Modeling the dynamic response of an activated sludge process

Previously collected data describing aerated synthetic waste water, treated in a continuous stirred-tank reactor, are analyzed to understand better the dynamic response to step changes in the dilution rate,D. Comparing a change inD between steady states leads to hysteresis trajectories on both the graph of specific growth rate, μ, vs limiting substrate level (S) and the graph of (S) vs the cell level (X). Qualitative differences between the three different monitored cases will be compared to simulations of simple models at various dilution level changes in order to gain understanding of the dynamics of the process.

     

Modeling activated states of GPCRs: the rhodopsin template

Activation of G Protein-Coupled Receptors (GPCRs) is an allosteric mechanism triggered by ligand binding and resulting in conformational changes transduced by the transmembrane domain. Models of the activated forms of GPCRs have become increasingly necessary for the development of a clear understanding of signal propagation into the cell. Experimental evidence points to a multiplicity of conformations related to the activation of the receptor, rendered important physiologically by the suggestion that different conformations may be responsible for coupling to different signaling pathways. In contrast to the inactive state of rhodopsin (RHO) for which several high quality X-ray structures are available, the structure-related information for the active states of rhodopsin and all other GPCRs is indirect. We have collected and stored such information in a repository we maintain for activation-specific structural data available for rhodopsin-like GPCRs, . Using these data as structural constraints, we have applied Simulated Annealing Molecular Dynamics to construct a number of different active state models of RHO starting from the known inactive structure. The common features of the models indicate that TM3 and TM5 play an important role in activation, in addition to the well-established rearrangement of TM6. Some of the structural changes observed in these models occur in regions that were not involved in the constraints, and have not been previously tested experimentally; they emerge as interesting candidates for further experimental exploration of the conformational space of activated GPCRs. We show that none of the normal modes calculated from the inactive structure has a dominant contribution along the path of conformational rearrangement from inactive to the active forms of RHO in the models. This result may differentiate rhodopsin from other GPCRs, and the reasons for this difference are discussed in the context of the structural properties and the physiological function of the protein. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. An erratum to this article can be found at     

Modeling reactive blending: An experimental approach

We present an experimental study of polymer–polymer reaction kinetics at the interfaces between two immiscible polymer phases under flow in a batch mixer of type Haake Rheocord. To that end, we have developed a model chemical system that is composed of a mixture of polystyrene (PS) and poly(methyl methacrylate) (PMMA). A small fraction of PS bear hydroxyl terminal group (PS-OH) and that of PMMA contain nonclassical isocyanate moieties that are randomly distributed along the PMMA chains (PMMA-r-NCO). This reactive system is particularly pertinent to modeling practical reactive blending processes because the amount and rate of copolymer formation can be determined with great accuracy (on the order of ppm). This study shows that the overall reaction rate is controlled primarily by interfacial generation through convective mixing. Most reaction and morphological development are accomplished within a very short period of time (1–3 min). For a PS/PMMA (60/40) reactive blend, the ultimate size of the PMMA particles is as small as 0.2 μm and is reached within 2 to 3 min. A surface coverage of about 0.5 of the PMMA particles by a monolayer of the copolymer is enough to prevent dynamic coalescence, whereas a much higher surface coverage is needed to eliminate static coalescence. In the nonentangled regime (M_n of the PS-OH = 7800 g/mol), temperature has a significant effect on the reaction rate, while it has little effect in the entangled regime (M_n of the PS-OH = 53,200 g/mol). © 1998 John Wiley & Sons, Inc. J. Polym. Sci. B Polym. Phys. 36: 2153–2163, 1998     

Modeling the sorption dynamics of NaH using a reactive force field

We have parametrized a reactive force field for NaH, ReaxFF(NaH), against a training set of ab initio derived data. To ascertain that ReaxFF(NaH) is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFF(NaH) was done. The results and trend of ReaxFF(NaH) are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFF(NaH). There is a good match between the two results, showing that ReaxFF(NaH) is correctly parametrized by the ab initio training set. ReaxFF(NaH) has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFF(NaH) properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments.     

Surface properties of liquid reactive oligomers

Spreading coefficients and the work of adhesion of oligomers to different substrates are calculated based on the results of studying the wettability and surface tension of ED-20 epoxy oligomer and oligooxyethyleneoxypropylene triols. It is shown that the addition of surfactant (ethoxylated alkyl phenols) considerably enhances the wettability of the studied oligomers. It is established that the addition of surfactant imparted to the properties of oligomers and surface energy characteristics of composites based on these oligomers nonlinearly depend on the degree of ethoxylation.     

Kinetic modeling of liquid-phase adsorption of reactive dyes on activated carbon

In this paper, adsorption equilibrium and kinetics of three reactive dyes from their single-component aqueous solutions onto activated carbon were studied in a batch reactor. Effects of the initial concentration and adsorbent particle size on adsorption rate were investigated Adsorption equilibrium data were then correlated with several well-known equilibrium isotherm models. The kinetic data were fitted using the pseudo-first-order equation, the pseudo-second-order equation, and the intraparticle diffusion model. The respective characteristic rate constants were presented. A new adsorption rate model based on the pseudo-first-order equation has been proposed to describe the experimental data over the whole adsorption process. The results show that the modified pseudo-first-order kinetic model generates the best agreement with the experimental data for the three single-component adsorption systems.     

Regio- and diastereoselective dearomatizations of N-alkyl activated azaarenes: the maximization of the reactive sites

An unprecedented base-promoted multi-component one-pot dearomatization of N-alkyl activated azaarenes was developed, which enabled the synthesis of complex and diverse bridged cyclic polycycles with multiple stereocenters in a highly regio- and diastereoselective manner. Besides, we realized the step-controlled dearomative bi- and trifunctionalization of quinolinium salts. These transformations not only achieved the maximization of the reaction sites of pyridinium, quinolinium and isoquinolinium salts to enhance structural complexity and diversity, but also opened up a new reaction mode of these N-activated azaarenes. A unique feature of this strategy is the use of easily accessible and bench-stable N-alkyl activated azaarenes to provide maximum reactive sites for dearomative cascade cyclizations. In addition, the salient characteristics including high synthetic efficiency, short reaction time, mild conditions and simple operation made this strategy particularly attractive.

An unprecedented base-promoted multi-component one-pot dearomatization of N-alkyl activated azaarenes was developed to construct complex and diverse bridged cyclic polycycles with multiple stereocenters in a highly regio- and diastereoselective manner.     

Discriminating among the discriminator bases of tRNAs

Aminoacyl-tRNA synthetases must select their specific tRNAs from the 20 structurally similar tRNAs present in a cell. The discriminator base, at position 73 of the tRNA, is important for this selection but its effects on aminoacylation are variable depending on context Recent structural studies provide insight into this variability.     

A semiclassical reactive flux method for the calculation of condensed phase activated rate constants

A semi classical reactive flux algorithm for calculating thermally activated rate constants is presented which is based on a semi-classical transition state theory due to Chapman, Garrett and Miller [J. Chem. Phys. 63 (1975) 2710]. This reactive flux technique, when combined with the semiclassical TST, enables one to describe dynamical recrossings of the transition state on the same footing as tunneling effects. Most importantly, the method is readily applied to nonlinear multidimensional systems over a wide range of temperatures. It will be shown that the method works very well for a variety of existing models.     

Modeling the adsorption of dyes onto activated carbon by using experimental designs

We used experimental design methodologies to obtain the response surface of the adsorption process for three acid dyes used in the dyeing step of a tanning process. The dyes were Acid Red 97, Acid Orange 61 and Acid Brown 425. The adsorption process was evaluated determining the concentrations of individual and total dyes remaining in solution at the end of the process. These concentrations were determined simultaneously in a single step using sequential injection analysis with multivariate curve resolution alternating least squares (SIA-MCR-ALS). This method involves fractional factorial designs and the steepest ascent method to find a zone of efficient adsorption and a response surface-modeling step to fit the relevant adsorption factors for the response.     

Adsorption of a reactive dye on chemically modified activated carbons--influence of pH

The surface chemistry of a commercial activated carbon with a slightly basic nature was modified by appropriate treatments in order to obtain two additional samples, respectively with acidic and basic properties, without changing its textural parameters significantly. Different techniques (N2 adsorption at 77 K, temperature programmed desorption, and determination of acidity, basicity, and pH at the point of zero charge) were used to characterize the adsorbents. Kinetic and equilibrium adsorption data of a selected textile reactive dye (Rifafix Red 3BN, C.I. reactive red 241) on the mentioned materials were obtained at the pH values of 2, 7, and 12. The kinetic curves are fitted using the second-order model. The respective rate constants seem to diminish progressively with the initial concentration for the more diluted solutions tested, reaching a constant value at higher concentrations, which depends on the experimental system under consideration (adsorbent and pH). In general, the Langmuir model provides the best fit for the equilibrium data. The different uptakes obtained are discussed in relation to the surface chemical properties of the adsorbents. It is shown that the adsorption of the reactive (anionic) dye on the basic sample (prepared by thermal treatment under H2 flow at 700 degrees C) is favored. This conclusion is explained on the basis of the dispersive and electrostatic interactions involved. Moreover, it is also shown that the optimal adsorption condition for all the activated carbons tested corresponds to solution pH values not higher than the pH(pzc) of the adsorbents, which may be interpreted by taking into account the electrostatic forces present.     

Adsorption properties of iodine-doped activated carbon fiber

Iodine-doped activated carbon fibers (ACFs) were prepared by the iodine immersion method on pitch-based ACF. Then iodine-doped ACFs were heated in argon at 523 K for 4 h and at 673 K for 2 h. The iodine structure of the resultant iodine-doped ACFs was examined using X-ray photoelectron spectroscopy. The micropore structures were determined by N(2) adsorption at 77 K. The surface area and micropore volume of iodine-doped ACFs are less than those of pristine ACFs. However, the pore width does not change with the iodine doping. The effects of iodine doping on adsorption properties of ACFs for H(2)O and NO at 303 K were examined. The iodine doping affected remarkably the adsorptivities of ACFs for H(2)O and NO. In particular, iodine-doped ACFs treated at 673 K show enhanced adsorptivities for H(2)O and NO. This result suggests that iodine molecules doped on the micropores should be charged by heat treatment at 673 K.     

Effect of acid treatment on the properties of an activated carbon

The enhancement of the activity of a carbon treated with HF is due to the drastic diminution of its inorganic impurities, which produces an increase of the surface area of the carbon, a stronger Pt-C interaction and a higher Pt dispersity.

---

, HF, , , Pt-C Pt.

     

Scalable synthesis of activated carbon with superparamagnetic properties

Magnetic activated carbons were obtained by in situ formation of coated superparamagnetic iron nanoparticles in the pores of carbons initially impregnated with ferric salt solution.     

Modeling and experimental study of vanadium adsorption by iron-nanoparticle-impregnated activated carbon

Research on Chemical Intermediates - Iron-nanoparticle-impregnated activated carbon (IrAC) nanocomposite was synthesized as a new vanadium adsorbent. The vanadium adsorption rate for commercial...     

A general approach for the generation of orthogonal tRNAs

BACKGROUND: The addition of new amino acids to the genetic code of Escherichia coli requires an orthogonal suppressor tRNA that is uniquely acylated with a desired unnatural amino acid by an orthogonal aminoacyl-tRNA synthetase. A tRNA(Tyr)(CUA)-tyrosyl-tRNA synthetase pair imported from Methanococcus jannaschii can be used to generate such a pair. In vivo selections have been developed for selecting mutant suppressor tRNAs with enhanced orthogonality, which can be used to site-specifically incorporate unnatural amino acids into proteins in E. coli. RESULTS: A library of amber suppressor tRNAs derived from M. jannaschii tRNA(Tyr) was generated. tRNA(Tyr)(CUA)s that are substrates for endogenous E. coli aminoacyl-tRNA synthetases were deleted from the pool by a negative selection based on suppression of amber nonsense mutations in the barnase gene. The remaining tRNA(Tyr)(CUA)s were then selected for their ability to suppress amber nonsense codons in the beta-lactamase gene in the presence of the cognate M. jannaschii tyrosyl-tRNA synthetase (TyrRS). Four mutant suppressor tRNAs were selected that are poorer substrates for E. coli synthetases than M. jannaschii tRNA(Tyr)(CUA), but still can be charged efficiently by M. jannaschii TyrRS. CONCLUSIONS: The mutant suppressor tRNA(Tyr)(CUA) together with the M. jannaschii TyrRS is an excellent orthogonal tRNA-synthetase pair for the in vivo incorporation of unnatural amino acids into proteins. This general approach may be expanded to generate additional orthogonal tRNA-synthetase pairs as well as probe the interactions between tRNAs and their cognate synthetases.     

Modeling properties of the HF dimer in argon clusters

We compare geometry configurations, vibrational properties, and electronic structures of (HF)₂ in a free state and inside argon atom shells Ar_n. For the first stage, molecular dynamics calculations for the (HF)₂ · Ar₆₂ heterocluster are performed with the help of model potentials HF(SINGLE BOND)HF, Ar(SINGLE BOND)Ar, and Ar(SINGLE BOND)HF. Then, ab initio quantum chemistry analysis is carried out for the smaller systems (HF)₂ · Ar₁₅ and (HF)₂ · Ar₆ when keeping the argon atoms closest to the trapped dimer. We conclude that the hydrogen-bonded complex (HF)₂ gains some extra stability inside the argon shells, originating primarily from a decrease of intermolecular distance R_FF. Electronic structure calculations are in accord with the changes in dynamical properties, namely, a noticeable increase in the vibrational frequency assigned to the F(SINGLE BOND)F stretching mode (+25 cm⁻¹) and decrease in rms deviations for the corresponding coordinate δ_FF. In addition to these changes, the argon atoms of the nearest solvent shell donate a small fraction of electron charge which is spent for an increase of population of the antibonding orbital σ^* of the free monomer unit and shift orbital energies primarily of the lone-pair fluorine species. These shifts are greater than the changes due to geometry alterations and the possible inaccuracies of the calculation scheme. © 1997 John Wiley & Sons, Inc.