A central partition of molecular conformational space. II. Embedding 3D structures

A combinatorial model of molecular conformational space that was previously developped (J. Gabarro-Arpa, Comp. Biol. and Chem. 27, (2003) 153-159), had the drawback that structures could not be properly embedded beacause it lacked explicit rotational symmetry. The problem can be circumvented by sorting the elementary 3D components of a molecular system into a finite set of classes that can be separately embedded. This also opens up the possibility of encoding the dynamical states into a graph structure

A Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells

In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells, that encodes the set of cells in conformational space that are visited by the system in its thermal wandering. Here we outline a set of procedures for extracting useful information from this structure: 1st) interesting regions in the volume occupied by the system in conformational space can be bounded by a polyhedral cone whose faces are determined empirically from a set of relations between the coordinates of the molecule, 2nd) it is also shown that this cone can be decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a cone can be encoded by a simple combinatorial sequence.Comment: added an intrduction and reference

A Central Partition of Molecular Conformational Space.III. Combinatorial Determination of the Volume Spanned by a Molecular System

In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into a hierarchical set of cells that can be encoded by the face lattice poset of the arrangement. The model however, lacked explicit rotational symmetry which made impossible to distinguish rotated structures in conformational space. This problem was solved in a second work [physics/0404052] by sorting the elementary 3D components of the molecular system into a set of morphological classes that can be properly oriented in a standard 3D reference frame. This also made possible to find a solution to the problem that is being adressed in the present work: for a molecular system immersed in a heat bath we want to enumerate the subset of cells in conformational space that are visited by the molecule in its thermal wandering. If each visited cell is a vertex on a graph with edges to the adjacent cells, here it is explained how such graph can be built

Azimuthons in weakly nonlinear waveguides of different symmetries

We show that weakly guiding nonlinear waveguides support stable propagation of rotating spatial solitons (azimuthons). We investigate the role of waveguide symmetry on the soliton rotation. We find that azimuthons in circular waveguides always rotate rigidly during propagation and the analytically predicted rotation frequency is in excellent agreement with numerical simulations. On the other hand, azimuthons in square waveguides may experience spatial deformation during propagation. Moreover, we show that there is a critical value for the modulation depth of azimuthons above which solitons just wobble back and forth, and below which they rotate continuously. We explain these dynamics using the concept of energy difference between different orientations of the azimuthon.Comment: 12 pages, 8 figure

Perbedaan Jumlah Koloni Staphylococcus Epidermidis Pada Media Nutrient Agar Yang Menggunakan Pelarut Akuades Dan Air Minum Dalam Kemasan

Background : The regrowing process is conducted to investigate the contamination of Staphylococcus epidermidis. The inoculation in the specific culture media can be used to regrow the microorganism. Nutrient agaris one of the culture medium used to inoculate. In the preparation of microbiology medium, distilled water is the most-used solvent due to its purity and hygienist. However, pure distilled water is sometimes hard to find and relatively has a high price. The alternative solvent such as bottled-drinking water should be made to substitute the use of distilled water as the solvent. The distilled water and bottled-drinking water have a similar characteristic and both types of water are obtained by almost similar technology process such as filtration and sterilization. Moreover, the small amount of mineral which possibly contains in the bottled-drinking water is safe for microorganism cultivation and it also can not contaminate the culture medium. Thus, the substitution of distilled water with bottled-drinking water is possible as the alternative solvent. The present research aims to investigate the different number of Staphylococcus epidermidis colonies regrowth in nutrient agar which dissolved in distilled water and bottled-drinking water. Method : The present research is categorized as the pre-experiment with comparative statics study. The sample which is the pure colonies suspension of Staphylococcus epidermidisis diluted to 1 million times and inoculated on nutrient agar with a specific solvent. To investigate the effect of solvent, distilled water, and bottled-drinking water are used as the solvent. The inoculated-medium is incubated at 37oC for 48 hours. After 48 hours, the number of colonies is calculated, and the obtained data is parametrically analyzed using the paired t-test. Result: The research has been conducted for 20 times to ensure that the obtained data is repeatable. The result showed that the colonies number of Staphylococcus epidermidisregrowth in nutrient agar which dissolved in distilled water and bottled-drinking water is 113 and 114. The statistical analysis using Paired Sample T-Test supports that there is no significant difference of colonies number in nutrient agar dissolved in distilled water and bottled-drinking water. Conclusion: The research and the statistical analysis show that there is no significant difference of colonies number in nutrient agar dissolved in distilled water and bottled-drinking water