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PubMedDate not supplied

[Homeostasis of the auto-oscillation period in a model of a cellular circadian clock].

A mathematical model was numerically investigated which describes the autooscillatory temporal organization of futile cycles of the carbohydrate branch of energy metabolism. Using an optimization method we found a region in the parametric space of the model in which the circadian oscillation period was practically constant, although the major eight parameters varied in a wide range. Such homeostasis of the period is due to synergistic effects of the four feed-back mechanisms regulating activities of the key enzymes. The result obtained supports the metabolic theory of the circadian cell clock.

Carbohydrate Metabolism↗

PubMed2003

First X-ray characterization and theoretical study of pi-alkyne, alkynyl-hydride, and vinylidene isomers for the same transition metal fragment [Cp*Ru(PEt3)2]+.

The reaction of the chloro-complex [CpRuCl(PEt(3))(2)] with acetylene gas in methanol gave the pi-alkyne complex [CpRu(eta(2)-HCtbd1;CH)(PEt(3))(2)][BPh(4)] (1), which has been structurally characterized by X-ray analysis. The alkyne complex undergoes spontaneous isomerization even at low temperature, yielding the metastable alkynyl-hydride complex [CpRu(H)(Ctbd1;CH)(PEt(3))(2)][BPh(4)] (2), as the result of the oxidative addition of the alkyne C-H bond. This compound has also been structurally characterized despite it tautomerizes spontaneously into the stable primary vinylidene [CpRu(=C=CH(2))(PEt(3))(2)][BPh(4)] (3). This species has been alternatively prepared by a two-step deprotonation/protonation synthesis from the pi-alkyne complex. Moreover, the reaction of the initial chloro-complex with monosubstituted alkynes HCtbd1;CR (R = SiMe(3), Ph, COOMe, (t)Bu) has been studied without detection of pi-alkyne intermediates. Instead of this, alkynyl-hydride complexes were obtained in good yields. They also rearrange to the corresponding substituted vinylidenes. In the case of R = SiMe(3), the isomerization takes place followed by desilylation, yielding the primary vinylidene complex. X-ray crystal structures of the vinylidene complexes [CpRu(=C=CH(2))(PEt(3))(2)][BPh(4)] (3) and [CpRu(=C=CHCOOMe)(PEt(3))(2)][BPh(4)] (10) have also been determined. Both, full ab initio and quantum mechanics/molecular mechanics (QM/MM) calculations were carried out, respectively, on the model system [CpRu(C(2)H(2))(PH(3))(2)](+) (A) and the real complex [CpRu(C(2)H(2))(PEt(3))(2)](+) (B) to analyze the steric and electronic influence of ligands on the structures and relative energies of the three C(2)H(2) isomers. QM/MM calculations have been employed to evaluate the role of the steric effects of real ligands, whereas full ab initio energy calculations on the optimized QM/MM model have allowed recovering the electronic effects of ligands. Additional pure quantum mechanics calculations on [CpRu(C(2)H(2))(PH(3))(2)](+) (C) and [CpRu(C(2)H(2))(PMe(3))(2)](+) (D) model systems have been performed to analyze in more detail the effects of different ligands. Calculations have shown that the steric effects induced by the presence of bulky substituents in phosphine ligand are responsible for experimentally observed alkyne distortion and for relative destabilization of the alkyne isomer. Moreover, increasing the phosphine basicity and sigma donor capabilities of ligands causes a relative stabilization of an alkynyl-hydride isomer. The combination of both steric and electronic effects, makes alkyne and alkynyl-hydride isomers to be close in energy, leading to the isolation of both complexes.

Journal Article↗

PubMed2002

Optimality in the developing vascular system: branching remodeling by means of intussusception as an efficient adaptation mechanism.

The theory of bifurcating vascular systems predicts vessel diameters that are related to optimality criteria like minimization of pumping energy or of building material. However, mechanisms for producing the postulated optimality have not been described so far, and quantitative data on bifurcation diameters during development are scarce. We used an embryonic vascular bed that rapidly grows and adapts to changing hemodynamic conditions, the chicken chorioallantoic membrane (CAM), and correlated vascular cast and tissue section morphology with in vivo time-lapse video monitoring. The bifurcation exponent delta and associated parameters were quantitatively assessed in arterial and venous microvessels ranging in diameter from 30 to 100 microm. We observed emergence of optimality by means of intussusception, i.e., formation of transvascular tissue pillars. In addition to intussusceptive microvascular growth (IMG = expansion of capillary networks) and intussusceptive arborization (IAR = formation of feeding vessels from capillaries) the observed intussusception at bifurcations represents a third variant of nonsprouting angiogenesis. We call it intussusceptive branching remodeling (IBR). IBR occurred in vessels of considerable diameter by means of two alternative mechanisms: either through pillars arising close to a bifurcation, which increased in girth until they merged with the connective tissue in the bifurcation angle; or through pillars arising at some distance from the bifurcation point, which then expanded by formation of ingrowing tissue folds until they became connected to the tissue of the bifurcation angle. Morphologic evidence suggests that IBR is a wide-spread phenomenon, taking place also in lung, intestinal, kidney, eye, etc., vasculature. Irrespective of the mode followed, IBR led to a branching pattern close to the predicted optimum, delta = 3.0. Significant differences were observed between delta at arterial bifurcations (2.70 to 2.90) and delta at venous bifurcations (2.93 to 3.75). IBR, by means of eccentric pillar formation and fusion, was also involved in vascular pruning. Experimental changes in CAM hemodynamics (by locally increasing blood flow) induced onset of IBR within less than 1 hr. Our study provides morphologic and quantitative evidence that a similar cellular machinery is used for all three variants of vascular intussusception, IMG, IAR, and IBR. It thus provides a mechanism of efficiently generating complex blood transport systems from limited genetic information. Differential quantitative outcome of IBR in arteries and veins, and the experimental induction of IBR strongly suggest that hemodynamic factors can instruct embryonic vascular remodeling toward optimality.

Allantois↗

PubMed2003

On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations.

Using molecular mechanics force field partial atomic charges, we show the nonuniqueness of the parametrization of continuum electrostatics models with respect to solute atomic radii and interior dielectric constant based on hydration (vacuum-to-water transfer) free energy data available for small molecules. Moreover, parameter sets that are optimal and equivalent for hydration free energy calculations lead to large variations of calculated absolute and relative electrostatic binding free energies. Hence, parametrization of solvation effects based on hydration data, although a necessary condition, is not sufficient to guarantee its transferability to the calculation of binding free energies in solution.

Journal Article↗

PubMed2004

'Optimal' vortex rings and aquatic propulsion mechanisms.

Fishes swim by flapping their tail and other fins. Other sea creatures, such as squid and salps, eject fluid intermittently as a jet. We discuss the fluid mechanics behind these propulsion mechanisms and show that these animals produce optimal vortex rings, which give the maximum thrust for a given energy input. We show that fishes optimize both their steady swimming efficiency and their ability to accelerate and turn by producing an individual optimal ring with each flap of the tail or fin. Salps produce vortex rings directly by ejecting a volume of fluid through a rear orifice, and these are also optimal. An important implication of this paper is that the repetition of vortex production is not necessary for an individual vortex to have the 'optimal' characteristics.

Animals↗

PubMed1996

Control of the dehydration process in production of intermediate-moisture meat products: a review.

IM meat products are produced by lowering the aw to 0.90 to 0.60. Such products are stable at ambient temperature and humidity and are produced in nearly every country in the world, especially in developing areas where refrigeration is limited or unavailable. Traditionally IM meats use low cost sources of energy for drying, such as sun drying, addition of salt, or fermentation. Products produced by different processes are of interest since they do not require refrigeration during distribution and storage. Many different IM meat products can be produced by utilizing modern processing equipment and methods. Production can be achieved in a relatively short period of time and their advantages during marketing and distribution can be utilized. Nevertheless, a better understanding of the principles involved in heat transfer and efficiency of production are still needed to increase efficiency of processing. A basic understanding of the influence of water vapor pressure and sorption phenomena on water activity can materially improve the efficiency of drying of IM meats. Predrying treatments, such as fermentation and humidity control, can also be taken advantage of during the dehydration process. Such information can lead to process optimization and reduction of energy costs during production of IM meats. The development of sound science-based methods to assure the production of high-quality and nutritious IM meats is needed. Finally, such products also must be free of pathogenic microorganisms to assure their success in production and marketing.

Absorption↗

PubMed1994

Comparison of radiation dosimetry in water and in solid phantom materials for I-125 and Pd-103 brachytherapy sources: EGS4 Monte Carlo study.

A model based on the EGS4 Monte Carlo system is developed for calculating dose rate to water from an embedded low-energy brachytherapy source, given measurement data of dose rate to water within a water-substitute solid phantom for a source of given strength. The EGS4-based model is used to calculate point source dose rate distributions per unit source strength for water and for several species of solid phantoms. As a model for the dose rate distribution to an infinitesimal water inhomogeneity embedded in the solid phantom, the Monte Carlo is used to calculate dose rate to a thin spherical shell of water contained within the solid phantom at various distances centered on the source. Comparing this distribution to that calculated for a homogeneous water phantom, one can derive correction factors to determine dose rate to homogeneous water medium from measurements with water dose-calibrated detectors within the solid phantom. These factors are calculated for polymethylmethacrylate (PMMA or acrylic), solid water (WT1), and RW-1, a material optimized for low-energy dosimetry, with photon spectra from Pd-103 and from two commercial models of I-125 seed used as input. For model 6711 I-125 seeds at 1 cm in PMMA and WT1, the calculated ratios of dose rate to water to dose rate to water in the solid phantom are 0.893 and 1.038, respectively. Applying these factors to published, apparently divergent measurements of the specific dose rate constant based on measurements in PMMA and WT1 phantoms, the specific dose rate constant inferred for the model 6711 seed are found to be in excellent agreement: 0.878 cGy h-1U-1 (1.115 cGy- cm2h-1mCi-1) from the mean of the WT1 measurements and 0.879 cGy h-1U-1 from the PMMA measurements. Among the phantoms studied for Pd-103 and I-125, measurements in RW-1 would most closely approximate those for water.

Biophysical Phenomena↗

PubMed2001

What are the dielectric "constants" of proteins and how to validate electrostatic models?

Implicit models for evaluation of electrostatic energies in proteins include dielectric constants that represent effect of the protein environment. Unfortunately, the results obtained by such models are very sensitive to the value used for the dielectric constant. Furthermore, the factors that determine the optimal value of these constants are far from being obvious. This review considers the meaning of the protein dielectric constants and the ways to determine their optimal values. It is pointed out that typical benchmarks for validation of electrostatic models cannot discriminate between consistent and inconsistent models. In particular, the observed pK(a) values of surface groups can be reproduced correctly by models with entirely incorrect physical features. Thus, we introduce a discriminative benchmark that only includes residues whose pK(a) values are shifted significantly from their values in water. We also use the semimacroscopic version of the protein dipole Langevin dipole (PDLD/S) formulation to generate a series of models that move gradually from microscopic to fully macroscopic models. These include the linear response version of the PDLD/S models, Poisson Boltzmann (PB)-type models, and Tanford Kirkwwod (TK)-type models. Using our different models and the discriminative benchmark, we show that the protein dielectric constant, epsilon(p), is not a universal constant but simply a parameter that depends on the model used. It is also shown in agreement with our previous works that epsilon(p) represents the factors that are not considered explicitly. The use of a discriminative benchmark appears to help not only in identifying nonphysical models but also in analyzing effects that are not reproduced in an accurate way by consistent models. These include the effect of water penetration and the effect of the protein reorganization. Finally, we show that the optimal dielectric constant for self-energies is not the optimal constant for charge-charge interactions.

Ions↗

PubMed1991

[Lactose--a potential dietary fiber. The regulation of its microecologic effect in the intestinal tract. 4. Dietary fiber action of lactose: evaluation with multivariate statistical analysis].

The conditions and the intestinal processes responsible for the action of lactose as a potential dietary fibre are described. The beta-galactosidase activity in the rat caecum and colon is influenced by dietary factors: It declines with increasing lactose concentration and it rises with increasing protein and phosphate concentration in the diet. The enzyme activity correlates negatively with the content of lactose, and positively with the content of protein and phosphate in the chymus. The products of lactose hydrolysis are degraded by microbial glycolysis in caecum and colon. The glycolytic products are mainly absorbed and energetically utilized by the macroorganism. Phosphate stimulates the microbial metabolism and, therefore, accelerates the consumption of the energy substrate lactose. Mathematical optimization gives the necessary composition of the diet which causes an intended microecological effect. To minimize the chymus pH (5.1 in the colon ascendens; 4.6 in the colon descendens; 4.3 in the faeces) the lactose content of the diet has to be greater than or equal to 160 mumol/g, the protein content less than or equal to 10 mg/g, and the phosphate content less than or equal to 5.5 mumol/g. The minimal pH value depends to a greater extent on variations in the supply of protein and phosphorus with the diet whereas the response to changes in lactose concentration is less noticeable.

Animals↗

PubMed2006

Active control of passive acoustic fields: passive synthetic aperture/Doppler beamforming with data from an autonomous vehicle.

The maneuverability of autonomous underwater vehicles (AUVs) equipped with hull-mounted arrays provides the opportunity to actively modify received acoustic fields to optimize extraction of information. This paper uses ocean acoustic data collected by an AUV-mounted two-dimensional hydrophone array, with overall dimension one-tenth wavelength at 200-500 Hz, to demonstrate aspects of this control through vehicle motion. Source localization is performed using Doppler shifts measured at a set of receiver velocities by both single elements and a physical array. Results show that a source in the presence of a 10-dB higher-level interferer having exactly the same frequency content (as measured by a stationary receiver) is properly localized and that white-noise-constrained adaptive beamforming applied to the physical aperture data in combination with Doppler beamforming provides greater spatial resolution than physical-aperture-alone beamforming and significantly lower sidelobes than single element Doppler beamforming. A new broadband beamformer that adjusts for variations in vehicle velocity on a sample by sample basis is demonstrated with data collected during a high-acceleration maneuver. The importance of including the cost of energy expenditure in determining optimal vehicle motion is demonstrated through simulation, further illustrating how the vehicle characteristics are an integral part of the signal/array processing structure.

Acoustics↗

PubMed2000

Optimizing the window size for multiple least squares fitting of electron energy loss spectra.

The purpose of this study was to determine the effect of the fitting window size used with the linear least squares fit method when quantitating trace elements with electron energy loss spectroscopy. Theory and computer simulation with a simple model of two 'signals' show that, when the background underlying the signal is slowly varying and the signal is localized, there exists a minimum window optimal for fitting raw spectra. The width of the minimum fitting window can be determined directly from the reference standard spectrum of the signal alone and the estimates of signal and background are related. Use of narrower than the minimum window will increase the fitting uncertainty of the signal and yield less reliable results. More complicated experimental spectra must be fitted to more than two standards and a simple analytical expression of the minimum fitting window cannot be derived, but can be determined empirically. Our study shows that the empirical value obtained from experimental spectra is only slightly larger than the theoretical value derived from the simple model, indicating that this conclusion is still valid. When fitting difference spectra with a slowly varying background, the estimates of signal and background are independent and windows wider than the size of the signal will yield the same fitting uncertainty. In the presence of a non-slowly varying background, common in difference spectra, the minimum window size depends on the fine structure of the signal and the background.

Calcium↗

PubMed2003

A systematic study of techniques for elective cervical nodal irradiation with anterior or opposed anterior and posterior beams.

PURPOSE: To assess target coverage and dose homogeneity using conventional radiotherapy (RT) and intensity-modulated RT (IMRT) with anterior and posterior beams for elective irradiation of the cervical lymph nodes in patients with head and neck cancer. MATERIALS AND METHODS: A planning study was performed in six patients who had undergone radical RT for head and neck cancer. RT plans to irradiate the cervical lymph nodes using a single anterior field, or opposed anterior and posterior fields, with 6 or 10 MV photons were compared. Plans using IMRT for missing-tissue compensation were also studied. An algorithm was developed to guide clinicians to the most appropriate treatment technique depending on the nodal groups to be irradiated. RESULTS: With 6 MV single field (SF) irradiation significant under-dose (minimum dose <70% of prescription dose) was seen in nodal groups II and V, due to their posterior position. With SF 10 MV the mean dose to level II was higher (p<0.001) and dose homogeneity to levels Ib and II was improved. Using opposed fields (OF), minimum doses to the nodes in levels II and V were improved. OF using 10 MV showed significant advantage over 6 MV with reduction of maximum doses to levels II, III and V. SF 10 MV IMRT improved maximum doses to levels Ib and II compared to SF 6 MV IMRT. OF IMRT gave the best dose distributions with optimal mean dose and dose homogeneity. Beam energy made no difference with OF IMRT. CONCLUSIONS: The optimal technique for elective cervical node irradiation depends on the lymph node levels within the PTV. If irradiation of the level II or V nodes is required, then the OF IMRT technique with either 6 or 10 MV gives the best dose distributions. In the absence of IMRT, then OF conventional techniques are best. If the aim is to irradiate levels III and IV or level IV only, then 6 MV SF non-IMRT is the simplest technique.

Algorithms↗

PubMed2002

Universality classes for self-avoiding walks in a strongly disordered system.

We study the behavior of self-avoiding walks (SAWs) on square and cubic lattices in the presence of strong disorder. We simulate the disorder by assigning random energy epsilon taken from a probability distribution P(epsilon) to each site (or bond) of the lattice. We study the strong disorder limit for an extremely broad range of energies with P(epsilon) is proportional to 1/epsilon. For each configuration of disorder, we find by exact enumeration the optimal SAW of fixed length N and fixed origin that minimizes the sum of the energies of the visited sites (or bonds). We find the fractal dimension of the optimal path to be d(opt)=1.52+/-0.10 in two dimensions (2D) and d(opt)=1.82+/-0.08 in 3D. Our results imply that SAWs in strong disorder with fixed N are much more compact than SAWs in disordered media with a uniform distribution of energies, optimal paths in strong disorder with fixed end-to-end distance R, and SAWs on a percolation cluster. Our results are also consistent with the possibility that SAWs in strong disorder belong to the same universality class as the maximal SAW on a percolation cluster at criticality, for which we calculate the fractal dimension d(max)=1.64+/-0.02 for 2D and d(max)=1.87+/-0.05 for 3D, values very close to the fractal dimensions of the percolation backbone in 2D and 3D.

Journal Article↗

PubMed2004

Minimizing energy below the glass thresholds.

Focusing on the optimization version of the random K -satisfiability problem, the MAX- K -SAT problem, we study the performance of the finite energy version of the survey propagation algorithm. We show that a simple (linear time) backtrack decimation strategy is sufficient to reach configurations well below the lower bound for the dynamic threshold energy and very close to the analytic prediction for the optimal ground states. A comparative numerical study on one of the most efficient local search procedures is also given.

Journal Article↗

PubMed2005

Optimal position estimation for the automatic alignment of a high-energy laser.

The alignment of high-energy laser beams for potential fusion experiments demands high precision and accuracy by the underlying positioning algorithms whether it be for actuator control or for monitoring the beam line for potential anomalies. The feasibility of employing on-line optimal position estimators in the form of model-based processors to achieve the desired results is examined. We discuss the modeling, the development, the implementation, and the processing of model-based processors applied to both simulated and actual beamline data.

Journal Article↗

PubMed1995

Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis.

Fluorescent dye-labeled DNA primers have been developed that exploit fluorescence energy transfer (ET) to optimize the absorption and emission properties of the label. These primers carry a fluorescein derivative at the 5' end as a common donor and other fluorescein and rhodamine derivatives attached to a modified thymidine residue within the primer sequence as acceptors. Adjustment of the donor-acceptor spacing through the placement of the modified thymidine in the primer sequence allowed generation of four primers, all having strong absorption at a common excitation wavelength (488 nm) and fluorescence emission maxima of 525, 555, 580, and 605 nm. The ET efficiency of these primers ranges from 65% to 97%, and they exhibit similar electrophoretic mobilities by gel electrophoresis. With argon-ion laser excitation, the fluorescence of the ET primers and of the DNA sequencing fragments generated with ET primers is 2- to 6-fold greater than that of the corresponding primers or fragments labeled with single dyes. The higher fluorescence intensity of the ET primers allows DNA sequencing with one-fourth of the DNA template typically required when using T7 DNA polymerase. With single-stranded M13mp18 DNA as the template, a typical sequencing reaction with ET primers on a commercial sequencer provided DNA sequences with 99.8% accuracy in the first 500 bases. ET primers should be generally useful in the development of other multiplex DNA sequencing and analysis methods.

Bacteriophage M13↗

PubMed1986

Indo-mo investigation of gas-phase acidities of carbamates and thiocarbamates.

Gas-phase anion proton affinities of carbamic (I), thiol- (II), thio- (III) and dithiocarbamic (IV) acids are calculated by the INDO-MO method employing energy gradients for full geometry optimizations. The effect of d-type functions on sulphur on the calculated proton affinities has been examined. Detailed energy partitioning analysis enabled a much better understanding of the protonation process. Energetics of the isomerization II --> III have been computed and discussed.

Journal Article↗

PubMedDate not supplied

Enhancement of electron beam dose distributions by longitudinal magnetic fields: Monte Carlo simulations and magnet system optimization.

A Monte Carlo electron-photon transport code was developed in order to determine the effects of static, longitudinal, magnetic fields on dose distributions produced by high-energy electron beams, and to optimize the design of a superconducting magnet system. As a result of these simulations, a 20-cm-i.d., 30-cm-o.d., 15-cm-tall, single-coil, magnet system was designed that could be incorporated into a mobile treatment table for use with a standard radiation therapy accelerator. Operating at a current density of 18 kA/cm2, the magnet would produce field strengths of 1-4 T in the phantom and 0.01 T at the accelerator exit window. Magnetically enhanced dose distributions, calculated for 20- and 30-MeV electron beams, show a pronounced Bragg peak, steeper gradients to the sides and rear, and a roughly fourfold increase in the peak dose to entrance dose ratios relative to those similarly calculated without a magnetic field. These magnetically enhanced dose distributions have the potential for sparing intervening tissue when high-energy electrons are used for the treatment of deep-seated tumors.

Electrons↗