Quantitative measurements of Ge surface segregation during SiGe alloy growth

Ge segregation during the growth of Si_{1 − x}Ge_x alloys (x = 5, 10, 20, and 40%) was studied using X-ray photoelectron spectroscopy. The alloys were grown in thicknesses up to 20.0 nm at 500°C to measure quantitatively the amount of segregated surface Ge. The length of alloy needed to reach steady-state growth edge was found to decrease with increasing alloy concentration (4.8, 2.8, 2.4, and 2.0 nm, respectively). It was found that each alloy had a complete monolayer of Ge on the surface and an increasing amount of segregated Ge in the second layer (20, 55, 80, and 95%, respectively) during steady-state growth. An increase in the temperature of alloy growth (400–750°C) resulted in an increase in the leading edge of alloy growth but did not change the amount of segregated Ge during steady-state growth. We propose that film stress is responsible for the amount of Ge segregation.     

How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?

We estimate the statistical distribution of relative orientations between contacting residues from a database of protein structures and evaluate the potential of mean force for relative orientations between contacting residues. Polar angles and Euler angles are used to specify two degrees of directional freedom and three degrees of rotational freedom for the orientation of one residue relative to another in contacting residues, respectively. A local coordinate system affixed to each residue based only on main chain atoms is defined for fold recognition. The number of contacting residue pairs in the database will severely limit the resolution of the statistical distribution of relative orientations, if it is estimated by dividing space into cells and counting samples observed in each cell. To overcome such problems and to evaluate the fully anisotropic distributions of relative orientations as a function of polar and Euler angles, we choose a method in which the observed distribution is represented as a sum of delta functions each of which represents the observed orientation of a contacting residue, and is evaluated as a series expansion of spherical harmonics functions. The sample size limits the frequencies of modes whose expansion coefficients can be reliably estimated. High frequency modes are statistically less reliable than low frequency modes. Each expansion coefficient is separately corrected for the sample size according to suggestions from a Bayesian statistical analysis. As a result, many expansion terms can be utilized to evaluate orientational distributions. Also, unlike other orientational potentials, the uniform distribution is used for a reference distribution in evaluating a potential of mean force for each type of contacting residue pair from its orientational distribution, so that residue-residue orientations can be fully evaluated. It is shown by using decoy sets that the discrimination power of the orientational potential in fold recognition increases by taking account of the Euler angle dependencies and becomes comparable to that of a simple contact potential, and that the total energy potential taken as a simple sum of contact, orientation, and (phi,psi) potentials performs well to identify the native folds.     

Long‐Wavelength Fluorescent Reporters for Monitoring Protein Kinase Activity

In vivo optical imaging must contend with the limitations imposed by the optical window of tissue (600–1000 nm). Although a wide array of fluorophores are available that are visualized in the red and near‐IR region of the spectrum, with the exception of proteases, there are few long wavelength probes for enzymes. This situation poses a particular challenge for studying the intracellular biochemistry of erythrocytes, the high hemoglobin content of which optically obscures subcellular monitoring at wavelengths less than 600 nm. To address this, tunable fluorescent reporters for protein kinase activity were developed. The probing wavelength is preprogrammed by using readily available fluorophores, thereby enabling detection within the optical window of tissue, specifically in the far‐red and near‐IR region. These agents were used to monitor endogenous cAMP‐dependent protein kinase activity in erythrocyte lysates and in intact erythrocytes when using a light‐activatable reporter.     

Synthesis and characterization of donor-acceptor chromophores for unidirectional electron transfer

[reaction: see text] A series of electron-transfer chromophores containing a donor and acceptor linked by an alkyl spacer were synthesized, and their electronic spectra were investigated. By inclusion with amylose, the supramolecularly encapsulated chromophores exhibit enhanced fluorescence quenching with discrete distance dependence and acquire the ability to sustain self-assemblies of a densely packed supramolecular array on a SiOH/Si substrate.     

Sterically bulky tris(triazolyl)borate ligands as water-soluble analogues of tris(pyrazolyl)borate

The recently synthesized 3-tert-butyl-5-methyl-1,2,4-triazole reacted with KBH4 to give the new potassium tris(3-tert-butyl-5-methyl-1,2,4-triazolyl)borate K(Ttz(tBu,Me)) ligand. Ttz(tBu,Me) formed a four-coordinate (Ttz(tBu,Me))CoCl complex and five-coordinate (Ttz(tBu,Me))CoNO3 and (Ttz(tBu,Me))ZnOAc complexes. When these complexes were compared to their Tp(tBu,Me) analogues, it was found that Ttz(tBu,Me) resulted in negligible steric differences. K(Ttz(tBu,Me)) is more water-soluble than K(Tp(tBu,Me)), so bulky tris(triazolyl)borate ligands should lead to functional models for enzyme active sites in an aqueous environment and the creation of water-soluble analogues of Tp catalysts.     

Synthesis of zinc, copper, nickel, cobalt, and iron complexes using tris(pyrazolyl)methane sulfonate ligands: a structural model for N,N,O binding in metalloenzymes

Ligands of intermediate steric bulk were designed to mimic metalloenzymes with histidine and carboxlyate binding sites. The reaction between tris(3-isopropylpyrazolyl)methane and butyllithium followed by SO3NMe3 in THF yielded the new ligand lithium tris(3-isopropylpyrazolyl)methane sulfonate (LiTpmsiPr). Various metal salts reacted with LiTpmsiPr to give the octahedral complexes M(TpmsiPr)2 (M = Zn, Cu, Ni, Co, Fe) in which each ligand has N,N,O binding to the metal. In the reaction between LiTpmsiPr and ZnCl2, in addition to the major product Zn(TpmsiPr)2, [LiTpmsiPrZnCl2].2THF was also formed as a minor product with a tetrahedral zinc atom coordinated to either N,N,Cl,Cl in the solid phase or N,N,N,Cl in acetonitrile solution. Although TpmsiPr is coordinatively flexible and can act as a bipodal or tripodal ligand, it appears to favor the formation of octahedral L2M complexes.     

Intercalation ofn-alkylamines into α-titanium phosphate from aqueous solutions

Journal of Inclusion Phenomena and Macrocyclic Chemistry - The intercalation reactions betweenn-alkylamines and α-titanium phosphate in aqueous media have been investigated. The compounds with...     

Parameter and moment bounds for a nonlinear stochastic ecology model

A differential equation model of a marine ecosystem is formulated as a stochastic process. The ecosystem is modeled by considering the random exchange of a chemical nutrient between three components of the ecosystem. The Chapman-Kolmogorov equations and the moment or cumulant generating functions for the process are derived to examine analytically the behavior of the moments of the process. Through the use of differential inequalities, bounds on the exchange rate parameters are derived to reflect component extinction. Bounds on the moments of the process are also obtained.