Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

Direct Writing of Copper Film Patterns by Laser-Induced Decomposition of Copper Acetate

Direct writing of patterns is being widely attempted in the field of microelectronic circuit/device manufacture. Use of this technique eliminates the need for employing photolithographic process. Laser induced direct writing can be achieved by (i) Photochemical reaction [i] , (ii) Evaporation from target material [2], and (iii) decomposition.Micron size features of palladium and copper through decomposition of palladium acetate and copper formate respectively on quartz and silicon using Argon ion laser have been reported [3,4] .In this commuication we report a technique for both single line and large area depositon of copper through decomposition of copper acetate,(CH3COO)2Cu, on alumina substrates.Nd:YAG laser known for its reliability and low maintenance cost as compared to excimer and other gas lasers is used. This technique offers an attractive and economical alternative for manufacture of thin film microcircuits.

Synergistic use of thermogravimetric and electrochemical techniques for thermodynamic study of TiOx (1.67 <= x <= 2.0) at 1573 K

A thermodynamic study of the Ti-O system at 1573 K has been conducted using a combination of thermogravimetric and emf techniques. The results indicate that the variation of oxygen potential with the nonstoichiometric parameter delta in stability domain of TiO2-delta with rutile structure can be represented by the relation, Delta mu o(2) = -6RT In delta - 711970(+/-1600) J/mol. The corresponding relation between non-stoichiometric parameter delta and partial pressure of oxygen across the whole stability range of TiO2-delta at 1573 K is delta proportional to P-O2(-1/6). It is therefore evident that the oxygen deficient behavior of nonstoichiometric TiO2-delta is dominated by the presence of doubly charged oxygen vacancies and free electrons. The high-precision measurements enabled the resolution of oxygen potential steps corresponding to the different Magneli phases (Ti-n O2n-1) up to n = 15. Beyond this value of n, the oxygen potential steps were too small to be resolved. Based on composition of the Magneli phase in equilibrium with TiO2-delta, the maximum value of n is estimated to be 28. The chemical potential of titanium was derived as a function of composition using the Gibbs-Duhem relation. Gibbs energies of formation of the Magneli phases were derived from the chemical potentials of oxygen and titanium. The values of -2441.8(+/-5.8) kJ/mol for Ti4O7 and -1775.4(+/-4.3) kJ/mol for Ti3O5 Obtained in this study refine values of -2436.2(+/-26.1) kJ/mol and-1771.3(+/-6.9) kJ/mol, respectively, given in the JANAF thermochemical tables.

Delamination and solvothermal decomposition of layered zinc hydroxysalt: Formation of bimodal zinc oxide nanostructures

Dodecylsulphate-intercalated zinc hydroxysalt, Zn-5(OH)(8)(DS)(2)center dot mH(2)O delaminates to give monolayer colloidal dispersions in alcohols such as 1-butanol and ethylene glycol. The extent of delamination and the stability of the colloidal dispersion are comparable to those of layered double hydroxides. The solvothermal decomposition of the colloidal dispersion of the hydroxysalt in ethylene glycol yields a bimodal ZnO having a nanotubular structure decorated with nanosheets. (C) 2010 Elsevier Masson SAS. All rights reserved.

Chemistry of the incomplete decomposition of ammonium perchlorate (AP)

Results are presented to show that as the thermal decomposition of orthorhombic ammonium perchlorate proceeds there is an accumulation, in the solid, of hydrochloric and nitric acids, the concentrations of which increase up to 15% decomposition after which they decrease until they reach the original values.

Composite signal decomposition by digital inverse filtering

Inverse filters are conventionally used for resolving overlapping signals of identical waveshape. However, the inverse filtering approach is shown to be useful for resolving overlapping signals, identical or otherwise, of unknown waveshapes. Digital inverse filter design based on autocorrelation formulation of linear prediction is known to perform optimum spectral flattening of the input signal for which the filter is designed. This property of the inverse filter is used to accomplish composite signal decomposition. The theory has been presented assuming constituent signals to be responses of all-pole filters. However, the approach may be used for a general situation.

Spinodal decomposition of a Co-Ti-Nb alloy

The microstructural evolution on aging a Co-3 wt pct Ti-2 wt pct Nb alloy has been followed by transmission electron microscopy and diffraction to show that the solid solution decomposed by the spinodal mode. The strengthening observed has been correlated with the differences in lattice parameters of the coexisting phases. The several stages of coarsening have been documented to yield information about their kinetics and morphological changes.Formerly Visiting Assistant Professor, Department of Mechanical and Industrial Engineering, University of Illinois at Urbana-Champaign, 1206 West Green Street, Urbana, IL 61801, is with .

Effect of electric field on ammonium perchlorate decomposition

A novel method of detecting the charge-carrying species in inorganic decomposable salts is described. In ammonium perchlorate it is observed that the charge-carrying species at temperatures 150 and 230°C are oppositely charged; i.e., they are negatively charged (ClO−4 ions) at 230°C and positively charged (H+ or NH+4) at 150°C.

Effect of electric field on ammonium perchlorate decomposition

A novel method of detecting the charge-carrying species in inorganic decomposable salts is described. In ammonium perchlorate it is observed that the charge-carrying species at temperatures 150 and 230°C are oppositely charged; i.e., they are negatively charged (ClO−4 ions) at 230°C and positively charged (H+ or NH+4) at 150°C.

Kinetics and mechanism of thermal decomposition of tetramethylammonium nitrate

The mechanism of thermal decomposition of tetramethylammonium nitrate has been investigated by thermogravimetry and mass spectrometry. The activation energy for the decomposition has been determined by isothermal decomposition technique using thermogravimetry and by monitoring mass spectrometrically the formation of trimethylamine. The activation energies determined in both the cases compare well, suggesting that the decomposition proceeds via dissociation of tetramethylammonium nitrate into trimethylamine and methylnitrate.

Effect of trimethylammonium perchlorate on the decomposition and combustion of potassium perchlorate and potassium perchlorate-polyurethane propellants

Addition of trimethylammonium perchlorate to potassium perchlorate (KP) catalyzes its thermal decomposition. However, although the additive sensitises KP-PU propellant decomposition, its combustion is desensitised. The observed effects have been explained in terms of the role played by the early formation of potassium chloride.

Thermogravimetric and mass-spectrometric study of the thermal decomposition of PBCT resins

The thermal decomposition of three commercial samples of carboxy-terminated polybutadiene (PBCT) resins was studied by thermogravimetric analysis (TGA) at heating rates varying from 2° to 100°C/min. Kinetic parameters of the decomposition process at different heating rates were evaluated by means of the Fuoss method.1 The decomposition process and the activation energy values are found to be dependent on heating rate. Mass-spectrometric analysis of the decomposition products shows that the pyrolysis products of PBCT resins are mainly low molecular weight hydrocarbons: ethylene, acetylene, butadiene, propadiene, vinylcyclohexene, etc. The rates of evolution of these hydrocarbon products vary with the carboxy content of the PBCT resin. Based on this, a carbonium ion mechanism has been suggested for the thermal decomposition. The data generated from this work are of importance for a consideration of the mechanism of combustion of composite solid propellants based on PBCT binders.