomena, whose origin is yet to be clarified. Here, the authors use GPU molecular dynamics simulations for various binary mixtures in the supercooled regime to show the validity of a quasiuniversal excess-entropy scaling relation for viscosity and diffusion