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PubMed2004

Efficiency optimization for systems and components in microwave power engineering.

The paper is concerned with one aspect of optimization of microwave thermal processing, namely, with optimization of energy coupling interpreted as a numerical characteristic of system efficiency. Since in computer-aided design coupling can be evaluated through the computed reflections, an optimization scheme is presented that is particularly suitable for minimizing the reflection coefficient in typical systems and elements of microwave power engineering. Based on response surface methodology and the sequential quadratic programming for constrained optimization, the procedure is linked with the full-wave 3-D FDTD electromagnetic simulator QuickWave-3D. Credibility and effectiveness of the method is illustrated by four examples: dimensional optimization is performed for a dry waveguide load, a waveguide T-junction with a partial-height post, a water cylinder in a cavity, and a slotted waveguide-backed radiating element.

Journal Article↗

PubMed2006

Emerging therapies for the management of decompensated heart failure: from bench to bedside.

While pharmaceutical innovation has been highly successful in reducing mortality in chronic heart failure, this has not been matched by similar success in decompensated heart failure syndromes. Despite outstanding issues over definitions and end points, we argue in this paper that an unprecedented wealth of pharmacologic innovation may soon transform the management of these challenging patients. Agents that target contractility, such as cardiac myosin activators and novel adenosine triphosphate-dependent transmembrane sodium-potassium pump inhibitors, provide inotropic support without arrhythmogenic increases in cytosolic calcium or side effects of more traditional agents. Adenosine receptor blockade may improve glomerular filtration and diuresis by exerting a direct beneficial effect on glomerular blood flow while vasopressin antagonists promote free water excretion without compromising renal function and may simultaneously inhibit myocardial remodeling. Urodilatin, the renally synthesized isoform of atrial natriuretic peptide, may improve pulmonary congestion via vasodilation and enhanced diuresis. Finally, metabolic modulators such as perhexiline may optimize myocardial energy utilization by shifting adenosine triphosphate production from free fatty acids to glucose, a unique and conceptually appealing approach to the management of heart failure. These advances allow optimism not only for the advancement of our understanding and management of decompensated heart failure syndromes but for the translational research effort in heart failure biology in general.

Antidiuretic Hormone Receptor Antagonists↗

PubMed2003

Shock wave application enhances pertussis toxin protein-sensitive bone formation of segmental femoral defect in rats.

UNLABELLED: Extracorporeal shock waves (ESWs) elicit a dose-dependent effect on the healing of segmental femoral defects in rats. After ESW treatment, the segmental defect underwent progressive mesenchymal aggregation, endochondral ossification, and hard callus formation. Along with the intensive bone formation, there was a persistent increase in TGF-beta1 and BMP-2 expression. Pretreatment with pertussis toxin reduced ESW-promoted callus formation and gap healing, which presumably suggests that Gi proteins mediate osteogenic signaling. INTRODUCTION: Extracorporeal shock waves (ESWs) have previously been used to promote bone repair. In our previous report, we found that ESWs promoted osteogenic differentiation of mesenchymal cells through membrane perturbation and activation of Ras protein. In this report, we show that ESWs elicit a dose-dependent effect on the healing of segmental defects and that Gi proteins play an important role in mediating ESW stimulation. MATERIALS AND METHODS: Rats with segmental femoral defects were subjected to ESW treatment at different energy flux densities (EFD) and impulses. Bone mass (mineral density and calcium content), osteogenic activities (bone alkaline phosphatase activity and osteocalcin content), and immunohistochemistry were assessed. RESULTS: An optimal ESW energy (500 impulses at 0.16 mJ/mm2 EFD) stimulated complete bone healing without complications. ESW-augmented healing was characterized by significant increases (p < 0.01) in callus size, bone mineral density, and bone tissue formation. With exposure to ESW, alkaline phosphatase activity and osteocalcin production in calluses were found to be significantly enhanced (p < 0.05). After ESW treatment, the histological changes we noted included progressive mesenchymal aggregation, endochondral ossification, and hard callus formation. Intensive bone formation was associated with a persistent increase in transforming growth factor-beta 1 (TGF-beta1) and bone morphogenetic protein-2 (BMP-2) expression, suggesting both growth factors were active in ESW-promoted bone formation. We also found that pertussis toxin, an inhibitor of membrane-bound Gi proteins, significantly reduced (p < 0.01) ESW promotion of callus formation and fracture healing. CONCLUSION: ESW treatments enhanced bone formation and the healing of segmental femoral defects in rats. It also seems likely that TGF-beta1 and BMP-2 are important osteogenic factors for ESW promotion of fracture healing, presumably through Gi protein-mediated osteogenic signaling.

Absorptiometry, Photon↗

PubMed2000

Two-wave mixing in (111)-cut Bi12SiO20 and Bi12TiO20 crystals: characterization and comparison with the general orientation

We study the process of two-wave mixing (TWM) in optically active, electro-optic, and elasto-optic BSO and BTO crystals. We calculate the TWM gain for arbitrary crystal cut and optimize the energy exchange. For the (111) cut, by choosing an appropriate coordinate system, we obtain a simple analytical solution for the components of the coupling tensor which allows us to optimize analytically the TWM gain with respect to the grating orientation and the initial light polarization.

Journal Article↗

PubMed1998

Definition of an energy function for the random neural to solve optimization problems.

In this paper, we propose a general energy function for a new neural model, the random neural model of Gelenbe. This model proposes a scheme of interaction between the neurons and not a dynamic equation of the system. We then apply this general energy function on different optimization problems: the graph partitionning problem and the minimum node covering problem.

Journal Article↗

PubMed2004

Flaw tolerant bulk and surface nanostructures of biological systems.

Bone-like biological materials have achieved superior mechanical properties through hierarchical composite structures of mineral and protein. Gecko and many insects have evolved hierarchical surface structures to achieve extraordinary adhesion capabilities. We show that the nanometer scale plays a key role in allowing these biological systems to achieve their superior properties. We suggest that the principle of flaw tolerance may have had an overarching influence on the evolution of the bulk nanostructure of bone-like materials and the surface nanostructure of gecko-like animal species. We demonstrate that the nanoscale sizes allow the mineral nanoparticles in bone to achieve optimum fracture strength and the spatula nanoprotrusions in Gecko to achieve optimum adhesion strength. In both systems, strength optimization is achieved by restricting the characteristic dimension of the basic structure components to nanometer scale so that crack-like flaws do not propagate to break the desired structural link. Continuum modeling and atomistic simulations have been conducted to verify the concept of flaw tolerance at nanoscale. A simple tension-shear chain model has been developed to model the stiffness and fracture energy of biocomposites. It is found that, while the problem of low toughness of mineral crystals is alleviated by restricting the crystal size to nanoscale, the problem of low modulus of protein has been solved by adopting a large aspect ratio for the mineral platelets. The fracture energy of biocomposites is found to be proportional to the effective shear strain and the effective shear stress in protein along its path of deformation to fracture. The bioengineered mineral-protein composites are ideally suited for fracture energy dissipation as the winding paths of protein domain unfolding and slipping along protein-mineral interfaces lead to very large effective strain before fracture. The usual entropic elasticity of biopolymers may involve relatively small effective stress and may not be able to ensure simultaneous domain unfolding and interface slipping. Cross-linking mechanisms such as Ca++ induced sacrificial bonds in bone can increase the shear stress in protein and along the protein-mineral interface, effectively converting the behavior of entropic elasticity to one that resembles metal plasticity. The sacrificial bond mechanism not only builds up a large effective stress in protein but also allows protein deformation and interface slipping to occur simultaneously under similar stress levels, making it possible to engineer a very long range of deformation under significant stress in order to maximize energy absorption. Optimization of mineral platelets near theoretical strength is found to be crucial for allowing a large effective stress to be built up in protein via cross-linking mechanisms such as Ca++ induced sacrificial bonds. Similarly, for gecko adhesion, the strength optimization of individual spatulas is found to play a critical role in enhancing adhesion energy at the higher hierarchical level.

Biocompatible Materials↗

PubMed2006

On the electronic origin of strain energy: QTAIM study of perfluorocycloalkanes.

The strain energies (SE) of the five smallest perfluorocycloalkanes (c-CnF2n; n=3, 4, 5, 6, and 7) were calculated by means of several homodesmotic processes using B3LYP/6-31++G(d,p) optimized molecular energies. These values were compared with the energy difference between the linear and cyclic CF2 groups calculated by means of the quantum theory of atoms in molecules (QTAIM) applied on charge densities obtained at the same computational level. The differences between the values computed with both methods vary from 255 (n=3) to 629 (n=7) kJ mol-1. These differences arise because QTAIM-computed SE contain the energy involved in opening the ring to give rise to nearly transferable central CF2 fragments of linear perfluoroalkanes, whereas homodesmotic energies contain energy terms corresponding to transformation of nontransferable linear CF2 fragments and a ring-opening energy, which depending on the process, transforms CF2 cyclic compounds into nearly transferable or nontransferable linear CF2 groups.

Journal Article↗

PubMed1990

Theoretical studies of protein conformation by means of energy computations.

In this review we describe fundamental concepts and applications of conformational energy computations, with emphasis on some recent advances and problems being investigated. The formulation of potential energy functions is described, including the nature of the intramolecular force field, the representation of interactions with the solvent, and considerations of entropy contributions. Approaches to the search for the optimal potential energy are summarized. Examples cited among applications of conformational energy computations include refinement of X-ray crystallographic structures, the use of computations in conjunction with NMR data, prediction of the structures of proteins based on either homology or on other procedures that surmount the multiple-minima problem, the analysis of hierarchical levels of structure and assembly, and interactions in enzyme-substrate complexes.

Algorithms↗

PubMed2002

HAMMER: hierarchical attribute matching mechanism for elastic registration.

A new approach is presented for elastic registration of medical images, and is applied to magnetic resonance images of the brain. Experimental results demonstrate very high accuracy in superposition of images from different subjects. There are two major novelties in the proposed algorithm. First, it uses an attribute vector, i.e., a set of geometric moment invariants (GMIs) that are defined on each voxel in an image and are calculated from the tissue maps, to reflect the underlying anatomy at different scales. The attribute vector, if rich enough, can distinguish between different parts of an image, which helps establish anatomical correspondences in the deformation procedure; it also helps reduce local minima, by reducing ambiguity in potential matches. This is a fundamental deviation of our method, referred to as the hierarchical attribute matching mechanism for elastic registration (HAMMER), from other volumetric deformation methods, which are typically based on maximizing image similarity. Second, in order to avoid being trapped by local minima, i.e., suboptimal poor matches, HAMMER uses a successive approximation of the energy function being optimized by lower dimensional smooth energy functions, which are constructed to have significantly fewer local minima. This is achieved by hierarchically selecting the driving features that have distinct attribute vectors, thus, drastically reducing ambiguity in finding correspondence. A number of experiments demonstrate that the proposed algorithm results in accurate superposition of image data from individuals with significant anatomical differences.

Aged↗

PubMed2005

Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface.

Continuum electrostatic methods are a powerful tool for the analysis and design of biomolecular complexes, with methodologies that allow for the detailed analysis of the electrostatic contributions to binding affinities and procedures for computing the properties of electrostatically optimal ligands. We have applied these methods to the design of improved inhibitors of HIV-1 cell entry. HIV infection of a cell requires viral-cell membrane fusion, an event partially driven by a large-scale conformational change in the viral membrane glycoprotein gp41. This transformation involves the docking of a helix from the C-terminal region of three gp41 chains against a pre-formed trimeric-coiled coil; several protein constructs that inhibit membrane fusion act by binding to an isolated C-terminal helix and blocking the formation of the fusogenic structure. A detailed analysis of the electrostatic contributions to the binding of one such inhibitor (5-Helix) to a C-terminal helix was performed using the X-ray crystal structure of the core of the HIV-1 gp41 ectodomain as a structural model, and several residues on 5-Helix that make substantial contributions to binding, both favorable and unfavorable, were identified. An electrostatic affinity optimization methodology was applied to the side chains of 5-Helix, with the results showing that significant improvements in binding affinity are possible if the electrostatic contributions to the binding free energy are optimized. Several mutations accessible by experimental methods are suggested, with calculated improvements in binding affinity of as much as 500-fold and greater.

Amino Acid Sequence↗

PubMed2003

A unified variational approach to denoising and bias correction in MR.

We propose a novel bias correction method for magnetic resonance (MR) imaging that uses complementary body coil and surface coil images. The former are spatially homogeneous but have low signal intensity; the latter provide excellent signal response but have large bias fields. We present a variational framework where we optimize an energy functional to estimate the bias field and the underlying image using both observed images. The energy functional contains smoothness-enforcing regularization for both the image and the bias field. We present extensions of our basic framework to a variety of imaging protocols. We solve the optimization problem using a computationally efficient numerical algorithm based on coordinate descent, preconditioned conjugate gradient, half-quadratic regularization, and multigrid techniques. We show qualitative and quantitative results demonstrating the effectiveness of the proposed method in producing debiased and denoised MR images.

Algorithms↗

PubMed2006

Optimization of the molecular orbital energies of conjugated polymers for optical amplification of fluorescent sensors.

Cationic water-soluble poly(fluorene-co-phenylene)s with electron withdrawing or donating substituents on the conjugated backbone were designed and synthesized. Fluorescence resonance energy transfer (FRET) experiments between these conjugated polymers and dye-labeled single-stranded DNA (ssDNA-C*) reveal the importance of matching donor and acceptor orbital energy levels to improve the sensitization of C* emission. Quenching of polymer fluorescence with ssDNA-C* and differences in C* emission suggest involvement of photoinduced charge transfer (PCT) as an energy wasting mechanism. The HOMO and LUMO energy levels of the conjugated polymers and C serve as a preliminary basis to understand the competition between FRET and PCT. Dilution of C in polymer/ssDNA-C complexes by addition of ssDNA yields insight into C*...C self-quenching. Under optimized conditions, where there is no probe self-quenching and minimum PCT, efficient signal amplification is demonstrated despite poor spectral overlap between polymer and C.

Biosensing Techniques↗

PubMed1990

Protein and energy relationships in the diet of the American alligator (Alligator mississippiensis).

First-year alligators (Alligator mississippiensis) averaging 377-857 g body weight were fed diets containing various levels of protein, fat and carbohydrate. In experiment 1, nine diets arranged in a centrally rotatable composite design contained 0-36% extruded corn and 4-20% total fat. Response surface analysis predicted maximum responses in performance criteria at 6.3-18.8% corn and 15.8-27.4% fat. Corn inclusion at up to 27-36% of diet resulted in equal or improved performance compared to carbohydrate-free diets of equal fat content. Energy digestibility averaged 84.3%. Protein digestibility averaged 86.7%. Maximum responses in performance criteria were predicted at 42.5-48.7% digestible protein and 4367-4421 kcal/kg digestible energy. In two additional experiments, alligators were either fasted or fed for various numbers of days/week. Carbohydrate-supplementation of high protein diets led to equal or significantly improved performances. Performance was maximized by feeding the alligators 5-6 d/w. Regression of body weight changes against energy and protein intake yielded estimates of daily maintenance requirements of 5.7-8.4 kcal and 0.49-0.89 g protein/kg live body weight. Dietary fat and carbohydrate in the forms and amounts fed to young alligators were well-utilized. Optimal digestible energy:crude protein ratios (8.2-10.9:1 kcal/g protein) were similar to those of other aquatic ectotherms of equal size.

Alligators and Crocodiles↗

PubMed2004

Cyclic perfluorocarbon radicals and anions having high global warming potentials (GWPs): structures, electron affinities, and vibrational frequencies.

Adiabatic electron affinities, optimized molecular geometries, and IR-active vibrational frequencies have been predicted for small cyclic hydrocarbon radicals C(n)H(2)(n)(-)(1) (n = 3-6) and their perfluoro counterparts C(n)F(2)(n)(-)(1) (n = 3-6). Total energies and optimized geometries of the radicals and corresponding anions have been obtained using carefully calibrated (Chem. Rev. 2002, 102, 231) density functional methods, namely, the B3LYP, BLYP, and BP86 functionals in conjunction with the DZP++ basis set. The predicted electron affinities show that only the cyclopropyl radical tends to bind electrons among the hydrocarbon radicals studied. The trend for the perfluorocarbon (PFC) radicals is quite different. The electron affinities increase with expanding ring size until n = 5 and then slightly decrease at n = 6. Predicted electron affinities of the hydrocarbon radicals using the B3LYP hybrid functional are 0.24 eV (C(3)H(5)/C(3)H(5)(-)), -0.19 eV (C(4)H(7)/C(4)H(7)(-)), -0.15 eV (C(5)H(9)/C(5)H(9)(-)), and -0.11 eV (C(6)H(11)/C(6)H(11)(-)). Analogous electron affinities of the perflurocarbon radicals are 2.81 eV (C(3)F(5)/C(3)F(5)(-)), 3.18 eV (C(4)F(7)/C(4)F(7)(-)), 3.34 eV (C(5)F(9)/C(5)F(9)(-)), and 3.21 eV (C(6)F(11)/C(6)F(11)(-)).

Journal Article↗

PubMed2005

Challenges of crystal structure prediction of diastereomeric salt pairs.

A methodology for the computational prediction of the crystal structures and resolution efficiency for diastereomeric salt pairs is developed by considering the polymorphic system of the diastereomeric salt pair (R)-1-phenylethylammonium (R/S)-2-phenylpropanoate. To alleviate the mathematical complexity of the search for minima in the lattice energy due to the presence of two flexible entities in the asymmetric unit, the range of rigid-body lattice energy global optimizations was guided by a statistical analysis of the Cambridge Structural Database for common ion-pair geometries and ion conformations. A distributed multipole model for the dominant electrostatic interactions and high-level ab initio calculations for the intramolecular energy penalty for conformational distortions are used to quantify the relative stabilities of the p- and n-salt forms. While the ab initio prediction of the known structure of the p-salt as the most stable structure was insensitive to minor changes in the rigid-ion conformations considered, the relative stabilities of the known polymorphs and hypothetical structures of the n-salt were very sensitive. Although this paper provides a significant advance over traditional search algorithms and empirical force fields in determining the structures and relative stabilities of diastereomeric salt pairs, the sensitivity of the computed lattice energies to the fine details of the ion conformations overtaxes current computational models and renders the design of diastereomeric resolution processes by computational chemistry a challenging problem.

Algorithms↗

PubMed2005

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.

The prediction of functional sites in newly solved protein structures is a challenge for computational structural biology. Most methods for approaching this problem use evolutionary conservation as the primary indicator of the location of functional sites. However, sequence conservation reflects not only evolutionary selection at functional sites to maintain protein function, but also selection throughout the protein to maintain the stability of the folded state. To disentangle sequence conservation due to protein functional constraints from sequence conservation due to protein structural constraints, we use all atom computational protein design methodology to predict sequence profiles expected under solely structural constraints, and to compute the free energy difference between the naturally occurring amino acid and the lowest free energy amino acid at each position. We show that functional sites are more likely than non-functional sites to have computed sequence profiles which differ significantly from the naturally occurring sequence profiles and to have residues with sub-optimal free energies, and that incorporation of these two measures improves sequence based prediction of protein functional sites. The combined sequence and structure based functional site prediction method has been implemented in a publicly available web server.

Algorithms↗

PubMed1996

Energy efficient neural codes.

In 1969 Barlow introduced the phrase "economy of impulses" to express the tendency for successive neural systems to use lower and lower levels of cell firings to produce equivalent encodings. From this viewpoint, the ultimate economy of impulses is a neural code of minimal redundancy. The hypothesis motivating our research is that energy expenditures, e.g., the metabolic cost of recovering from an action potential relative to the cost of inactivity, should also be factored into the economy of impulses. In fact, coding schemes with the largest representational capacity are not, in general, optimal when energy expenditures are taken into account. We show that for both binary and analog neurons, increased energy expenditure per neuron implies a decrease in average firing rate if energy efficient information transmission is to be maintained.

Action Potentials↗

PubMedDate not supplied

Microbial impacts to the near-field environment geochemistry: a model for estimating microbial communities in repository drifts at Yucca Mountain.

Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned 1 million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 degrees C and above relative humidities of 90% in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley et al. [FEMS Microbiol. Rev. 20 (1997) 545] by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift to perform two separate mass balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C(160)(H(280)O(80))N(30)P(2)S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature and pH at that time. This optimization maximizes those reactions that produce >15 kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated and unsaturated environments and in laboratory situations to establish microbial growth limitations. Other projected uses include investigations of contaminated locations where monitored natural attenuation or engineered bioremediation could be employed.

Carbon↗