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Results for “energy optimization”

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PubMed2001

Designability of lattice model heteropolymers.

Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20-letter lattice model of proteins which, relying only on the central limit theorem, has a generality which goes beyond the simple model used in its derivation. This expression displays an exponential dependence on the energy of the optimal sequence folding on the given conformation measured with respect to the lowest energy of the conformational dissimilar structures, an energy difference which constitutes the only parameter controlling designability. Accordingly, the designability of a native conformation is intimately connected to the stability of the sequences folding to them.

Algorithms↗

PubMed1986

Recognition of spectral patterns in the green treefrog: neurobiology and evolution.

The natural communication behavior of frogs has provided a framework for studying both the mechanisms and evolution of sound pattern recognition. In the green treefrog behavioral studies using synthetic stimuli have identified the pertinent acoustic properties of its complex but stereotyped vocal signals. There are two optimal frequency bands: the most effective signals have about the same amount of energy in the two bands. Neurophysiological studies revealed biases for these two frequency bands at the level of the peripheral auditory system. Furthermore, the neural response properties in an auditory thalamic area are especially well correlated with selective phonotaxis based on the appropriate combination of low- and high-frequency sound energy. Comparing the optimal frequency bands in terms of female preferences with the range of frequencies produced by males in natural populations suggests that intraspecific mate choice based on call frequency alone is unlikely.

Animal Communication↗

PubMed1985

[Effects of different types of continuous emission laser on human atheromatous plaques in vitro].

The laser beam is a punctual source of thermal energy which can be used to vaporize human atheroma. The physical characteristics of optimal utilisation (total energy, wave length, continuous or pulsed emission) have not been clearly defined. We carried out in vitro irradiations of human atheromatous material and healthy arterial wall with different combinations of power-emission time and three different wave lengths, using four continuous emission laser beams (Nd-Yag, two CO2 with different lenses, Argon). The beam emitted by the Nd-Yag was absorbed less than the CO2 and Argon lasers, which had comparable effects above a threshold of 2 to 14 joules. The weight of vaporized fibro-atheromatous material was 0.11 mg per joule of optical energy dissipated (CO2). No radical difference was observed in the nature of the effects of the three types of laser studied. The problems of using this technique on the beating heart remain unsolved (ballistics of the emerging ray). Other modes of emission (pulsed) and different wave lengths should be studied.

Argon↗

PubMed2005

The trust-region self-consistent field method in Kohn-Sham density-functional theory.

The trust-region self-consistent field (TRSCF) method is extended to the optimization of the Kohn-Sham energy. In the TRSCF method, both the Roothaan-Hall step and the density-subspace minimization step are replaced by trust-region optimizations of local approximations to the Kohn-Sham energy, leading to a controlled, monotonic convergence towards the optimized energy. Previously the TRSCF method has been developed for optimization of the Hartree-Fock energy, which is a simple quadratic function in the density matrix. However, since the Kohn-Sham energy is a nonquadratic function of the density matrix, the local energy functions must be generalized for use with the Kohn-Sham model. Such a generalization, which contains the Hartree-Fock model as a special case, is presented here. For comparison, a rederivation of the popular direct inversion in the iterative subspace (DIIS) algorithm is performed, demonstrating that the DIIS method may be viewed as a quasi-Newton method, explaining its fast local convergence. In the global region the convergence behavior of DIIS is less predictable. The related energy DIIS technique is also discussed and shown to be inappropriate for the optimization of the Kohn-Sham energy.

Algorithms↗

PubMedDate not supplied

Comparison of NaI(T1), CdTe, and HgI2 surgical probes: effect of scatter compensation on probe performance.

Spatial variation in the background source distribution makes tumor detection difficult for single-detector probes. Using a single energy window that brackets the photopeak helps discriminate against background events dominated by Compton scattering. Another approach is to use the information provided by an additional window in the Compton region. The performances of NaI(T1), CdTe, and HgI2 surgical probes have been compared under realistic simulations of a tumor-staging procedure using optimal single-sided energy windows and a two-window scatter-subtraction technique. Results showed that despite the differences in energy resolution of the detectors, the performances of the probes in a variable background were similar when optimal single energy windows were used. When the background variations were large, using information provided by a second window improved probe performance.

Cadmium↗

PubMed2006

Learning to minimize energy costs and maximize mechanical work in a bimanual coordination task.

The authors addressed the hypothesis that economy in motor coordination is a learning phenomenon realized by both reduced energy cost for a given workload and more external work at the same prepractice metabolic and attentional energy expenditure. "Self-optimization" of movement parameters has been proposed to reflect learned motor adaptations that minimize energy costs. Twelve men aged 22.3 -/+ 3.9 years practiced a 90 degrees relative phase, upper limb, independent ergometer cycling task at 60 rpm, followed by a transfer test of unpracticed (45 and 75 rpm) and self-paced cadences. Performance in all conditions was initially unstable, inaccurate, and relatively high in both metabolic and attentional energy costs. With practice, coordinative stability increased, more work was performed for the same metabolic and attentional costs, and the same work was done at a reduced energy cost. Self-paced cycling was initially below the metabolically optimal, but following practice at 60 rpm was closer to optimal cadence. Given the many behavioral options of the motor system in meeting a variety of everyday movement task goals, optimal metabolic and attentional energy criteria may provide a solution to the problem of selecting the most adaptive coordination and control parameters.

Adult↗

PubMed1997

Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86% of optimal.

This paper considers the protein energy minimization problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. We consider two side chain models: a lattice model that generalizes the HP model (Dill, 1985) to explicitly represent side chains on the cubic lattice and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. We describe algorithms with mathematically guaranteed error bounds for both of these models. In particular, we describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 86% of optimal in a face-centered cubic lattice, and we demonstrate how this provides a better than 70% performance guarantee for the HP-TSSC model. Our analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Ngo et al. (1994) concerning the complexity of protein folding models that include side chains.

Algorithms↗

PubMed2006

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.

BACKGROUND: Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs. RESULTS: Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free energy change of an input sequence pair can either be compared with the total free energy changes of a set of control sequence pairs, or be used in combination with sequence length and nucleotide frequencies as input to a classification support vector machine. The latter method is much faster, but slightly less sensitive at a given specificity. Additionally, the classification support vector machine method is shown to be sensitive and specific on genomic ncRNA screens of two different Escherichia coli and Salmonella typhi genome alignments, in which many ncRNAs are known. The Dynalign computational experiments are also compared with two other ncRNA detection programs, RNAz and QRNA. CONCLUSION: The Dynalign-based support vector machine method is more sensitive for known ncRNAs in the test genomic screens than RNAz and QRNA. Additionally, both Dynalign-based methods are more sensitive than RNAz and QRNA at low sequence pair identities. Dynalign can be used as a comparable or more accurate tool than RNAz or QRNA in genomic screens, especially for low-identity regions. Dynalign provides a method for discovering ncRNAs in sequenced genomes that other methods may not identify. Significant improvements in Dynalign runtime have also been achieved.

Algorithms↗

PubMed2004

Method for creating ideal tissue fusion in soft-tissue structures using radio frequency (RF) energy.

Bipolar radiofrequency (RF) energy can successfully seal vascular structures up to 7 mm by fusing collagen and elastin in the lumen. Valleylab has created a system to expand this technology beyond vessel sealing with the development of a closed-loop, feedback-control RF generator that closely monitors tissue fusion. This generator, operating with a loop time of approximately 250 micros, continuously adjusts energy output, creating optimized soft-tissue fusion through structural protein amalgamation. In the first study, RF energy was applied to canine lung using the new-generation generator and lung-prototype device. A lobectomy was completed, sealing the lobar bronchus, parenchyma, and pulmonary vasculature. Chronic performance of the seals was evaluated at necropsy on postoperative days 7 and 14. In a second study, RF energy was applied to porcine small intestine using the same closed-loop generator and anastomosis prototype device. Acute tissue fusion was assessed qualitatively for hemostasis and seal quality. Terminal tissue evaluation was completed on postoperative day 7 and analyzed histopathologically. Histopathology confirmed acute and chronic tissue fusion in both the lung and intestine. Normal pathological healing was substantiated by angiogenesis, granulation, and proliferation of fibroblasts. Preliminary studies using canine lung and porcine small intestine demonstrate the potential of this closed-loop generator for soft-tissue amalgamation. Advanced monitoring capabilities make this fusion system applicable in many soft-tissue structures with adequate collagen and elastin. Further investigation of potential surgical applications needs to be completed.

Anastomosis, Surgical↗

PubMed1994

Energetic basis for structural preferences in 5/6-hydroxy-5,6-dihydropyrimidines: products of ionizing and ultraviolet radiation action on DNA bases.

The structures of all diastereoisomers of 5/6-hydroxy-5,6-dihydropyrimidines have been optimized with ab initio quantum chemical calculations using a 6-31G basis set. The energies of the optimized structures were calculated at the MP2/6-31G* level. The hydroxyl group prefers an equatorial over an axial orientation at the C(5) position of pyrimidines by 3-4 kcal/mol. At the C(6) position, the axial orientation of hydroxyl is preferred by 3-4 kcal/mol. The factors responsible for the different preferences result from dipolar intramolecular interactions between the hydroxyl and C(4) = O(4) on the one hand, and the N(1)-H(1) on the other hand. As a consequence of these structural preferences, the pseudo axial positions at C(5) and C(6), which are perpendicular to the molecular plane, can be occupied by different substituents. These pseudo axial groups are expected to be a major source of distortions to DNA structure with more bulky groups having a greater effect. This may constitute a structural basis for interpretation of experimental results on the biological consequences of pyrimidine lesions. The conclusions drawn from the calculations correlate well with experimental observations on the biological activities of thymine lesions.

Calorimetry↗

PubMed1991

Reversible mechanosensitive ion pumping as a part of mechanoelectrical transduction.

To explain the ability of some mechanosensitive cells to reverse the process of mechanotransduction and to generate mechanical oscillations and emit sound, a piezo-conformational coupling model (PCC model) is proposed. The model includes a transport protein which changes either its volume (PV-coupling) or its area in the membrane (gamma A-coupling) when undergoing conformational transitions. Such a protein can interact with an oscillating pressure to pump ions and create a transmembrane gradient if the affinities of the protein for ions are different at the two sides of membrane. The frequency and concentration windows for mechanical energy transduction were determined. Under optimal conditions, the efficiency of energy transduction can approach the theoretical maximum of 100%. If the concentration gradient exceeds the static head value (quasi-equilibrium which can be built up and maintained by this transport system), the energy transduction reverses and the transporter becomes a generator of mechanical oscillations at the expense of a concentration gradient. Estimation of thermodynamic parameters of the pump shows that the PV-coupling model would require large pressure oscillations to work while the gamma A-coupling model could work in physiological conditions. The gamma A-coupling mechanism may be used by cells for two purposes. In the reverse mode, it can be a force generator for various applications. In the direct mode, it may serve bioenergetic purposes by harvesting the energy of mechanical oscillations and storing it in the form of a concentration gradient. This pump has an unusual thermodynamic feature: it can distinguish the two components of the electrochemical potential gradient,i.e., the concentration gradient and the electrical potential, the latter serving as a permissive switch to open, or close, the pump when the potential reaches the threshold value.Predictions of the PCC model and its probable involvement in biological mechanotransduction are dicussed.

Biological Transport, Active↗

PubMedDate not supplied

Genetic algorithm for the design of molecules with desired properties.

The design of molecules with desired properties is still a challenge because of the largely unpredictable end results. Computational methods can be used to assist and speed up this process. In particular, genetic algorithms have proved to be powerful tools with a wide range of applications, e.g. in the field of drug development. Here, we propose a new genetic algorithm that has been tailored to meet the demands of de novo drug design, i.e. efficient optimization based on small training sets that are analyzed in only a small number of design cycles. The efficiency of the design algorithm was demonstrated in the context of several different applications. First, RNA molecules were optimized with respect to folding energy. Second, a spinglass was optimized as a model system for the optimization of multiletter alphabet biopolymers such as peptides. Finally, the feasibility of the computer-assisted molecular design approach was demonstrated for the de novo construction of peptidic thrombin inhibitors using an iterative process of 4 design cycles of computer-guided optimization. Synthesis and experimental fitness determination of only 600 different compounds from a virtual library of more than 10(17) molecules was necessary to achieve this goal.

Algorithms↗

PubMed1993

Equilibration during mantle melting: a fractal tree model.

Many basalts from oceanic islands, ridges, and arcs show strong trace element evidence for melting at great depths, where garnet is a stable phase in mantle peridotites. If partial melts ascend to the surface by porous (intergranular) flow processes, the high-pressure garnet signature will be obliterated by diffusive reequilibration at shallower depths in the mantle. Spiegelman and Kenyon [Spiegelman, M. & Kenyon, P. (1992) Earth Planet Sci. Lett. 109, 611-620] argued that partial melts must therefore be focused into a coarser transport network, for high-speed delivery to the surface. Numerous natural network systems, such as rivers and the human vascular and bronchial systems, have fractal structures that are optimal for minimizing energy expenditure during material transport. I show here that a fractal magma "tree" with these optimal properties provides a network in which magma rapidly loses diffusive chemical "contact" with its host matrix. In this fractal network, magma conduits combine by twos, with the radius and flow velocities scaling as (2)n/3, where n is the generation number. For reasonable values of volume diffusivities, viscosities, and aspect ratios, melts will experience only limited diffusive reequilibration once they have traveled some hundreds of meters from their source. Melts thus represent rather local mantle domains, and there is little problem in delivering melts with deep (<100 km) geochemical signatures to the surface.

Journal Article↗

PubMed2002

Optimization of Ga-67 imaging for detection and estimation tasks: dependence of imaging performance on spectral acquisition parameters.

UNLABELLED: We have compared the use of two (93 and 185 keV) and three (93, 185, and 300 keV) photopeaks for Ga-67 tumor imaging and optimized the placement of each energy window. METHODS: The bases for optimization and evaluation were ideal and Bayesian signal-to-noise ratios (SNR) for the detection of spheres embedded in a realistic anthropomorphic digital torso phantom and ideal SNR for the estimation of their size and activity concentration. Seven spheres of radii ranging from 1 to 3 cm, located at several sites in the torso, were simulated using a realistic Monte Carlo program. We also calculated the ideal SNR for the detection from simple phantom acquisitions. RESULTS: For detection and estimation tasks, the optimum windows were identical for all sphere sizes and locations. For the 93 keV photopeak, the optimal window was 84-102 keV for the detection and 87-102 keV for estimation; these windows are narrower than the 20% window often used in the clinic (83-101 keV). For the 185 keV photopeak, the optimal window was 170-220 keV for the detection and 170-215 keV for estimation; these are substantially different than the 15% window used in our clinic (171-199 keV). For the 300 keV photopeak, the optimal window for detection was 270-320 keV, and for estimation, 280-320 keV. Using the three optimized, rather than only the two lower-energy, windows yielded a 9% increase in the SNR for the detection of the 3 cm diam sphere (a 12% increase for a 2 cm diam sphere) and a 7% increase in the SNR for estimation of its size. For the acquired phantom data, detection also increased by 9%-12% when using three, rather than two, energy windows.

Abdomen↗

PubMedDate not supplied

[Contribution of individual structural components to stabilization of the secondary structure of double-helical polynucleotides].

Contributions of individual structural components of the double-helical polynucleotide to the stabilization of its secondary structure have been studied. The energy of intramolecular interactions was calculated by the method of atom-atom potentials. Sections of the energy function were constructed according to the parameters determining mutual location of base pairs with the optimal conformation of ribose-phosphate backbone in the points close to A- and B-forms of DNA. A complicated nature of the contribution of different structural components of the polynucleotide to its stabilization was revealed by means of different parameters. Relationships between the change of conformational parameters corresponding to optimal values of energy for A- and B-families of nucleic acids were found.

DNA↗

PubMed2005

How optimal life history changes with the community size-spectrum.

This paper derives optimal life histories for fishes or other animals in relation to the size spectrum of the ecological community in which they are both predators and prey. Assuming log-linear size-spectra and well known scaling laws for feeding and mortality, we first construct the energetics of the individual. From these we find, using dynamic programming, the optimal allocation of energy between growth and reproduction as well as the trade-off between offspring size and numbers. Optimal strategies were found to be strongly dependent on size spectrum slope. For steep size spectra (numbers declining rapidly with size), determinate growth was optimal and allocation to somatic growth increased rapidly with increasing slope. However, restricting reproduction to a fixed mating season changed optimal allocations to give indeterminate growth approximating a von Bertalanffy trajectory. The optimal offspring size was as small as possible given other restrictions such as newborn starvation mortality. For shallow size spectra, finite optimal maturity size required a decline in fitness for large size or age. All the results are compared with observed size spectra of fish communities to show their consistency and relevance.

Animals↗

PubMedDate not supplied

Energetics and reproductive effort.

Natural selection favors the optimal allocation of energy and other limiting resources to reproduction. Human reproductive physiology displays characteristic patterns that can be viewed as mechanisms that help optimize reproductive effort in the face of environmental energetic constraints. Female ovarian function is particularly sensitive to energy balance and energy flux, resulting in a synchronization of conception with favorable energetic conditions. Reproductive effort during gestation is highly buffered from environmental energetic constraints, but the duration of gestation and final birthweight are both very sensitive to maternal energy availability. Milk production during lactation is relatively buffered from maternal energetic constraints as well, but the duration of lactational amenorrhea is sensitive to the relative metabolic load of lactation. Male gamete production is very insensitive to energetic constraints, but variation in testosterone production in response to both age and longer-lasting energetic conditions contributes to the modulation of somatic and behavioral aspects of male reproductive effort, aspects that are more energetically costly for a male. There is also new evidence that testosterone may also help to modulate the trade-off between male parenting and mating effort.

Amenorrhea↗

PubMed1994

Nutritional regulation of the insulin-like growth factors.

Nutrition is one of the main regulators of circulating IGF-I. In humans, serum IGF-I concentrations are markedly lowered by energy and/or protein deprivation. Both energy and proteins are critical in the regulation of serum IGF-I concentrations. Indeed, after fasting, optimal intake of both energy and protein is necessary for the rapid restoration of circulating IGF-I. We believe, however, that in adult humans energy may be somewhat more important than protein in this regard. While the lowest protein intake is able to increase IGF-I in the presence of adequate energy, there is a threshold energy requirement below which optimal protein intake fails to raise IGF-I after fasting. When energy intake is severely reduced, the carbohydrate content of the diet is a major determinant of responsiveness of IGF-I to GH. The essential amino acid content of the diet is also critical for the optimal restoration of IGF-I after fasting, when protein intake is reduced. The exquisite sensitivity of circulating IGF-I to nutrients, the nycthemeral stability of its concentrations and its relative short half-life constitute the basis for its use as a marker of both nutritional status and adequacy of nutritional rehabilitation. For these indications, IGF-I measurement is more sensitive and more specific than measurement of the other nutrient-related serum proteins (albumin, prealbumin, transferrin, retinol-binding protein). Animal models have been developed to investigate the mechanisms responsible for the nutritional regulation of IGF-I. There is no doubt that many mechanisms are involved (Fig. 12). Decline of serum IGF-I in dietary restriction is independent of the diet-induced alterations in pituitary GH secretion. The role of the liver GH receptors is dependent on the severity of the nutritional insult. In severe dietary restriction (fasting), a marked decrease of the number of somatogenic receptors supports the role of a receptor defect in the decline of circulating IGF-I. In contrast, in less severe forms of dietary restriction (protein restriction), the decline of IGF-I results from a postreceptor defect in the GH action at the hepatic level. Nutritional deprivation decreases hepatic IGF-I production by diminishing IGF-I gene expression. Decline in IGF-I gene expression is mainly caused by nutrient deficiency and less importantly by the nutritionally induced hormonal changes (insulin and T3). Diet restriction also increases the clearance and degradation of serum IGF-I through changes in the levels of circulating IGFBPs.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗