Reduction and solution of the chemical master equation using time scale separation and finite state projection

The dynamics of chemical reaction networks often takes place on widely differing time scales--from the order of nanoseconds to the order of several days. This is particularly true for gene regulatory networks, which are modeled by chemical kinetics. Multiple time scales in mathematical models often lead to serious computational difficulties, such as numerical stiffness in the case of differential equations or excessively redundant Monte Carlo simulations in the case of stochastic processes. We present a model reduction method for study of stochastic chemical kinetic systems that takes advantage of multiple time scales. The method applies to finite projections of the chemical master equation and allows for effective time scale separation of the system dynamics. We implement this method in a novel numerical algorithm that exploits the time scale separation to achieve model order reductions while enabling error checking and control. We illustrate the efficiency of our method in several examples motivated by recent developments in gene regulatory networks.     

Comparative Study of the CDW Systems

The physics of conducting trichalcogenides (NbSe 3) and organic metals (TTF-TCNQ) is considered from the point of view of 1d many body theories. It is argued that the former belong to the Peierls and the latter to the strongly correlated CDW limit.     

Resonance-enhanced multiphoton ionisation photoelectron spectroscopy of the ClO radical: the C 2 sigma- state

A (2 + 1) one-colour resonance-enhanced multiphoton ionisation study is carried out on the C 2 sigma- state of the ClO radical in the one-photon energy range 29,500-31,250 cm-1. The ClO radical is produced by one-photon photolysis of ClO2 employing 359.2 nm photons derived from a separate laser. In this way a significant concentration of vibrationally excited ClO in its spin-orbit split X 2 pi omega (omega = 3/2 or 1/2) electronic ground state is produced. In addition to mass-resolved excitation spectra, kinetic-energy resolved photoelectron spectra for the X 3 sigma-(v+)<--C 2 sigma-(v' = 3-5) transitions are measured. These transitions are not completely Frank-Condon diagonal, and indicate a decrease in bond length on removal of the Rydberg electron from the C 2 sigma- state. In addition to an unambiguous assignment of the C 2 sigma- state, valuable information is obtained on the degree of vibrational excitation with which the nascent ClO radical is formed in the photolysis of ClO2. Analysis of the photoelectron spectra is supported by Franck-Condon calculations based on potential energy curves either from experimental spectroscopic parameters, or obtained by theoretical ab initio methods.     

Phage display-derived inhibitor of the essential cell wall biosynthesis enzyme MurF

Background  

To develop antibacterial agents having novel modes of action against bacterial cell wall biosynthesis, we targeted the essential MurF enzyme of the antibiotic resistant pathogen Pseudomonas aeruginosa. MurF catalyzes the formation of a peptide bond between D-Alanyl-D-Alanine (D-Ala-D-Ala) and the cell wall precursor uridine 5'-diphosphoryl N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-diaminopimelic acid (UDP-MurNAc-Ala-Glu-meso-A2pm) with the concomitant hydrolysis of ATP to ADP and inorganic phosphate, yielding UDP-N-acetylmuramyl-pentapeptide. As MurF acts on a dipeptide, we exploited a phage display approach to identify peptide ligands having high binding affinities for the enzyme.     

ICP-MS Determination of Antimicrobial Metals in Microcapsules

Silver (Ag) and zinc (Zn) are very powerful antimicrobial metals. Therefore, in this research, a high-throughput, sensitive, and rapid method was developed for the determination of Ag and Zn in microcapsules using inductively coupled plasma mass spectrometry (ICP-MS). The sample preparation procedure employed simple microwave digestion of the microcapsules with 55.55% v/v HNO₃ and 44.45% v/v H₂O₂. The method was applied to determine Ag and Zn in microcapsule samples of different sizes (120 and 450 μm) after their preparation with and without chitosan. Prepared microcapsules, after characterization, were bonded to a polymer carrier by sol-gel procedure and the materials were characterized by FTIR spectroscopy and high-resolution optical microscopy. Significant differences were found in Ag and Zn levels between microcapsules samples prepared with and without chitosan. The results have shown that samples with chitosan had up to 20% higher levels of Zn than Ag: 120 μm microcapsules contained 351.50 μg/g of Ag and 85.51 μg/g of Zn, respectively. In contrast, samples prepared without chitosan showed larger overall variability: In microcapsules with a diameter of 120 μm, the amounts of antimicrobial metals were 98.32 μg/g of Ag and 106.75 μg of Zn, respectively. Moreover, 450 μm microcapsules contained 190.98 μg/g of Ag and 121.35 μg/g of Zn. Those quantities are high enough for efficient antimicrobial activity of newly prepared microcapsules, enabling the application of microcapsules in different antimicrobial coatings.     

Photoelastic determination of stresses in multiple-pin connectors

The design, fabrication, and testing of photoelastic models of double-lap, multiple-pin connectors are discussed. Interest is in the stresses in the inner laps. These stresses are determined by constructing models with photoelastic inner laps and transparent-acrylic outer laps. The connectors have two pins, in tandem, parallel to the load direction. A photoelastic-isotropic point is shown to permit the evaluation of load sharing between the two pins. A numerical scheme, utilizing the isochromatic- and isoclinic-photoelastic data and a finite-difference representation of the planestress equilibrium equations, is used to compute the stresses around the two pins. Representative stress distributions and stress-concentration factors are shown.     

PHOTOPHYSICAL BEHAVI0RS OF OLIGOMER BASED ON 1, 1′-BINAPHTHOL WITH 3, 3′-ACETYLENE SPACER*

The photophysical behaviors of the oligomer based on 1,1'-binaphthol with3,3'-acetylene spacer were investigated. The oligomer molecule has a naphthyl-acetylene-naphthyl effective conjugation segment. The atropic of the 1,1'-binaphthyl moiety led totwisted and rigid main chain in the oligomer. With the changes of the external environ-ment such as solvents used, solvent viscosity and ambient temperature, the wavelengthsof absorption and the intensities of fluorescence and absorption are changed slightly, butthe fluorescent intensity and quantum yield can be influenced. The luminescent behav-iors of the oligomer exhibit twisted intramolecular charge transfer characteristics, whichcould have a potential application in wavelength-stable light emitting material adaptableto ambient temperature and the solvents used in wide range.