Binary Substrate Research Articles

Solubility-dependent melting temperature depression of binary substrate mixtures: A model study

In formulating eutectic media, the role of solvent adjuvant is not well understood in depressing the melting temperature of a binary substrate mixture ( T MB ). Here, we demonstrated the effect of solubility on the depression of T MB by using combinatorial model mixtures of N -benzyloxycarbonyl- l -Asp (CBZ- l -Asp) with either an l -amino acid or a d -sugar in different solvent adjuvants. When CBZ- l -Asp was mixed with an individual l -amino acid at an equi-molar ratio, T MB values varied approximately from 34 to 113 °C according to the hydrophobicity of adjuvants. Similarly, CBZ- l -Asp/ d -sugar mixtures showed large variations of T MB values approximately from 43 to 112 °C according to the hydrophobicity of adjuvants. In the water adjuvant, T MB values in both CBZ- l -Asp/ l -amino acid and CBZ- l -Asp/ d -sugar showed strong correlations with the water solubility of either l -amino acids or d -sugars. In contrast, the hydrophobicity of individual compounds did not show any correspondence with T MB depression. The peak height of X-ray diffractions in the mixture of either CBZ- l -Asp/ l -Lys or CBZ- l -Asp/ l -Tyr was significantly reduced only when either l -Lys or l -Tyr was soluble in the adjuvant. These results show that the solubilization of a substrate component to an adjuvant contributed to the T MB depression, which may be caused by the enhanced structural homogeneity of a binary mixture.

Using polystyrene‐co‐maleic acid for molecularly imprinted membranes prepared in supercritical carbon dioxide

AbstractSupercritical CO2 (ScCO2) has been used to prepare molecularly imprinted polymers of poly(styrene‐co‐maleic acid) (PSMA) for targeted uracil (URA). The condition of ScCO2 was on 16 MPa between 35 and 50°C. The resultant imprinted membranes prepared at 35 and 50°C bound URA with 9.2 ± 0.10 and 12.6 ± 0.06 μmol g−1, respectively. Competitive binding studies were undertaken in binary substrate solution containing each of URA/DMURA, URA/Thymine, and URA/Cytosine with 2 μM. The URA imprinted membrane showed high separation factor (α) with 17 for both URA/DMURA and URA/Thymine and for URA/Cytosine, α = 13. Results strongly suggested that the URA imprinted membrane had effective selectivity hydrogen bonding to separately bind in the binary components to the template. Effect of organic solvents on the URA imprinting in ScCO2 was also studied, in addition to comparison of properties with those obtained in both ScCO2 and water. Evidence presented that ScCO2 medium was effective to prepare the URA imprinted membrane. We discussed that ScCO2 fluid was efficient to fix the shape of URA template into the PSMA membrane through hydrogen bonding. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008

Self-spreading Lipid Bilayer on Nano-structured Surface with Periodic Array of Metallic and Organic Nano-architectures

We investigated the lipid bilayer self-spreading behavior on glass substrates modified with complex array of nano-architectures. Simple way of constructing a binary array of metallic / organic nano-architectures was established. The metallic nano-architecture was prepared by nano-sphere lithography (NSL) method. By controlling the drying process in NSL, periodic array of donut-shaped organic nano-architectures, 200 nm in diameter and 4 nm in height, was also constructed on the substrate. In the presence of metallic nano-architectures, the self-spreading velocity was significantly reduced due to the energy cost imposed on passing through the nano-architectures. The self-spreading phenomenon was found to be intact even on the metallic / organic binary array substrate. Fluorescence microscope revealed that the organic nano-architectures kept their initial structures during the self-spreading around the architectures.

Mechanism of the Conformational Transitions in 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase as Revealed by NMR Spectroscopy,

6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), leading to the biosynthesis of folate cofactors. HPPK undergoes dramatic conformational changes during its catalytic cycle, and the conformational changes are essential for enzymatic catalysis. Thus, the enzyme is not only an attractive target for developing antimicrobial agents but also an excellent model system for studying the catalytic mechanism of enzymatic pyrophosphoryl transfer as well as the role of protein dynamics in enzymatic catalysis. In the present study, we report the NMR solution structures of the binary complex HPPK*MgAMPCPP and the ternary complex HPPK*MgAMPCPP*DMHP, where alpha,beta-methyleneadenosine triphosphate (AMPCPP) and 7, 7-dimethyl-6-hydroxypterin (DMHP) are the analogues of the substrates ATP and HP, respectively. The results suggest that the three catalytic loops of the binary complex of HPPK can assume multiple conformations in slow exchanges as evidenced by multiple sets of NMR signals for several residues in loops 2 and 3 and the very weak or missing NH cross-peaks for several residues in loops 1 and 3. However, the ternary complex shows only one set of NMR signals, and the cross-peak intensities are rather uniform, suggesting that the binding of the second substrate shifts the multiple conformations of the binary complex to an apparently single conformation of the ternary complex. The NMR behaviors and conformations of the binary complex HPPK*MgAMPCPP are significantly different from those of HPPK in complex with Mgbeta,gamma-methyleneadenosine triphosphate (MgAMPPCP). It is suggested that the conformational properties of the binary substrate complex HPPK*MgATP be represented by those of HPPK*MgAMPCPP, because MgAMPCPP is a better MgATP analogue for HPPK with respect to both binding affinity and bound conformation.

Growth kinetics of Pseudomonas putida in the biodegradation of single and mixed phenol and sodium salicylate

The kinetics of biodegradation of single phenol and sodium salicylate (SA) and their binary mixtures in water by suspended Pseudomonas putida CCRC 14365 was studied at 30 °C and pH 7.0. Experiments were performed at different total substrate concentrations (0–4.25 mM) and/or mole fractions of phenol. The initial cell concentration was fixed at 0.025 g/L. Based on the parameters of the Haldane model for specific growth rate of the cells on single phenol and SA (correlation coefficient R 2 > 0.9737), phenol had larger degradation rate than SA, whereas the inhibition of P. putida by phenol was less significant than by SA. That is, the cells were more favored to degrade phenol than SA under comparable conditions. On the other hand, the specific growth rate of the cells on binary substrates could be described by an extended Haldane equation ( R 2 = 0.9256). The substrate interactions were thus discussed according to the modeled parameters. The dynamics in the biodegradation of single and binary substrate systems was finally analyzed.

Biodegradation of phenol and sodium salicylate mixtures by suspended Pseudomonas putida CCRC 14365

The biodegradation of single phenol and sodium salicylate (SA) and their binary mixtures in water by free Pseudomonas putida ( P. putida) CCRC 14365 was experimentally studied at 30 °C and pH 7. The initial concentration of the cells, adapted with either phenol or SA, was maintained at 0.025 g/L. Single substrate experiments were performed in the substrate level range 0.53–3.18 mM. The Haldane model has shown that phenol was biodegraded more quickly ( μ max = 0.245 h −1) than SA (0.137 h −1) under the ranges studied, and SA had a more inhibitory effect on cell growth ( K I = 5.21 mM) than phenol (12.6 mM) at low substrate levels even by SA-adapted cells. Binary substrate experiments were carried out at two fixed total substrate levels of 1.06 and 3.18 mM, with a varying molar concentration ratio of 0.33–3.0. The presence of a small amount of phenol to SA could significantly enhance the biodegradation of SA, particularly when the phenol-adapted cells were employed. On the other hand, the addition of a small amount of SA to phenol would retard the biodegradation of phenol, especially at higher total substrate levels (3.18 mM).

Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel That Evolved by Gene Duplication

Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two (βα)8 barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys)3Zn site in the related enzymes, MetH and betaine–homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E·Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.

Interdiffusion in Compound Thin Film Grown on Binary Substrate under Time-Variable Boundary Conditions

Interdiffusion in an epitaxial layer of a ternary semiconductor grown on thick binary substrate is investigated theoretically under time-variable boundary conditions typically used in conventional epitaxial methods. Precise calculations are carried out for Cd1-xMnxTe/CdTe which make it possible to calculate the concentration of metallic components that diffuse from the grown film into the substrate and vice versa. The processes of degradation during crystal growth in such systems are discussed in the cases of an ultra thin inclusion, graded-band-gap structure and a multilayered structure (superlattice).

Effect of ethanol, acetate, and phenol on toluene degradation activity and tod-lux expression in Pseudomonas putida TOD102: evaluation of the metabolic flux dilution model.

The reporter strain Pseudomonas putida TOD102 (with a tod-lux fusion) was used in chemostat experiments with binary substrate mixtures to investigate the effect of potentially occurring cosubstrates on toluene degradation activity. Although toluene was simultaneously utilized with other cosubstrates, its metabolic flux (defined as the toluene utilization rate per cell) decreased with increasing influent concentrations of ethanol, acetate, or phenol. Three inhibitory mechanisms were considered to explain these trends: (1) repression of the tod gene (coding for toluene dioxygenase) by acetate and ethanol, which was quantified by a decrease in specific bioluminescence; (2) competitive inhibition of toluene dioxygenase by phenol; and (3) metabolic flux dilution (MFD) by all three cosubstrates. Based on experimental observations, MFD was modeled without any fitting parameters by assuming that the metabolic flux of a substrate in a mixture is proportional to its relative availability (expressed as a fraction of the influent total organic carbon). Thus, increasing concentrations of alternative carbon sources "dilute" the metabolic flux of toluene without necessarily repressing tod, as observed with phenol (a known tod inducer). For all cosubstrates, the MFD model slightly overpredicted the measured toluene metabolic flux. Incorporating catabolite repression (for experiments with acetate or ethanol) or competitive inhibition (for experiments with phenol) with independently obtained parameters resulted in more accurate fits of the observed decrease in toluene metabolic flux with increasing cosubstrate concentration. These results imply that alternative carbon sources (including inducers) are likely to hinder toluene utilization per unit cell, and that these effects can be accurately predicted with simple mathematical models.

Phase equilibria of A 3 B 5 quinary systems with an elastically strained solid phase

The contribution of the elastic component of the excess energy of mixing is determined for A3B5 quinary solid solutions. A relationship is derived for the activities of the components in an elastically strained solid phase of the quinary solid solutions. The correctness of the possible assumptions used in the calculation of the activity coefficients of the solid phase of a quinary solution is analyzed. The contact supercooling in the vicinity of the binary substrate isoperiods is calculated for a number of A3B5 quinary systems. It is shown that the negative contact supercoolings correspond to the thermodynamic instability boundaries of the quinary solid solutions.

Catabolic enzyme levels in bacteria grown on binary and ternary substrate mixtures in continuous culture.

Bacteria grow on multicomponent substrates in most natural and engineered environments. To advance our ability to model bacterial growth on such substrates, axenic cultures were grown in chemostats at a low specific growth rate and a constant total energy flux on binary and ternary substrate mixtures and were assayed for key catabolic enzymes for each substrate. The substrates were benzoate, salicylate, and glucose, and the enzymes were catechol 1,2-dioxygenase, gentisate 1,2-dioxygenase, and glucose-6-phosphate dehydrogenase, respectively. The binary mixtures were salicylate with benzoate and salicylate with glucose. Measurements were also made of oxygen uptake rate by whole cells in response to each substrate. The effects of the substrate mixture on the oxygen uptake rate paralleled the effects on the measured enzymes. Catechol 1,2-dioxygenase exhibited a threshold response before synthesis occurred. Below the threshold flux of benzoate through the chemostat, either basal enzyme levels or nonspecific enzymes kept reactor concentrations too low for enzyme synthesis. Above the threshold, enzyme levels were linearly related to the fraction of the total energy flux through the chemostat due to benzoate. Gentisate 1,2-dioxygenase exhibited a linear response to the salicylate flux when mixed with benzoate, but a threshold response when mixed with glucose. Glucose-6-phosphate dehydrogenase activity increased in direct proportion to the glucose flux through the chemostat over the entire range studied. The results from two ternary mixtures were consistent with those from the binary mixtures.

Ball grid array (BGA) substrate conduct paths inspection using two-dimensional wavelet transform

The objective of this paper is to implement two-dimensional wavelet transform (2-D WT) in the detection of mousebite, spur, open, and short defect candidates on ball grid array (BGA) substrate conduct paths. Once the defect candidates are located, traditional BGA substrate inspection algorithms can further detect true defects among these suspicious defects. Therefore, the scope and effort during the inspection stage can be significantly reduced. The binary BGA substrate image is processed that shows only conduct path boundaries, which are decomposed directly by 2-D WT. Then, the inter-scale ratio from the wavelet transform modulus sum (WTMS) across adjacent decomposition levels for the edge pixels on BGA substrate conduct path boundaries is calculated. Since irregular edges in a small domain can preserve much more wavelet energy, an edge pixel is considered as an abnormal one or a defect candidate if its inter-scale ratio is less than a predefined threshold. The proposed approach is template-free and easy to implement, so it is suitable for small batch production. Real BGA substrates with synthetic boundary defects are used as testing samples to evaluate the performance of the proposed approach. Experimental results show that the proposed method is able to capture all the true mousebite, spur, open, and short defects without any missing errors by appropriate wavelet basis, decomposition level, and image resolution.

An agent-based learning framework for modeling microbial growth

The overall idea of this paper is to study the intelligent behavior of microbes in a binary substrate environment with agent-based learning models. Study of microbial growth enables understanding of industrially relevant processes such as fermentation, biodegradation of pollutants, antibody production using hybridoma cells, etc. Artificial intelligence techniques such as genetic algorithms and agent-based learning methodologies have been used to study microbial growth. Specifically, the objective is to (1) qualitatively model the intelligent growth characteristics of the microbes using a minimal set of generic rules as against algebraic/differential mathematical relationships and (2) propose a suitable hypothesis that explains the origin of intelligence through learning in the microbes. A microbial cell has been modeled as a collection of agents characterized by a set of resources and an objective to survive and grow. The actions of the agents are governed by generic rules such as survival, growth and division as is common for any individual in a resource-limited competitive environment. The interaction of the agents with the environment and other fellow agents enables them to “learn” and “adapt” to the changes in the environment and thus defines the dynamics of the system. The origin of intelligence in the microbes has been studied by both a simple learning rule of imitation and rule discovery studies.

Effect of media composition on yield values of bacteria growing on binary and ternary substrate mixtures in continuous culture.

Pseudomonas aeruginosa 142 and a presumed variant were grown axenically in chemostats on salicylate/benzoate or salicylate/glucose binary feeds. Each substrate was supplied at 2, 10, 50, 90, 98, or 100% of the total energy flux. Two experiments were also run with ternary mixtures using the same substrates. Aliquots were transferred to fed-batch reactors receiving the same substrates at the same specific rates as the chemostat, but with one substrate radiolabeled with 14C. Radiolabel incorporated into biomass, 14CO2, and soluble microbial products over a period of 8 minutes was used to establish the biomass yield, CO2 yield, and product yield, respectively, associated with a given substrate. The effect of the percent substrate in the feed on the yields depended on the pair of substrates supplied. When benzoate comprised 50% or more of the applied substrate in salicylate/benzoate feeds, the fraction of benzoate in the feed had a small effect on the yield values associated with benzoate. However, when benzoate constituted 2% or 10% of the feed, CO2 yields were lower, biomass yields were slightly lower, and product yields were higher. In contrast, the percent of salicylate in the feed had little effect on any of the salicylate yields for cells growing on the salicylate/benzoate feeds. When salicylate was mixed with glucose, the yields associated with salicylate behaved quite differently. Biomass and CO2 yields were lower and product yields higher when salicylate was 2% or 10% of the feed than when it was higher. In the same substrate mixtures, glucose-based biomass yields were higher and CO2 yields were lower when glucose constituted 2% or 10% of the feed but were constant for higher percentages. The results suggest that the fate of a substrate is relatively independent of the feed composition as long as the substrate in question constitutes a significant percentage of the mixture. Thus, in those situations the assumption of a constant biomass yield in multicomponent substrate modeling is justified. However, when a given substrate constitutes a small percentage of the feed, significant changes in yield may occur.

Thermodynamics and nucleation kinetics of AlxGa1−xN/GaN and InxGa1−xN/GaN heterostructures

The initial stage of growth of group III-Nitride ternary compounds on binary substrate were analysed using the classical nucleation theory, incorporating the stress induced supercooling due to lattice mismatch between the grown alloy and substrate. The explicit expression for the growth of the chosen system was established and it was used to evaluate the nucleation parameters. It has been theoretically shown that the nucleation barrier for the formation of ternary alloy on binary substrate depends on the composition of the alloy.

In vitro biogeneration of pure thiosulfinates and propanethial-S-oxide.

A model reaction system was developed for generating pure thiosulfinates and propanethial-S-oxide (PTSO) using an isolated alliinase (EC 4.4.1.4) and isolated or synthetic alk(en)yl-L-cysteine sulfoxides (ACSO). Reaction yields ranged from 30 to 60% after 3 h at 21-23 degrees C, and organosulfur reaction products were extracted into CHCl3 to yield product preparations of controlled composition. A pure thiosulfinate or PTSO was derived from a single ACSO, and a preparation containing a mixture of four thiosulfinate species was derived from reaction mixtures employing binary ACSO substrate systems. Identities of homologous thiosulfinates and PTSO were confirmed by 1H NMR. This approach has the potential to be used as a preparative tool for yielding pure thiosulfinates and PTSO to facilitate the study of chemical and biological properties of this group of compounds or as a means to study the dynamics of organosulfur chemistry in preparations from Allium spp.

Interaction between binary alloy thin films and silicon substrate: the conditions of bilayer formation and the effect of additional component

From a physical chemistry point of view the conditions of B/ASi bilayer structure occurrence as a result of silicon interaction with films of various binary alloys A–B (where A = for example Pt, Pd, Co, Ni; B = W, V, Ti, Zr, Hf, Ta) are analyzed. It is shown that the bilayer formation is observed when either the primary dissolution of extremely small amount of A in Si in comparison to the dissolution of Si in A occurs that is estimated by the enthalpies of mixing in extremely indefinitely diluted solutions of A in Si, and Si in A, or the higher surface activity of component A in the couple with silicon in comparison to the B-Si couple occurs that is estimated by the heats of sublimation. The possible segregation of A on the grain boundaries of alloy is taken into account. If in system A–B the intermetallic compounds AxBy have been formed, the driving force of alloy depletion process by component A is reduced. It is reasonable that at the appropriate choice of a additional component C (where C = boron,carbon, nitrogen) it is possible to increase the driving force of this process and to form the bilayer structure BC+AxBy/ASi. The analysis results are compared to some experimental data.

MBE growth of GaInAsSb p/n junction diodes for thermophotovoltaic applications

Abstract This paper reports recent progress in the development of quaternary III–V thermophotovoltaic (TPV) devices based on MBE grown Ga x In 1− x As y Sb 1− y . TPV is of great interest for a variety of applications (1st and 2nd NREL Conf. on Thermophotovoltaic Generation of Electricity, AIP Conf. Proc. 321 (1994), 358 (1995)). The objective of this work is to develop a TPV cell which is “tunable” to the emission spectrum of a heated blackbody, at temperatures in the range of 1200–1473 K. One aspect of this “tuning” is to match the band gap, E gap , of the photovoltaic device to the peak output of the heat source. An advantage of the quaternary III–V semiconductor systems is that devices can be fabricated by molecular beam epitaxy on a suitable binary substrate, such as GaSb or InAs, and the band gap and lattice constant can be adjusted more or less independently, to match requirements. Quaternary cells, with band-gaps in the 0.5–0.72 eV range, have been fabricated and tested. For 0.54 eV devices we obtained open circuit voltage V OC = 0.3 V and short circuit current I SC = 1.5 A/cm 2 under infrared illumination of a 1200 K blackbody. Under high illumination levels the V OC and I SC ranged from 0.5 V at 3 A/cm 2 for 0.72 eV devices to 0.31 V at 1.2 A/cm 2 for 0.5 eV devices, indicating good photovoltaic device characteristics over the range of bandgaps. The diode ideality factor for 0.54 eV devices ranged from 2.45 at low illumination indicating tunneling-dominated dark current, to 1.7 at high illumination intensity indicating recombination-generation dominated dark currents.

2.0 A resolution structure of a ternary complex of pig muscle phosphoglycerate kinase containing 3-phospho-D-glycerate and the nucleotide Mn adenylylimidodiphosphate.

The crystal structure of a ternary complex of pig muscle phosphoglycerate kinase (PGK) containing 3-phosphoglycerate (3-PG) and manganese adenylylimidodiphosphate (Mn AMP-PNP) has been determined and refined at 2.0 A resolution. The complex differs from the true substrate ternary complex only in the presence of an imido- rather than an oxylink between beta- and gamma-phosphates of the bound nucleotide. The 3-PG is bound in a similar manner to that observed in binary complexes. The nucleotide is bound in a similar manner to Mg ADP except that the metal ion is coordinated by all three alpha-, beta-, and gamma-phosphates, but not by the protein. The gamma-phosphate, which is transferred in the reaction, is not bound by the protein. One further characteristic of the ternary complex is that Arg-38 moves to a position where its guanidinium group makes a triple interaction with the N-terminal domain, the C-terminal domain, and the 1-carboxyl group of the bound 3-PG. Although a hinge-bending conformation change is seen in the ternary complex, it is no larger than that observed in the 3-PG binary complex. To reduce that distance between two bound substrates to a value consistent with the direct in-line transfer known to occur in PGK, we modeled the closure of a pronounced cleft in the protein structure situated between the bound substrates. This closure suggested a mechanism of catalysis that involves the "capture" of the gamma-phosphate by Arg-38 and the N-terminus of helix-14, which has a conserved Gly-Gly-Gly phosphate binding motif. We propose that nucleophilic attack by the 1-carboxyl group of the 3-PG on the gamma-phosphorus follows the capture of the gamma-phosphate, leading to a pentacoordinate transition state that may be stabilized by hydrogen bonds donated by the NH groups in the N-terminus of helix 14 and the guanidinium group of Arg-38. During the course of the reaction the metal ion is proposed to migrate to a position coordinating the alpha- and beta-phosphates and the carboxyl group of Asp-374. The mechanism is consistent with the structural information from binary and ternary substrate complexes and much solution data, and gives a major catalytic role to Arg-38, as indicated by site-directed mutagenesis.

Stimulation of Crystalline Lattice Stabilization of Ga-In-P-As Layers during Heteroepitaxy

Every process of heteroepitaxial synthesis from liquid phase of AIIIBV compounds is based on the contact of saturated solution with the binary substrate. The initial difference in the crystalline lattice parameters or in the radii of mutually substituting atoms of the interface causes the shift of the thermodynamic balance point of the system. The change in the total energy of the system connected with this effect causes the deviation of the actual composition of the crystallising solution with respect to the planed one. In the present paper there are shown the results of the theoretical and experimental analysis of the effect of InP substrates on parameters of the GaxIn1-xPyAs1-y layer crystallised from liquid phase.