Morphological Phase Diagram for Lipid Membrane Domains with Entropic Tension

Circular domains in phase-separated lipid vesicles with symmetric leaflet composition commonly exhibit three stable morphologies: flat, dimpled, and budded. However, stable dimples (i.e., partially budded domains) present a puzzle since simple elastic theories of domain shape predict that only flat and spherical budded domains are mechanically stable in the absence of spontaneous curvature. We argue that this inconsistency arises from the failure of the constant surface tension ensemble to properly account for the effect of entropic bending fluctuations. Formulating membrane elasticity within an entropic tension ensemble, wherein tension represents the free energy cost of extracting membrane area from thermal bending of the membrane, we calculate a morphological phase diagram that contains regions of mechanical stability for each of the flat, dimpled, and budded domain morphologies

A Rule-Based Approach to Analyzing Database Schema Objects with Datalog

Database schema elements such as tables, views, triggers and functions are typically defined with many interrelationships. In order to support database users in understanding a given schema, a rule-based approach for analyzing the respective dependencies is proposed using Datalog expressions. We show that many interesting properties of schema elements can be systematically determined this way. The expressiveness of the proposed analysis is exemplarily shown with the problem of computing induced functional dependencies for derived relations. The propagation of functional dependencies plays an important role in data integration and query optimization but represents an undecidable problem in general. And yet, our rule-based analysis covers all relational operators as well as linear recursive expressions in a systematic way showing the depth of analysis possible by our proposal. The analysis of functional dependencies is well-integrated in a uniform approach to analyzing dependencies between schema elements in general.Comment: Pre-proceedings paper presented at the 27th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR 2017), Namur, Belgium, 10-12 October 2017 (arXiv:1708.07854

Modelling the atomic structure of very high-density amorphous ice

The structure of very high-density amorphous (VHDA) ice has been modelled by positionally disordering three crystalline phases, namely ice IV, VI and XII. These phases were chosen because only they are stable or metastable in the region of the ice phase diagram where VHDA ice is formed, and their densities are comparable to that of VHDA ice. An excellent fit to the medium range of the experimentally observed pair-correlation function g(r) of VHDA ice was obtained by introducing disorder into the positions of the H2O molecules, as well as small amounts of molecular rotational disorder, disorder in the O--H bond lengths and disorder in the H--O--H bond angles. The low-k behaviour of the experimental structure factor, S(k), is also very well reproduced by this disordered-crystal model. The fraction of each phase present in the best-fit disordered model is very close to that observed in the probable crystallization products of VHDA ice. In particular, only negligible amounts of ice IV are predicted, in accordance with experimental observation.Comment: 4 pages, 3 figures, 1 table, v2: changes made in response to referees' comments, the justification for using certain ice phases is improved, and ice IV is now disordered as wel

Doming Modes and Dynamics of Model Heme Compounds

Synchrotron far-IR spectroscopy and density-functional calculations are used to characterize the low-frequency dynamics of model heme FeCO compounds. The “doming” vibrational mode in which the iron atom moves out of the porphyrin plane while the periphery of this ring moves in the opposite direction determines the reactivity of oxygen with this type of molecule in biological systems. Calculations of frequencies and absorption intensities and the measured pressure dependence of vibrational modes in the model compounds are used to identify the doming and related normal modes

An iterative procedure to obtain inverse response functions for thick-target correction of measured charged-particle spectra

A new method for correcting charged-particle spectra for thick target effects is described. Starting with a trial function, inverse response functions are found by an iterative procedure. The variances corresponding to the measured spectrum are treated similiarly and in parallel. Oscillations of the solution are avoided by rebinning the data to finer bins during a correction iteration and back to the original or wider binning after each iteration. This thick-target correction method has been used for data obtained with the MEDLEY facility at the The Svedberg Laboratory, Uppsala, Sweden, and is here presented in detail and demonstrated for two test cases.Comment: 14 pages, 8 figures, submitted to NIM