Using eigenstructure of the Hessian to reduce the dimension of the intensity modulated radiation therapy optimization problem

Optimization is of vital importance when performing intensity modulated radiation therapy to treat cancer tumors. The optimization problem is typically large-scale with a nonlinear objective function and bounds on the variables, and we solve it using a quasi-Newton sequential quadratic programming method. This study investigates the effect on the optimal solution, and hence treatment outcome, when solving an approximate optimization problem of lower dimension. Through a spectral decompostion, eigenvectors and eigenvalues of an approximation to the Hessian are computed. An approximate optimization problem of reduced dimension is formulated by introducing eigenvector weights as optimization parameters, where only eigenvectors corresponding to large eigenvalues are included. The approach is evaluated on a clinical prostate case. Compared to bixel weight optimization, eigenvector weight optimization with few parameters results in faster initial decline in the objective function, but with inferior final solution. Another approach, which combines eigenvector weights and bixel weights as variables, gives lower final objective values than what bixel weight optimization does. However, this advantage comes at the expense of the pre-computational time for the spectral decomposition. A preliminary version of this paper was presented at the AAPM 46th annual meeting, held July 25–29, 2004 in Pittsburgh, PA.     

Texture of MFI films grown from seeds

This review describes how the texture of MFI films grown from seed crystal is developed during film preparation. Reports published during the last 5 years are in focus. Relative growth rates in various crystallographic directions, competitive growth, properties of the seed layer, defects, grain boundaries and other parameters influencing the film properties are discussed. Mathematical models describing competitive growth are also discussed. Suitable characterization methods for defects are described. The last part of the review is devoted to diffusion. Diffusion models accounting for texture in MFI films and the influence of texture on diffussion are discussed.     

Mechanically manipulating the DNA threading intercalation rate

The dumbbell shaped binuclear ruthenium complex DeltaDelta-P requires transiently melted DNA in order to thread through the DNA bases and intercalate DNA. Because such fluctuations are rare at room temperature, the binding rates are extremely low in bulk experiments. Here, single DNA molecule stretching is used to lower the barrier to DNA melting, resulting in direct mechanical manipulation of the barrier to DNA binding by the ligand. The rate of DNA threading depends exponentially on force, consistent with theoretical predictions. From the observed force dependence of the binding rate, we demonstrate that only one base pair must be transiently melted for DNA threading to occur.     

Photochemical modification and patterning of SU-8 using anthraquinone photolinkers

Bioactive protein patterns and microarrays achieved by selective localization of biomolecules find various applications in biosensors, bio-microelectromechanical systems (bio-MEMS), and in basic protein studies. In this paper we describe simple photochemical methods to fabricate two-dimensional patterns on a Novolac A derivative polymer (SU-8) and, subsequently, their functionalization with biomolecules. Anthraquinone (AQ) derivatives are used to chemically modify and pattern SU-8 surfaces. Features as small as 20 mum are obtained when using uncollimated light. The X-Y spatial resolution of micropatterned AQ molecules is improved to 1.5 mum when a collimated light source is used. This micropatterning process will be important for the functionalization of MEMS-based biosensors. The method saves several processing steps and can be integrated in cleanroom fabrication thus avoiding contamination of the sensor surfaces.     

Complex DNA binding kinetics resolved by combined circular dichroism and luminescence analysis

We recently reported that ruthenium complexes, with general structure [mu-bidppz(bipy)4Ru2](4+) (B) or [mu-bidppz(phen)4Ru2](4+) (P) (bidppz=11,11'-bi(dipyrido[3,2- a:2',3'-c]phenazinyl)), show extreme kinetic selectivity for long AT tracts over mixed-sequence calf thymus DNA (ct-DNA), a selectivity that also varies markedly with the size (between B and P) and sense of chirality of the complex. Earlier studies, exploiting the great increase in luminescence intensity when the compound intercalates, have yielded complex kinetics indicating the presence of both first- and second-order processes. Even with a homogeneous DNA sequence, such as poly(dAdT)2, the luminescence kinetics generally requires more than a single exponential for a satisfactory fit. We here reveal that at least part of the complexity is a result of the extreme sensitivity of the effective quantum yield of the complexes, so that the luminescence trajectories also reflect subtle variations in the environment and binding geometry that the complex is sampling on its path to its final binding site. By monitoring the rearrangement process using circular dichroism (CD), we show that threading of both enantiomers of B and P into poly(dAdT)2 is effectively a monoexponential process, as expected if the compounds are not affecting each other during the intercalation process. Thus, the complex luminescence trajectories may be explained by slow relaxations in the binding geometry (DNA conformation) and associated changes in the environment of the entering complexes. To further disentangle the intriguing features of the threading intercalation kinetics, and how they may depend on the flexibility and size of the ruthenium complexes, we have also designed and studied two new ruthenium complexes, [mu-dtpf(phen)4Ru2](4+) (F) (dtpf=4,5,9,12,16,17,21,25-octaaza-23 H-ditriphenyleno[2,3-b:2,3-h]fluorene), in which the bridging ligand is made totally rigid, and [mu-bidppz([12]aneS4) 2Ru2](4+) (S), which has less bulky, nonaromatic ancillary ligands. The threading of F into poly(dAdT)2, also found to be a monoexponential process, is about 3 times slower than for P, indicating that the flexibility of the bridging ligand is an important factor for the intercalation rate. Surprisingly, in contrast to all other compounds, S requires two exponentials to fit its binding kinetics as monitored by CD. Also surprisingly, in view of the smaller steric bulk, even the fastest phase is roughly 2 times slower for S than for B and P. Thus, not only the size of the ancillary ligand but also other properties that can influence the energy landscape of the threading path are rate-determining factors. With mixed-sequence ct-DNA, threading of B and that of P are both multiphasic processes when monitored with CD as well as with luminescence. The rate constants for threading into ct-DNA show much larger variations between complexes than for poly(dAdT)2, confirming earlier results based on luminescence data.     

SPE and HPLC/UV of resin acids in colophonium-containing products

A new method, involving SPE and HPLC/UV diode-array detection (DAD), was developed for the quantification of colophonium components in different consumer products, such as cosmetics. Colophonium is a common cause of contact dermatitis since its components can oxidize into allergens on exposure to air. Three different resin acids were used as markers for native and oxidized colophonium, abietic acid (AbA), dehydroabietic acid (DeA), and 7-oxodehydroabietic acid (7-O-DeA). The SPE method, utilizing a mixed-mode hydrophobic and anion exchange retention mechanism, was shown to yield very clean extracts. The use of a urea-embedded C(12) HPLC stationary phase improved the separation of the resin acids compared to common C(18). Concentrations higher than 2 mg/g of both AbA and DeA were detected in wax strips. In this product also 7-O-DeA, a marker for oxidized colophonium, was detected at a level of 28 microg/g. The LODs were in the range of 7-19 microg/g and the LOQs 22-56 microg/g. The method is simple to use and can be applied on many types of technical products, not only cosmetics. For the first time, a method for technical products was developed, which separates AbA from pimaric acid.     

Front Cover: Dynamic Covalent Chemistry for Synthesis and Co-conformational Control of Mechanically Interlocked Molecules (Eur. J. Org. Chem. 8/2023)

Mechanically interlocked molecules have found extensive applications in areas all across the physical sciences, from materials to catalysis and sensing. However, introducing mechanical bonds and entanglements at the molecular level is still a significant challenge due to the inherent restriction in entropy needed to preorganize strands before interlocking. Over the last decade, dynamic covalent chemistry has emerged as one of the most efficient methods of forming rotaxanes, catenanes and molecular knots. By using reversible bonds such as imines, disulfides and boronate esters, one can use the inherent error-correction in these linkages to form interlocked architectures with high fidelity and often in excellent yields. This review reports on recent advances in the use of dynamic covalent chemistry to make mechanically interlocked molecules, systematically surveying clipping, capping and templating approaches with dynamic bonds. Furthermore, it is also discussed how dynamic bonds can be used to control motion, co-conformational expression and catalytic activity in mechanically interlocked molecular machinery.     

Computer screen photo-excited surface plasmon resonance imaging

Angle and spectra resolved surface plasmon resonance (SPR) images of gold and silver thin films with protein deposits is demonstrated using a regular computer screen as light source and a web camera as detector. The screen provides multiple-angle illumination, p-polarized light and controlled spectral radiances to excite surface plasmons in a Kretchmann configuration. A model of the SPR reflectances incorporating the particularities of the source and detector explain the observed signals and the generation of distinctive SPR landscapes is demonstrated. The sensitivity and resolution of the method, determined in air and solution, are 0.145 nm pixel⁻¹, 0.523 nm, 5.13 × 10⁻³ RIU degree⁻¹ and 6.014 × 10⁻⁴ RIU, respectively, encouraging results at this proof of concept stage and considering the ubiquity of the instrumentation.     

Liquid crystalline phases and their dispersions in aqueous mixtures of glycerol monooleate and glyceryl monooleyl ether

The aqueous phase behavior of mixtures of 1-glycerol monooleate (GMO) and its ether analogue, 1-glyceryl monooleyl ether (GME) has been investigated by a combination of polarized microscopy, X-ray diffraction, and NMR techniques. Three phase diagrams of the ternary GMO/GME/water system have been constructed at 25, 40, and 55 degrees C. The results demonstrate that the increasing amount of GME favors the formation of the reversed phases, evidenced by the transformation of the lamellar and bicontinuous cubic liquid crystalline phases of the binary GMO/water system into reversed micellar or reversed hexagonal phases. For a particular liquid crystalline phase, increasing the GME content has no effect on the structural characteristics and hydration properties, thus suggesting ideal mixing with GMO. Investigations of dispersed nanoparticle samples using shear and a polymeric stabilizer, Pluronic F127, show the possibility of forming two different kinds of bicontinuous cubic phase nanoparticles by simply changing the GMO/GME ratio. Also NMR self-diffusion measurements confirm that the block copolymer, Pluronic F127, used to facilitate dispersion formation, is associated with nanoparticles and provides steric stabilization.     

Molecular dynamics of a biodegradable biomimetic ionomer studied by broadband dielectric spectroscopy

Broadband dielectric spectroscopy was used to investigate the bulk molecular dynamics of a recently developed biodegradable biomimetic ionomer potentially useful for biomedical applications. Isothermal dielectric spectra were gathered for a phosphoryl choline (PC)-functionalized poly(trimethylene carbonate) (PTMC) ionomer and unfunctionalized PTMC at temperatures ranging from 2 to 60 degrees C over a broad frequency range of 10(-3) to 10(6) Hz. Four relaxations were clearly identified, two of which were shown to stem from the PTMC polymer backbone. A detailed analysis showed that the formation of zwitterionic aggregates was responsible for the material's bulk functionality and that bulk conduction processes may provide useful information for assessing the PC ionomer as a candidate for drug delivery applications. Finally, it was concluded that absorbed water concentrates around the aggregates, resulting in an increased mobility of the PC end-groups.