Tight binding of the antitumor drug ditercalinium to quadruplex DNA

The structural selectivity of the DNA-binding antitumor drug ditercalinium was investigated by competition dialysis with a series of nineteen different DNA substrates. The 7H-pyridocarbazole dimer was found to bind to double-stranded DNA with a preference for GC-rich species but can in addition form stable complexes with triplex and quadruplex structures. The preferential interaction of the drug with four-stranded DNA structures was independently confirmed by electrospray mass spectrometry and a detailed analysis of the binding reaction was performed by surface plasmon resonance (SPR) spectroscopy. The BIAcore SPR study showed that the kinetic parameters for the interaction of ditercalinium with the human telomeric quadruplex sequence are comparable to those measured with a duplex sequence. Slow association and dissociation were observed with both the quadruplex and duplex structures. The newly discovered preferential binding of ditercalinium to the antiparallel quadruplex sequence d(AG(3)[T(2)AG(3)](3)) provides new perspectives for the design of drugs that can bind to human telomeres.     

Floor shape optimization for green building design

Shape is an important consideration in green building design due to its significant impact on energy performance and construction costs. This paper presents a methodology to optimize building shapes in plan using the genetic algorithm. The building footprint is represented by a multi-sided polygon. Different geometrical representations for a polygon are considered and evaluated in terms of their potential problems such as epistasis, which occurs when one gene pair masks or modifies the expression of other gene pairs, and encoding isomorphism, which occurs when chromosomes with different binary strings map to the same solution in the design space. Two alternative representations are compared in terms of their impact on computational effectiveness and efficiency. An optimization model is established considering the shape-related variables and several other envelope-related design variables such as window ratios and overhangs. Life-cycle cost and life-cycle environmental impact are the two objective functions used to evaluate the performance of a green building design. A case study is presented where the shape of a typical floor of an office building defined by a pentagon is optimized with a multi-objective genetic algorithm.     

Open-Source Model Checking

We present GMC², a software model checker for GCC, the open-source compiler from the Free Software Foundation (FSF). GMC², which is part of the GMC static-analysis and model-checking tool suite for GCC under development at SUNY Stony Brook, can be seen as an extension of Monte Carlo model checking to the setting of concurrent, procedural programming languages. Monte Carlo model checking is a newly developed technique that utilizes the theory of geometric random variables, statistical hypothesis testing, and random sampling of lassos in Büchi automata to realize a one- sided error, randomized algorithm for LTL model checking. To handle the function call/return mechanisms inherent in procedural languages such as C/C++, the version of Monte Carlo model checking implemented in GMC² is optimized for pushdown-automaton models. Our experimental results demonstrate that this approach yields an efficient and scalable software model checker for GCC.     

Dynamic diffusion model for tracing the real-time potential response of polymeric membrane ion-selective electrodes

A numerical solution for the prediction of the time-dependent potential response of a polymeric-based ion-selective electrode (ISE) is presented. The model addresses short- and middle-term potential drifts that are dependent on changes in concentration gradients in the aqueous sample and organic membrane phase. This work has important implications for the understanding of the real-time response behavior of potentiometric sensors with low detection limits and with nonclassical super-Nernstian response slopes. As a model system, the initial exposure of membranes containing the well-examined silver ionophore O,O' '-bis[2-(methylthio)ethyl]-tert-butylcalix[4]arene was monitored, and the large observed potential drifts were compared to theoretical predictions. The model is based on an approximate solution of the diffusion equation for both aqueous and organic diffusion layers using a numerical scheme (finite difference in time and finite elements in space). The model may be evaluated on the basis of experimentally available parameters and gives time-dependent information previously inaccessible with a simpler steady-state diffusion model. For the cases studied, the model gave a very good correlation with experimental data, albeit with lower than expected diffusion coefficients for the organic phase. This model may address numerous open questions regarding the response time and memory effects of low-detection-limit ion-selective electrodes and for other membrane electrodes where ion fluxes are relevant.     

Securing Pocket Hard Drives

Today, affordable storage media comes in various form factors with a wide range of capacities. USB is the most popular PC interface, offering data transfer rates as high as 480 Mbps (version 2.0), with enough power to operate storage devices such as 2.5" hard-disk drives. The Fire Wire interface offers similar capabilities. A few vendors offer software that lets users synchronize their email and network folders with USB storage. This lets them access these data items from several different computers. The U3 industry consortium promotes a model that lets users run programs, such as a Firefox Web browser, directly from the USB storage device, so users can access these applications even on PCs that don't have these applications preinstalled. Similarly, commonly used live CD-ROMs let you boot a PC from an OS resident on the CD-ROM. In this new mobile computing model called portable storage-based personalization, users can personalize a computer by booting from the USB storage media. Users' portable storage devices act as a pocket hard drive.     

Study of photoactivity of tungsten trioxide (WO3) for water splitting

The paper presents the properties of WO₃ films considering the possibility to build a photoelectrochemical cell (PECC) for hydrogen production. The photocurrent response of the PECC containing WO₃/TCO as photoanode and Pt as cathode was analysed. The morphology, crystalline structure and electrical aspects were investigated. Tungsten trioxide (WO₃) thin film with porous morphology and high crystallinity was obtained using the spray pyrolysis deposition technique.     

Evolutionary algorithms for continuous-space optimisation

From a global viewpoint, evolutionary algorithms (EAs) working on continuous search-spaces can be regarded as homogeneous Markov chains (MCs) with discrete time and continuous state. We analyse from this viewpoint the (1?+?1)EA on the inclined plane fitness landscape, and derive a closed-form expression for the probability of occupancy of an arbitrary target zone, at an arbitrary iteration of the EA. For the hitting-time of an arbitrary target zone, we provide lower and upper bounds, as well as an asymptotic limit. Discretization leads to an MC with discrete time, whose simple structure is exploited to carry out efficient numerical investigations of the theoretical results obtained. The numerical results thoroughly confirm the theoretical ones, and also suggest various conjectures which go beyond the theory.