Automated estimation of rare event probabilities in biochemical systems

In biochemical systems, the occurrence of a rare event can be accompanied by catastrophic consequences. Precise characterization of these events using Monte Carlo simulation methods is often intractable, as the number of realizations needed to witness even a single rare event can be very large. The weighted stochastic simulation algorithm (wSSA) [J. Chem. Phys. 129, 165101 (2008)] and its subsequent extension [J. Chem. Phys. 130, 174103 (2009)] alleviate this difficulty with importance sampling, which effectively biases the system toward the desired rare event. However, extensive computation coupled with substantial insight into a given system is required, as there is currently no automatic approach for choosing wSSA parameters. We present a novel modification of the wSSA--the doubly weighted SSA (dwSSA)--that makes possible a fully automated parameter selection method. Our approach uses the information-theoretic concept of cross entropy to identify parameter values yielding minimum variance rare event probability estimates. We apply the method to four examples: a pure birth process, a birth-death process, an enzymatic futile cycle, and a yeast polarization model. Our results demonstrate that the proposed method (1) enables probability estimation for a class of rare events that cannot be interrogated with the wSSA, and (2) for all examples tested, reduces the number of runs needed to achieve comparable accuracy by multiple orders of magnitude. For a particular rare event in the yeast polarization model, our method transforms a projected simulation time of 600 years to three hours. Furthermore, by incorporating information-theoretic principles, our approach provides a framework for the development of more sophisticated influencing schemes that should further improve estimation accuracy.     

Graft copolymer directed synthesis of micron-thick organized mesoporous TiO2 films for solid-state dye-sensitized solar cells

Micron thick, well-organized mesoporous TiO(2) films with high porosity and good connectivity were synthesized by templating an amphiphilic graft copolymer for solid-state dye-sensitized solar cells.     

Highly efficient triplet chain isomerization of Dewar benzenes: adiabatic rate constants from cage kinetics

Quantum yields as high as 120 were achieved for triplet-sensitized photoisomerizations of several Dewar benzene reactants, R, to the corresponding benzene products, P. Considerable chain amplification is maintained even at high conversion. All relevant rate constants of this triplet chain reaction were extracted from laser flash photolysis plus steady-state photolysis experiments. The crucial rate constant ka for adiabatic isomerization of the triplet reactant to triplet product (R* --> P*) cannot be directly measured because it is so large relative to the bimolecular rate of R* formation via sensitization. However, ka was obtained indirectly using a cage/encounter complex model to analyze the competition between the dissociation of encounter pairs with the sensitizer, e.g., S/R* --> S + R*, and the in-cage processes, S/R* --> S/P* --> S*/P, in nonviscous and viscous solvents. These measurements yielded ka values of (approximately 4-9) x 10(9) s(-1), which suggests that only a small (approximately 3 kcal/mol) energy barrier exists along the potential energy surface from R* to P*. Steady-state data indicated that the chain-terminating rate constant R* --> R is negligibly small, an ideal condition for chain amplification. Triplet energy transfer from a series of sensitizers to the Dewar benzene derivatives shows a nonclassical falloff in rate constants with decreasing sensitizer triplet energy, suggesting energy transfer to thermally distorted configurations having lower singlet-triplet energy gaps. As a result of distorted geometries of R* and P*, the chain-propagating energy transfer from P* to R proceeds with a rate constant of only approximately 2 x 10(7) M(-1) s(-1), despite strong exothermicity. The isomerization reaction can release over 100 kcal/kcal of absorbed photons due to the high-energy content of the reactant together with the large chain length.     

On fuzzy B-algebras

The fuzzification of (normal) B-subalgebras is considered, and some related properties are investigated. A characterization of a fuzzy B-algebra is given.     

Future Direction for a Diffusion Barrier in Future High-Density Volatile and Nonvolatile Memory Devices

This article reviews the current status of high-density capacitor for volatile memory devices. The dielectric properties for both the Ta₂O₅ film and the (Ba, Sr)TiO₃ (BST) dielectric materials using either the metal organic chemical vapor deposition (MOCVD) or the atomic layer deposition (ALD) are reviewed briefly. New challenges of dielectric material for the next generation, and serious problems emerged during integration to date using Ta₂O₅ and BST. The material characteristics of many electrode materials for the high dielectric materials are introduced. We present the basic properties and integration issued for MOCVD-ruthenium (Ru). The second part of this review summarized the failure mechanisms from barrier properties of previously reported diffusion barriers and emphasizes new design concepts of diffusion barrier for high-density memory devices. Finally, the future direction for a diffusion barrier to advance high-density memory capacitors is suggested.     

Determination of acoustic attenuation in the Hudson River Estuary by means of ship noise observations

Analysis of sound propagation in a complex urban estuary has application to underwater threat detection systems, underwater communication, and acoustic tomography. One of the most important acoustic parameters, sound attenuation, was analyzed in the Hudson River near Manhattan using measurements of acoustic noise generated by passing ships and recorded by a fixed hydrophone. Analysis of the ship noise level for varying distances allowed estimation of the sound attenuation in the frequency band of 10-80 kHz. The effective attenuation coefficient representing the attenuation loss above cylindrical spreading loss had only slight frequency dependence and can be estimated by the frequency independent value of 0.058 dBm.     

Water-stable biphasic nanocolloids with potential use as anisotropic imaging probes

Electrified co-jetting of two aqueous polymer solutions followed by a thermal cross-linking step was used to create water-stable biphasic nanocolloids. For this purpose, aqueous solution mixtures of poly(acrylamide-co-acrylic acid) and poly(acrylic acid) were employed as jetting solutions. When the biphasic nanocolloids created by side-by-side electrified co-jetting were thermally treated, a cross-linking reaction occurred between amide groups and carboxylic groups to form stable imide groups. Infrared spectroscopy was employed to monitor the reaction. The quality and the integrity of the resulting biphasic nanocolloids were confirmed by confocal laser scanning microscopy, flow cytometry analysis, and dynamic light scattering. Selective encapsulation of two biomolecules in each phase of the biphasic colloids was maintained even after thermal reaction and suspension in aqueous environment. Well-dispersed spherical colloids with stable dye loadings in each hemisphere were kept intact without aggregation or dissolution for several weeks. Finally, biphasic nanocolloids were selectively surface-modified with a biotin-dextran resulting in water-stable particles to ensure binding of proteins only to a single hemisphere.     

Curcumin Loaded Dendrimers Specifically Reduce Viability of Glioblastoma Cell Lines

Glioblastoma (GB) is a deadly and aggressive cancer of the CNS. Even with extensive resection and chemoradiotherapy, patient survival is still only 15 months. To maintain growth and proliferation, cancer cells require a high oxidative state. Curcumin, a well-known anti-inflammatory antioxidant, is a potential candidate for treatment of GB. To facilitate efficient delivery of therapeutic doses of curcumin into cells, we encapsulated the drug in surface-modified polyamidoamine (PAMAM) dendrimers. We studied the in vitro effectiveness of a traditional PAMAM dendrimer (100% amine surface, G4 NH₂), surface-modified dendrimer (10% amine and 90% hydroxyl-G4 90/10-Cys), and curcumin (Cur)-encapsulated dendrimer (G4 90/10-Cys-Cur) on three species of glioblastoma cell lines: mouse-GL261, rat-F98, and human-U87. Using an MTT assay for cell viability, we found that G4 90/10-Cys-Cur reduced viability of all three glioblastoma cell lines compared to non-cancerous control cells. Under similar conditions, unencapsulated curcumin was not effective, while the non-modified dendrimer (G4 NH₂) caused significant death of both cancerous and normal cells. By harnessing and optimizing the components of PAMAM dendrimers, we are providing a promising new route for delivering cancer therapeutics. Our results with curcumin suggest that antioxidants are good candidates for treating glioblastoma.