Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

Organopolysiloxanes as Chemically Sensitive Coatings for Optical Fibers

Various types of UV-curable organically modified siloxanes have been synthesized by the sol-gel method with the aim of fabricating chemically sensitive coatings for silica optical fibers. The refractive index of the coating material can be tailored in the range from 1.46 to 1.56 and sensitivity towards CO2 is achieved by incorporation of amino groups. The interaction of the cured layers with CO2 or with hydrocarbons has been studied in immersion experiments. Both the reaction of CO2 with incorporated amino groups and the penetration of hydrocarbons into the layer induce changes of the light absorption coefficient and the refractive index of the coating which are detected by measuring the output light intensity from the fiber.     

In situ prepared polypyrrole for low humidity QCM sensor and related theoretical calculation

In situ preparation of polypyrrole (Ppy) by photo-polymerization coated on a quartz crystal microbalance (QCM) as a low humidity sensor was reported. Different concentrations of Ppy films say 0 wt.% (as blank), 0.1, 1, and 10 wt.% were investigated to measure humidity concentrations between 14.7 and 5412.5 ppm_v. The adsorption/desorption behavior was also examined at humidity concentration 510.2 ppm_v. The sensitivities of 0, 0.1 and 1 wt.% Ppy films at 51.5 ppm_v were 0.143, 0.219 and 0.427, respectively. For 1 wt.% Ppy, the highest sensitivity was obtained. The slope and correlation coefficients (R²) for 1 wt.% Ppy at the ranges of 14.7–898.6 ppm_v were 0.0646 and 0.9909, respectively. A series of molecular simulations have been carried out to calculate bond energy for the water molecule interaction with Ppy, which was found to be 3 kcal/mol indicating the existence of hydrogen bonding during the sorption process. Based on Langmuir isotherm adsorption assumption, for 0.1 and 1 wt.% Ppy films, the association constants were 2606.30 and 5792.98, respectively. This larger association constant for 1 wt.% Ppy film explains higher sensitivity.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Membrane-oxide semiconductor field-effect transistor (MOSFET) sensors

MOSFET-sensors can be considered as membrane-oxide-semiconductor field-effect transistors. MOSFETs can be divided into ISFETs, GasFETs, BioFETs, these sensors being sensitive to ion, gas, biomolecules respectively and there is also a possibility to fabricate MOSFET reference electrode (RefFET). The development and theoretical treatment of various type of MOSFET-sensors are presented in this paper.     

Chemical diffusion of oxygen in tin dioxide: Effects of dopants and oxygen partial pressure

Tin dioxide SnO_2−δ is a pronounced n-type electron conductor due to its oxygen deficiency. This study investigates the rate of chemical diffusion of oxygen in SnO_2−δ single crystals, which is a crucial step in the overall stoichiometry change of the material. The chemical diffusion coefficient D^δ was determined from conductivity- and EPR-relaxation methods. The temperature dependence was found to be . The dependence on crystal orientation, dopant content and oxygen partial pressure was below experimental error. The latter observation leads to the conclusion that the chemical diffusion coefficient is close to the diffusion coefficient of oxygen vacancies. Along with the relaxation process resulting from the chemical diffusion of oxygen, additional processes were observed. One of these was attributed to complications in the defect chemistry of the material. The relevance of the results for the kinetics of drift processes of Taguchi sensors is discussed.     

A discrete method of optimal control based upon the cell state space concept

A discrete method of optimal control is proposed in this paper. The continuum state space of a system is discretized into a cell state space, and the cost function is discretized in a similar manner. Assuming intervalwise constant controls and using a finite set of admissible control levels (u) and a finite set of admissible time intervals (), the motion of the system under all possible interval controls (u, ) can then be expressed in terms of a family of cell-to-cell mappings. The proposed method extracts the optimal control results from these mappings by a systematic search, culminating in the construction of a discrete optimal control table.The possibility of expressing the optimal control results in the form of a control table seems to give this method a means to make systems real-time controllable.Dedicated to G. LeitmannThe material is based upon work supported by the National Science Foundation under Grant No. MEA-82-17471. The author is also indebted to Professor G. Leitmann for his many helpful comments.     

Detection of Tumor Necrosis Factor Gene by Piezoelectric Nucleic Acid Senosr

A piezoelectric nucleic acid sensor was constructed ofr detection of tumor necrosis factor gene.Two methods were employed for immobilization of nucleic acid probe on gold electrode of piezoelectric crystal.The results show that polyethyleneimine adbesion and glutaraldehyde cross-linking method has higher sensitivity,stability and selectivity than protein A method.The solid-phase nucleic acid hybridization of oligo unclecotides and tumor necrosis factor target gene sequence were monitorde using this sensor.Tumor necrosis factor gene sequence(580bp) was detected by this nucleic acid sensor for the first time.     

味觉电化学传感器的研究——Ⅰ.甜、酸、苦、咸物质对模拟生物膜电位振动频率的影响

本文以十六烷基三甲基溴化铵/含苦味酸的硝基苯/蔗糖溶液为研究体系,发现甜、酸、苦、咸物质均能使体系的振动波形和频率发生变化,初步建立了测定有味物质的定性、定量方法,并对该味觉电化学传感器的响应机理进行了探讨。     

2,2’-联吡啶-1,1’-二氧化物与Mn(Ⅱ)的三聚体配合物的合成及性能

Mn( )能与许多氮氧化合物形成配合物 ,Wilde对 Mn( )与 2 ,2 -联吡啶及 1 ,1 -二氮杂菲的均配配合物作过详细研究 [1,2 ] ;Mn( )与 2 ,2 -联吡啶 - 1 ,1 -二氧化物 ( bipy O2 )的配合物也有综述 [3] .Mn( )与 bipy O2 的配合物大多是以 Cl O- 4、NO- 3、[Pt Cl4 ]2 -为阴离子 ,少数是卤离子 .它们均形成配位体数目为 3的单核螯合物 ,这些配合物是在水或乙醇中合成的 .Mn( )与 bipy O2 的多核聚合物还未见报道 .本文用 DMF为溶剂 ,以无水 Mn Cl2 和 2 ,2 -联吡啶 - 1 ,1 -二氧化物为原料 ,合成了 Mn( )与bipy O2 的三聚…