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PubMed2000

Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score.

Two methods were proposed recently to derive energy parameters from known native protein conformations and corresponding sets of decoys. One is based on finding, by means of a perceptron learning scheme, energy parameters such that the native conformations have lower energies than the decoys. The second method maximizes the difference between the native energy and the average energy of the decoys, measured in terms of the width of the decoys' energy distribution (Z-score). Whereas the perceptron method is sensitive mainly to "outlier" (i.e., extremal) decoys, the Z-score optimization is governed by the high density regions in decoy-space. We compare the two methods by deriving contact energies for two very different sets of decoys: the first obtained for model lattice proteins and the second by threading. We find that the potentials derived by the two methods are of similar quality and fairly closely related. This finding indicates that standard, naturally occurring sets of decoys are distributed in a way that yields robust energy parameters (that are quite insensitive to the particular method used to derive them). The main practical implication of this finding is that it is not necessary to fine-tune the potential search method to the particular set of decoys used.

Algorithms↗

PubMed2001

Extremal collision sequences of particles on a line: optimal transmission of kinetic energy.

The transmission of kinetic energy through chains of inelastically colliding spheres is investigated for the case of constant coefficient of restitution epsilon=const and impact-velocity-dependent coefficient epsilon(v) for viscoelastic particles. We derive a theory for the optimal distribution of particle masses which maximize the energy transfer along the chain and check it numerically. We found that for epsilon=const, the mass distribution is a monotonous function which does not depend on the value of epsilon. In contrast, for epsilon(v) the mass distribution reveals a pronounced maximum, depending on the particle properties and on the chain length. The system investigated demonstrates that even for small and simple systems, the velocity dependence of the coefficient of restitution may lead to new effects with respect to the same systems under the simplifying approximation epsilon=const.

Journal Article↗

PubMed2001

Evaluation of scatter compensation methods by their effects on parameter estimation from SPECT projections.

Three algorithms for scatter compensation in Tc-99m brain single-photon emission computed tomography (SPECT) were optimized and compared on the basis of the accuracy and precision with which lesion and background activity could be simultaneously estimated. These performance metrics are directly related to the clinically important tasks of activity quantitation and lesion detection, in contrast to measures based solely on the fidelity of image pixel values. The scatter compensation algorithms were (a) the Compton-window (CW) method with a 20% photopeak window, a 92-126 keV scatter window, and an optimized "k-factor," (b) the triple-energy window (TEW) method, with optimized widths of the photopeak window and the abutting scatter window, and (c) a general spectral (GS) method using seventeen 4 keV windows with optimized energy weights. Each method was optimized by minimizing the sum of the mean-squared errors (MSE) of the estimates of lesion and background activity concentrations. The accuracy and precision of activity estimates were then determined for lesions of different size, location, and contrast, as well as for a more complex Bayesian estimation task in which lesion size was also estimated. For the TEW and GS methods, parameters optimized for the estimation task differed significantly from those optimized for global normalized pixel MSE. For optimal estimation, the CW bias of activity estimates was larger and varied more (-2% to 22%) with lesion location and size than that of the other methods. The magnitude of the TEW bias was less than 7% across most conditions, although its precision was worse than that of CW estimates. The GS method performed best, with bias generally less than 4% and the lowest variance; its root-mean square (rms) estimation error was within a few percent of that achievable from primary photons alone. For brain SPECT, estimation performance with an optimized, energy-based, subtractive correction may approach that of an ideal scatter-rejection procedure.

Algorithms↗

PubMed2005

Beam hardening artefacts in computed tomography with photon counting, charge integrating and energy weighting detectors: a simulation study.

Photon counting x-ray imaging provides efficient rejection of the electronics noise, no pulse height (Swank) noise, less noise due to optimal photon energy weighting and the possibility of energy resolved image acquisition. These advantages apply also to CT when projection data are acquired using a photon counting detector. However, photon counting detectors assign a weighting factor of 1 to all detected photons whereas the weighting factor of a charge integrating detector is proportional to the energy of the detected photon. Therefore, data collected by photon counting and charge integrating detectors represent the 'hardening' of the photon beam passed through the object differently. This affects the beam hardening artefacts in the reconstructed CT images. This work represents the first comparative evaluation of the effect of photon counting, charge integrating and energy weighting photon detectors on beam hardening artefacts in CT. Beam hardening artefacts in CT images were evaluated for 20 cm and 14 cm diameter water cylinders with bone and low contrast inserts, at 120 kVp and 90 kVp x-ray tube voltages, respectively. It was shown that charge integrating results in 1.8% less beam hardening artefacts from bone inserts (i.e., CT numbers in the 'shadow' of the bone are less by 1.8% as compared to CT numbers over the periphery of the image), as compared to photon counting. However, optimal photon energy weighting, which provides highest SNR, results in 7.7% higher beam hardening artefacts from bone inserts as compared to photon counting. The magnitude of the 'cupping' artefacts was lower by 1% for charge integrating and higher by 6.1% for energy weighting acquisitions as compared to photon counting. Only the photon counting systems provide an accurate representation of the beam hardening effect due to its flat energy weighting. Because of their energy dependent weighting factors, the charge integrating and energy weighting systems do not provide accurate representation of the beam hardening effect.

Computer Simulation↗

PubMed2004

Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors.

As an effort to develop therapeutics for cancer treatments, a number of effective histone deacetylase inhibitors with structural diversity have been discovered. To gain insight into optimizing the activity of an identified lead compound, a computational protocol sequentially involving homology modeling, docking experiments, molecular dynamics simulation, and free energy perturbation calculations was applied for rationalizing the relative activities of known histone deacetylase inhibitors. With the newly developed force field parameters for the coordination environment of the catalytic zinc ion in hand, the computational strategy proved to be successful in predicting the rank orders for 12 derivatives of three hydroxamate-based inhibitor scaffolds with indole amide, pyrrole, and sulfonamide moieties. The results showed that the free energy of an inhibitor in aqueous solution should be an important factor in determining the binding free energy. Hence, in order to enhance the inhibitory activity by adding or substituting a chemical group, the increased stabilization in solution due to the structural changes must be overcome by a stronger enzyme-inhibitor interaction. It was also found that to optimize inhibitor potency, the hydrophobic head of an inhibitor should be elongated or enlarged so that it can interact with Pro29 and His28 that are components of the flexible loop at the top of the active site.

Amino Acid Sequence↗

PubMed2005

Hydrogen bond vs proton transfer in HZSM5 zeolite. A theoretical study.

The interaction of a large set of bases covering a wide range of the basicity scale with HZSM5 medium-size zeolites has been investigated through the use of two model clusters, namely 5T and 7T:63T. The 5T cluster has been treated fully ab initio at the B3LYP level, whereas the 63T cluster has been treated with the ONIOM2 scheme using the B3LYP:MNDO combination for geometry optimizations and B3LYP:HF/3-21G for adsorption energies. The optimized geometries of the different hydrogen bond (HB) and ion pair (IP) complexes obtained with both models are rather similar. However, there are significant dissimilarities as far as the adsorption energies are concerned, in particular when dealing with IP clusters whose intrinsic stability is largely underestimated when the simpler 5T model is used. 5T clusters could be used to obtain reasonable estimates of adsorption energies provided these are scaled by a factor of 1.1 for HB complexes and 1.4 for IP complexes. The zeolite cavity favors the proton transfer process, similarly to that found by third polar partners in gas-phase HB trimers. The intrinsic basicity of the base and its adsorption energy within the zeolite are correlated. From this correlation, is possible to conclude that, in general, bases with proton affinities (PA) larger than 200 kcal mol(-1) should lead to the formation of IPs, whereas bases with PA smaller than this value should form HB complexes.

Adsorption↗

PubMed1994

Biological electron energy loss spectroscopy in the field-emission scanning transmission electron microscope.

The dedicated scanning transmission electron microscope (STEM) combined with parallel electron energy loss spectroscopy (EELS) provides a very sensitive means of detecting specific elements in small structures. EELS is more sensitive than optimized energy-dispersive X-ray spectroscopy by a factor of about three for calcium. Measurement of such low concentrations requires special processing methods such as difference-acquisition techniques and multiple least squares procedures for fitting reference spectra. By analyzing data recorded at each pixel in a spectrum-image it is possible to map quantitatively the elemental distributions in a specimen. It is possible to prepare cryosections that are sufficiently thin to avoid excessive plural inelastic scattering so analysis can be performed at 100 keV beam energy. Under optimal conditions, a resolution of 10 nm and detection limits of a few atoms are achievable for elements such as calcium, phosphorus and iron. In the field emission STEM certain types of chemical information can be extracted from biological specimens. Valence EELS has been exploited to measure water distributions in frozen hydrated cryosections.

Animals↗

PubMedDate not supplied

Theoretical optimization of dual-energy x-ray imaging with application to mammography.

Detection of a target object in a radiological image is often impeded by an obscuring background "clutter" resulting from the contrast between various materials in the neighborhood of the target. Dual-energy techniques can reduce or remove this clutter. In order for the target to be detectable in the image after dual-energy processing, the signal-to-noise ratio (SNR), defined as the difference between the target and the background divided by the photon noise in the difference, must exceed some threshold. A given SNR may be obtained for a wide range of the energies of the two x-ray beams and the ratio of their fluences. A theoretical model is developed which permits the choice of beams to be optimized with respect to some critical parameter--in this case, patient dose. The analysis is applied to the detection of calcifications in mammography. For an ideal imaging system, we predict that the optimum beam energies are 19 and 68 keV. A dose of 0.42 cGy is required to obtain an SNR of 5 for detection of a 0.02-cm cubic calcification in the resulting clutter-free image. This can be reduced to 0.16 cGy if the higher energy image is smoothed, prior to dual-energy processing, such that its variance is reduced to one-fourth of its unsmoothed value.

Female↗

PubMed1989

A theoretical study of glucosamine synthase. Part I. Molecular mechanics calculations on substrate binding.

Glucosamine synthase transfers the gamma-amino group of glutamine to fructose, producing 1-glucosamine which is the key constituent of bacterial and fungal cell walls. In this study, model calculations were performed on substrate binding to the enzyme active site. Two models of the active site of glucosamine synthase were proposed, which assume two different sequences of aminoacids, Cys-Gly-Ile and Cys-Ala-Cys, the first one being the N-terminal sequence of the Escherichia coli enzyme. Several initial geometries were assumed for these tripeptides, the energy was then optimized by means of molecular mechanics. It has been found that the structure which is both energy optimal and satisfies the assumed cysteine sulphur arrangement consists of combinations of C7eq and C7ax conformations of single residues. Molecular mechanics calculations were then performed on glutamine and D-fructose-6-phosphate, which are the substrates of the enzymatic catalysis, and on their complex with the enzyme glutamine-binding site. The spatial configuration of the compounds under study, which is optimal as far as the reaction path is concerned, also turned out to be an energy minimum.

Alanine↗

PubMed2000

The role of gravity in human walking: pendular energy exchange, external work and optimal speed.

During walking on Earth, at 1.0 g of gravity, the work done by the muscles to maintain the motion of the centre of mass of the body (W(ext)) is reduced by a pendulum-like exchange between gravitational potential energy and kinetic energy. The weight-specific W(ext) per unit distance attains a minimum of 0.3 J x kg(-1) x m(-1) at about 4.5 km x h(-1) in adults. The effect of a gravity change has been studied during walking on a force platform fixed to the floor of an aircraft undergoing flight profiles which resulted in a simulated gravity of 0.4 and 1.5 times that on Earth. At 0.4 g, such as on Mars, the minimum W(ext) was 0.15 J x kg(-1) x m(-1), half that on Earth and occurred at a slower speed, about 2.5 km x h(-1). The range of walking speeds is about half that on Earth. At 1.5 g, the lowest value of W(ext) was 0.60 J x kg(-1) x m(-1), twice that on Earth; it was nearly constant up to about 4.3 km x h(-1) and then increased with speed. The range of walking speeds is probably greater than that on Earth. A model is presented in which the speed for an optimum exchange between potential and kinetic energy, the 'optimal speed', is predicted by the balance between the forward deceleration due to the lift of the body against gravity and the forward deceleration due to the impact against the ground. In conclusion, over the range studied, gravity increases the work required to walk, but it also increases the range of walking speeds.

Energy Metabolism↗

PubMed1989

Three example applications of optimization techniques to Department of Energy contractor radiation protection programs.

Six numerical examples of optimization of radiation protection are provided in the appendices of International Commission on Radiological Protection (ICRP) Publication No. 37 (1983). In each case, the calculations were based on well-defined parameters and assumptions. In this paper, we examined three different numerical examples that were based on empirical data and less-certain assumptions. In the first example, the optimum sampling frequency for a typical 3H bioassay program was found to be once every 2 mo. However, this result depended on assumed values for several variables that were difficult to evaluate. The second example showed that the optimum frequency for recalibrating a group of "cutie pie" (CP) ionization chamber survey instruments was once every 85 d. This result depended largely on the assumption that an improperly operating CP instrument could lead to a serious overexposure. In the third example, one continuous air monitor (CAM) was determined to be the optimum number in a workplace at a Department of Energy (DOE) Pu facility. The optimum location of the CAM was determined from past glove-box release studies. These examples demonstrated that cost-benefit analysis of individual elements of radiation protection programs can be useful even if limited data are available.

Air Pollution, Radioactive↗

PubMed2004

Making optimal use of empirical energy functions: force-field parameterization in crystal space.

Today's energy functions are not able yet to distinguish reliably between correct and almost correct protein models. Improving these near-native models is currently a major bottle-neck in homology modeling or experimental structure determination at low resolution. Increasingly accurate energy functions are required to complete the "last mile of the protein folding problem," for example during a molecular dynamics simulation. We present a new approach to reach this goal. For 50 high resolution X-ray structures, the complete unit cell was reconstructed, including disordered water molecules, counter ions, and hydrogen atoms. Simulations were then run at the pH at which the crystal was solved, while force-field parameters were iteratively adjusted so that the damage done to the structures was minimal. Starting with initial parameters from the AMBER force field, the optimization procedure converged at a new force field called YAMBER (Yet Another Model Building and Energy Refinement force field), which is shown to do significantly less damage to X-ray structures, often move homology models in the right direction, and occasionally make them look like experimental structures. Application of YAMBER during the CASP5 structure prediction experiment yielded a model for target 176 that was ranked first among 150 submissions. Due to its compatibility with the well-established AMBER format, YAMBER can be used by almost any molecular dynamics program. The parameters are freely available from www.yasara.org/yamber.

Computer Simulation↗

PubMed1989

Temporal parameters of low energy laser irradiation for optimal delay of post-traumatic degeneration of rat optic nerve.

Compression injury of a central nerve results in its degeneration with irreversible loss of function due to the inability of the mammalian central nervous system (CNS) to regenerate. In contrast, the CNS of lower vertebrates has a high capacity to regenerate. Recently, low energy laser irradiation was shown to attenuate degeneration in injured CNS nerves. The optic nerves of rats were subjected to moderate crush, calibrated so that some electrophysiological activity was preserved. The nerves were then subjected to low energy laser irradiation (10.5 mW, 2 min daily) for various periods. The electrical activity of the nerves, distal to the site of injury, was determined by measuring the compound action potential at the termination of the experiment. Two weeks of irradiation begun immediately after injury and continued daily thereafter, resulted in a compound action potential which was significantly higher (mean +/- S.E.M. 1856 +/- 535 microV) than that of non-irradiated injured nerves (351 +/- 120 microV). The effect was temporary and subsided within a week. This two-week irradiation was slightly more effective than a treatment lasting one week (1406 +/- 225 microV) and was significantly more effective than 4 days of irradiation (960 +/- 133 microV). The number of treatments is therefore important. The time at which the treatment commences relative to the injury is also critical. Irradiation initiated two hours after the crush was about half as effective as immediate irradiation (810 +/- 42 microV). No apparent effect was evident when the laser was applied for the first time 5 h, or longer, after the crush.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2000

Acute effects of methoxamine on left ventricular-arterial coupling in streptozotocin-diabetic rats: a pressure-volume analysis.

We determined the acute effects of methoxamine, a specific alpha1-selective adrenoceptor agonist, on the left ventricular-arterial coupling in streptozotocin (STZ)-diabetic rats, using the end-systolic pressure-stroke volume relationships. Rats given STZ 65 mg x kg(-1) iv (n = 8) were compared with untreated age-matched controls (n = 8). A high-fidelity pressure sensor and an electromagnetic flow probe measured left ventricular (LV) pressure and ascending aortic flow, respectively. Both LV end-systolic elastance E(LV,ES) and effective arterial elastance Ea were estimated from the pressure-ejected volume loop. The optimal afterload Q(load) determined by the ratio of Ea to E(LV,ES) was used to measure the optimality of energy transmission from the left ventricle to the arterial system. In comparison with controls, diabetic rats had decreased LV end-systolic elastance E(LV,ES), at 513 +/- 30 vs. 613 +/- 29 mmHg x mL(-1), decreased effective arterial elastance Ea, at 296 +/- 20 vs. 572 +/- 48 mmHg x mL(-1), and decreased optimal afterload Q(load), at 0.938 +/- 0.007 vs. 0.985 +/- 0.009. Methoxamine administration to STZ-diabetic rats significantly increased LV end-systolic elastance E(LV,ES), from 513 +/- 30 to 602 +/- 38 mmHg x mL(-1), and effective arterial elastance Ea, from 296 +/- 20 to 371 +/- 28 mmHg x mL(-1), but did not change optimal afterload Q(load). We conclude that diabetes worsens not only the contractile function of the left ventricle, but also the matching condition for the left ventricular-arterial coupling. In STZ-diabetic rats, administration of methoxamine improves the contractile status of the ventricle and arteries, but not the optimality of energy transmission from the left ventricle to the arterial system.

Adrenergic alpha-Agonists↗

PubMed1986

A unifying principle relating stress to trabecular bone morphology.

The relationships between cancellous bone apparent density, trabecular orientation, and stress are developed and a mathematical theory describing these relationships is proposed. The bone is assumed to be a self-optimizing material. Using a continuum model, sufficient conditions are developed which ensure that, for a given stress encountered during normal activity, the theory will predict both trabecular orientation and apparent density. Using two special approaches, one based on optimizing strain energy density (stiffness) and the other on optimizing strength, the relationship between apparent density and stress is derived. This is the first time that a single theory has been advanced to predict both the orientation and apparent density of cancellous bone.

Biomechanical Phenomena↗

PubMed1995

Homology modeling by the ICM method.

Five models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three-dimensional structure with sequence identity ranging from 25 to 77%. After alignment of the target sequence with the related three-dimensional structure, the modeling procedure consists of two subproblems: side-chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the nonconserved portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side-chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low-energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near-native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed.

Antibodies, Anti-Idiotypic↗

PubMed1976

Phototherapy of the cornea: some aspects to be considered.

To safeguard against and reduce possible harmful and undesired side effects of photon interaction with ocular structures during phototherapy of certain corneal diseases, precautionary measures should be taken. These include (1) Selection of the proper light source, strongly emitting in the effective spectral range. (2) Removal of potential harmful spectral bands which make no significant contribution to the therapeutic action. (3) Determination of the most optimal exposure energy (W/cm2). (4) Selection of the most optimal time-dose relationship. (5) Selection of the proper interval between vital staining and radiation exposure and considering possible repetition of therapeutic exposures. (6) Careful calibration of the light source to be used. (7) Adequate eye examination for visual acuity, pupillary diameter, signs of intraocular inflammation, mainly iritis with anterior chamber activity, and possible fundus pathology with special attention to maculopathy. These findings should be properly recorded before, during and after the period of phototherapy.

Corneal Diseases↗

PubMed1999

A dynamic programming algorithm for RNA structure prediction including pseudoknots.

We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of O(N6) in time and O(N4) in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA folding thermodynamic parameters augmented by a few parameters describing the thermodynamic stability of pseudoknots. We demonstrate the properties of the algorithm by using it to predict structures for several small pseudoknotted and non-pseudoknotted RNAs. Although the time and memory demands of the algorithm are steep, we believe this is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model.

Algorithms↗