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PubMed2001

A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base.

The electronic ground and first excited states of retinal and its Schiff base are optimized for the first time using the semiempirical AM1 Hamiltonian. The barrier for rotation about the C(11)-C(12) double bond is characterized by variation of both the twist angle delta(C(10)-C(11)-C(12)-C(13)) and the bond length d(C(11)-C(12)). The potential energy surface is obtained by varying these two parameters. The calculated ground state rotational barrier is equal to 15.6 kcal/mol for retinal and 20.5 kcal/mol for its Schiff base. The all-trans conformation is more stable by 3.7 kcal/mol than the 11-cis geometry. For the first excited state, S(1,) the 90 degrees twisted geometry represents a saddle point for retinal with the rotational barrier of 14.6 kcal/mol. In contrast, this conformation is an energy minimum for the Schiff base. It can be easily reached at room temperature from the planar minima since it is separated from them by a barrier of only 0.6 kcal/mol. The 90 degrees minimum conformation is more stable than the all-trans by 8.6 kcal/mol. We are thus able to present a reaction path on the S(1) surface of the retinal Schiff base with an almost barrier-less geometrical relaxation into a twisted minimum geometry, as observed experimentally. The character of the ground and first excited singlet states underscores the need for the inclusion of double excitations in the calculations.

Energy Transfer↗
PubMed2002

Intensity and energy modulated radiotherapy with proton beams: variables affecting optimal prostate plan.

Inverse planning for intensity- and energy-modulated radiotherapy (IEMRT) with proton beams involves the selection of (i) the relative importance factors to control the relative importance of the target and sensitive structures, (ii) an appropriate energy resolution to achieve an acceptable depth modulation, (iii) an appropriate beamlet width to modulate the beam laterally, and (iv) a sufficient number of beams and their orientations. In this article we investigate the influence of these variables on the optimized dose distribution of a simulated prostate cancer IEMRT treatment. Good dose conformation for this prostate case was achieved using a constellation of I factors for the target, rectum, bladder, and normal tissues of 500, 50, 15, and 1, respectively. It was found that for an active beam delivery system, the energy resolution should be selected on the basis of the incident beams' energy spread (sigmaE) and the appropriate energy resolution varied from 1 MeV at sigmaE = 0.0 to 5 MeV at sigmaE= 2.0 MeV. For a passive beam delivery system the value of the appropriate depth resolution for inverse planning may not be critical as long as the value chosen is at least equal to one-half the FWHM of the primary beam Bragg peak. Results indicate that the dose grid element dimension should be equal to or no less than 70% of the beamlet width. For this prostate case, we found that a maximum of three to four beam ports is required since there was no significant advantage to using a larger number of beams. However for a small number (< or = 4) of beams the selection of beam orientations, while having only a minor effect on target coverage, strongly influenced the sensitive structure sparing and normal tissue integral dose.

Algorithms↗
PubMed2002

Optimization of intensity-modulated very high energy (50-250 MeV) electron therapy.

This work evaluates the potential of very high energy (50-250 MeV) electron beams for dose conformation and identifies those variables that influence optimized dose distributions for this modality. Intensity-modulated plans for a prostate cancer model were optimized as a function of the importance factors, beam energy and number of energy bins, number of beams, and the beam orientations. A trial-and-error-derived constellation of importance factors for target and sensitive structures to achieve good conformal dose distributions was 500, 50, 10 and I for the target, rectum, bladder and normal tissues respectively. Electron energies greater than 100 MeV were found to be desirable for intensity-modulated very high energy electron therapy (VHEET) of prostate cancer. Plans generated for lower energy beams had relatively poor conformal dose distributions about the target region and delivered high doses to sensitive structures. Fixed angle beam treatments utilizing a large number of fields in the range 9-21 provided acceptable plans. Using more than 21 beams at fixed gantry angles had an insignificant effect on target coverage, but resulted in an increased dose to sensitive structures and an increased normal tissue integral dose. Minor improvements in VHEET plans utilizing a 'small' number (< or =9) of beams may be achieved if, in addition to intensity modulation, energy modulation is implemented using a small number (< or =3) of beam energies separated by 50 to 100 MeV. Rotation therapy provided better target dose homogeneity but unfortunately resulted in increased rectal dose, bladder dose and normal tissue integral dose relative to the 21-field fixed angle treatment plan. Modulation of the beam energy for rotation therapy had no beneficial consequences on the optimized dose distributions. Lastly, selection of beam orientations influenced the optimized treatment plan even when a large number of beams (approximately 15) were employed.

Electrons↗
PubMed1998

Theoretical studies employing an ab initio and molecular modeling combination method on the DNA binding of bis-benzimidazoles designed for bioreductive activation.

Ab initio calculations (Hartree-Fock) using the 3-21G and the STO-3G Gaussian basis sets were performed on synthetic analogues of the minor groove binding bis-benzimidazole Hoechst 33258 designed to be subject to bioreductive activation. Such compounds have been shown experimentally to react with DNA to exhibit sequence dependent inhibition of human placental helicase and display significant anticancer properties. Geometry optimized conformations and energies were derived. The binding of the optimized conformations of the drugs to both alternating and non-alternating (AT)n and to (G)n-(C)n sequences were studied. The energetics of reaction at alternative DNA base sites are calculated and compared.

Bisbenzimidazole↗
PubMed1996

Universality Classes of Optimal Channel Networks

Energy minimization of both homogeneous and heterogeneous river networks shows that, over a range of parameter values, there are only three distinct universality classes. The exponents for all three classes of behavior are calculated.

Journal Article↗
PubMed2006

Dual-energy mammography: simulation studies.

This paper presents a mammography simulator and demonstrates its applicability in feasibility studies in dual-energy (DE) subtraction mammography. This mammography simulator is an evolution of a previously presented x-ray imaging simulation system, which has been extended with new functionalities that are specific for DE simulations. The new features include incident exposure and dose calculations, the implementation of a DE subtraction algorithm as well as amendments to the detector and source modelling. The system was then verified by simulating experiments and comparing their results against published data. The simulator was used to carry out a feasibility study of the applicability of DE techniques in mammography, and more precisely to examine whether this modality could result in better visualization and detection of microcalcifications. Investigations were carried out using a 3D breast software phantom of average thickness, monoenergetic and polyenergetic beam spectra and various detector configurations. Dual-shot techniques were simulated. Results showed the advantage of using monoenergetic in comparison with polyenergetic beams. Optimization studies with monochromatic sources were carried out to obtain the optimal low and high incident energies, based on the assessment of the figure of merit of the simulated microcalcifications in the subtracted images. The results of the simulation study with the optimal energies demonstrated that the use of the DE technique can improve visualization and increase detectability, allowing identification of microcalcifications of sizes as small as 200 microm. The quantitative results are also verified by means of a visual inspection of the synthetic images.

Algorithms↗
PubMed2003

Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction.

Docking of metalloproteinase inhibitors remains a challenge due to the zinc multiple coordination geometries and the lack of appropriate force field parameters to model the metal/ligand interactions. In this study, we explore the docking accuracy and scoring reliability for the docking of matrix metalloproteinase (MMP) inhibitors using AutoDock 3.0. Potential problems associated with zinc ion were investigated by docking 16 matrix metalloproteinase ligands to their crystal structures. A good coordination between the zinc binding group (ZBG) and the zinc was shown to be a prerequisite for the ligand to fit the binding site. A simplex optimization of zinc parameters, including zinc radius, well depth, and zinc charges, was performed utilizing the 14 MMP complexes with good docking. The use of optimized zinc parameters (zinc radius: 0.87 A; well depth: 0.35 kcal/mol; and zinc charges: +0.95 e) shows improvement in both docking accuracy at the zinc binding site and the prediction of binding free energies. Although further improvement in the docking procedure, particularly the scoring function is needed, optimization of zinc parameters provides an efficient way to improve the performance of AutoDock as a drug discovery tool.

Binding Sites↗
PubMed2001

Optimizing nitrogen management in food and energy production and environmental protection: summary statement from the Second International Nitrogen Conference.

Human efforts to produce food and energy are changing the nitrogen (N) cycle of the Earth. Many of these changes are highly beneficial for humans, while others are detrimental to people and the environment. These changes transcend scientific disciplines, geographical boundaries, and political structures. They challenge the creative minds of natural and social scientists, economists, engineers, business leaders, and decision makers. The Second International Nitrogen Conference was designed to facilitate communications among all stakeholders in the "nitrogen community" of the world. The Conference participants" goal in the years and decades ahead is to encourage every country to make optimal choices about N management in food production and consumption, energy production and use, and environmental protection. Scientific findings and recommendations for decision makers that emerged from the Conference are presented.

Agriculture↗
PubMed2006

CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications.

We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface-area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR ensembles with 0.951+/-0.047 correlation and predicts relative solvation energy changes between members of individual ensembles with an accuracy of 15.8+/-9.6 kcal/mol. The energy of individual atoms in any of CIRSE's 17 types is predicted with at least 0.98 correlation. We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications. The CIRSE model shows some propensity to accumulate errors in energy minimization as well as rotamer optimization, but these errors are consistent enough that CIRSE correctly identifies the relative solvation energies of designed sequences as well as putative docked complexes. We analyze the errors accumulated by the CIRSE model during each type of simulation and suggest means of improving the model to be generally useful for all-atom simulations.

Models, Molecular↗
PubMed1987

Nutritional status and energy metabolism of crayfish (Procambarus clarkii, Girard) muscle and hepatopancreas.

1. Food deprivation resulted in significant decreases in muscle carbohydrate, lipid and water content and increased ATP, ADP, AMP and total adenylate levels over the 21-day experimental period. 2. In the hepatopancreas phosphoarginine was significantly higher on day 21 in the starved crayfish. 3. Muscle energy charges remained within optimal (unstressed) ranges, while hepatopancreatic energy charges of food-deprived crayfish fell into suboptimal (stressed) ranges, indicating the necessity of examining organs separately to accurately ascertain metabolic changes in response to stressors.

Adenine Nucleotides↗
PubMed2005

Iridium cyclometalated complexes with axial symmetry: time-dependent density functional theory investigation of trans-bis-cyclometalated complexes containing the tridentate ligand 2,6-diphenylpyridine.

A new series of iridium cyclometalated complexes with a C/N/C dppy-type ligand and a N/N/N tpy-type ligand have been synthesized and characterized by various techniques such as mass spectrometry, 1H and 13C NMR, cyclic voltammetry, both steady-state and time-resolved emission and absorption studies, and time-dependent DFT (TDDFT) calculations. The complexes exhibit strong visible absorptions and long-lived (1.6-2.0 micros) emissions (lambdamax, ca. 680 nm) in room-temperature solution. DFT calculations on the ground-state geometry match that of an X-ray crystal structure. TDDFT calculations give accurate predictions of the electronic absorption energies and intensities, while geometry optimizations on the lowest energy triplet state give accurate energies for the emission. Examination of the relevant molecular orbitals shows that the inherent asymmetry of the coordination environment offers a unique directional character to the emitting excited state, which is predominately LLCT (dppy --> tpy) in nature.

Journal Article↗
PubMed2004

Structure prediction of high-pressure phases for alkali metal sulfides.

For a given chemical system we present a systematic approach to predict structures, which may exist at high pressure, by investigating the global enthalpy landscape. We combine global optimizations, based on empirical potential energy functions, and local optimizations (volume, cell shape, and atomic positions) on both Hartree-Fock and density functional theory level. We predict the existence of high-pressure phases for the alkali metal sulfides of the composition M2S (M = Li, Na, K, Rb, Cs), together with the transition pressures among these phases.

Journal Article↗
PubMed2003

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding.

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Drug Design↗
PubMed2003

[Development of an optimized formulation of damask marmalade with low energy level using Taguchi methodology].

The goal of this present study was the development of an optimized formula of damask marmalade low in calories applying Taguchi methodology to improve the quality of this product. The selection of this methodology lies on the fact that in real life conditions the result of an experiment frequently depends on the influence of several variables, therefore, one expedite way to solve this problem is utilizing factorial desings. The influence of acid, thickener, sweetener and aroma additives, as well as time of cooking, and possible interactions among some of them, were studied trying to get the best combination of these factors to optimize the sensorial quality of an experimental formulation of dietetic damask marmalade. An orthogonal array L8 (2(7)) was applied in this experience, as well as level average analysis was carried out according Taguchi methodology to determine the suitable working levels of the design factors previously choiced, to achieve a desirable product quality. A sensory trained panel was utilized to analyze the marmalade samples using a composite scoring test with a descriptive acuantitative scale ranging from 1 = Bad, 5 = Good. It was demonstrated that the design factors sugar/aspartame, pectin and damask aroma had a significant effect (p < 0.05) on the sensory quality of the marmalade with 82% of contribution on the response. The optimal combination result to be: citric acid 0.2%; pectin 1%; 30 g sugar/16 mg aspartame/100 g, damask aroma 0.5 ml/100 g, time of cooking 5 minutes. Regarding chemical composition, the most important results turned out to be the decrease in carbohydrate content compaired with traditional marmalade with a reduction of 56% in coloric value and also the amount of dietary fiber greater than similar commercial products. Assays of storage stability were carried out on marmalade samples submitted to different temperatures held in plastic bags of different density. Non percetible sensorial, microbiological and chemical changes were detected after 90 days of storage under controlled conditions.

Dietary Fiber↗
PubMed1995

Comparison of treatment plans for irradiating adenocarcinoma of the prostate.

In a clinic with multiple megavoltage beams (Co-60, 6 MV, 10 MV, 18 MV) available, the optimal dose distributions depends on the radiation technique, patient size, and beam energy. To determine optimal dose distributions for external beam irradiation for patients with localized adenocarcinoma of the prostate, we investigated the dependence of beam energy, treatment technique, and patient size. Various radiation isodose plans were prepared at the central plane of the treatment field using computerized tomography scans of the pelvis for small, medium, and large patients. The dose uniformity in the target volume, the dose received by sensitive tissues such as bladder, rectum, and femoral heads, and the irradiated volume of these normal tissues were used as the criteria for comparing the plans. In all cases, the target volume was within the 95% isodose line with good dose uniformity (+/- 5%, of the prescribed dose). The volume of the rectum and bladder enclosed within the 90% isodose curve depended on the choice of the beam energy and the treatment technique for different patient sizes. For the small size patient the optimal dose distribution was achieved by using 10 MV box and arc or oblique boost. For the medium size patient, using 18 MV X-rays with box technique and oblique boost gave the optimal treatment plan. For the large size patient, using 18 MV or 10 MV X-rays box technique with arc boost were both acceptable.

Adenocarcinoma↗
PubMed2005

Optimizing the driving function for nonequilibrium free-energy calculations in the linear regime: a variational approach.

We consider the issue of optimizing linear-regime nonequilibrium simulations to estimate free-energy differences. In particular, we focus on the problem of finding the best-possible driving function lambda(t) that, for a given thermodynamic path, simulation algorithm, and amount of computational effort, minimizes dissipation. From the fluctuation-dissipation theorem it follows that, in the linear-response regime, the dissipation is controlled by the magnitude and characteristic correlation time of the equilibrium fluctuations in the driving force. As a result, the problem of finding the optimal switching scheme involves the solution of a standard problem in variational calculus: the minimization of a functional with respect to the switching function. In practice, the minimization involves solving the associated Euler-Lagrange equation subject to a set of boundary conditions. As a demonstration we apply the approach to the simple, yet illustrative problem of computing the free-energy difference between two classical harmonic oscillators with very different characteristic frequencies.

Journal Article↗
PubMed1976

Protein needs and possible modifications of the American diet.

The matter of protein needs is almost irrelevant in the discussion of appropriate modification of the American diet. Our total food supply system from the producer through the processor to the retail distributor is wasteful of energy and produces a food supply of less than optimal quality. The energy crisis may have a favorable effect on the food supply. We should and no doubt will contribute to the world food supply for a long time to come, but eventually the countries in need of food must solve their problems internally. In the long run, we can probably do more by attempting to conserve resources than by trying to feed the world.

Adult↗