Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. I. A DeVoe theory approach.

Infrared (IR) vibrational circular dichroism (VCD), absorption, and linear dichroism (LD) spectra of four homopolyribonucleotides, poly(rA), poly(rG), poly(rC), and poly(rU), have been calculated, in the 1750-1550 cm-1 spectral region, using the DeVoe polarizability theory. A newly derived algorithm, which approximates the Hilbert transform of imaginaries to reals, was used in the calculations to obtain real parts of oscillator polarizabilities associated with each normal mode. The calculated spectra of the polynucleotides were compared with previously measured solution spectra. The good agreement between calculated and measured polynucleotide spectra indicates, for the first time, that the DeVoe theory is a useful means of calculating the VCD and IR absorption spectra of polynucleotides. For the first time, calculated DeVoe theory VCD and IR absorption spectra of oriented polynucleotides are presented. The calculated VCD spectra for the oriented polynucleotides are used to predict the spectra for such measurements made in the future. The calculated IR spectra for the oriented polynucleotides are useful in interpreting the linear dichroism of the polynucleotides.     

Ab initio (CASPT2) excited state calculations, including circular dichroism, of helically twisted cyanine dyes

Ab initio calculations at the CASSCF/CASPT2 level were performed on helically twisted mono-, tri-, and pentamethine cyanine dyes in the all-Z-configurations. Excitation energies and oscillator and rotatory strengths were calculated for the five lowest energy singlet states. Both the long wavelength methine band and the cis-band could be identified unambiguously from their configurational parentage. The calculated state energies are within 0.09 eV of the experimental value for the methine band and within 0.16 eV for the cis-band. The calculated rotatory strengths of the methine band shows sign inversion as the length of the chromophore increases: negative for the short monomethine, strongly positive for the pentamethine. The trimethine presents a borderline case: the measured rotatory strength is almost nil, the calculated one depends on the geometry. There is good agreement between rotatory strengths calculated in the velocity and in the length formalism.     

In vivo dosimetry of the rectum in image-guided adaptive interstitial-intracavitary brachytherapy of cervix cancer – A feasibility study

Aim and backgroundTo investigate the feasibility of in vivo rectal dosimetry in image-guided adaptive brachytherapy of cervical cancer.Materials and methodsError of measurement of dose rate in a semiconductor diode probe was investigated depending on the distance and angle in water, and on temperature in a polymethyl methacrylate phantom using an Ir-192 source. Furthermore, the difference between the measured and calculated dose was analysed in the interstitial brachytherapy of 30 cervix cancer patients. The relationship between in vivo measured dose, calculated dose in the point of the diode, calculated maximal dose in the point of the diodes and calculated maximal dose of the rectum were examined.ResultsThe dosimeter measured with 85% accuracy at more than 5 cm from the source, but within a closer distance the accuracy decreased significantly. At 45–90° angle, the device measured with a 15% error. The error increased with the temperature, 22% at 35 °C. In 8 cases (26.7%) the maximal dose was measured in the correct diode. The device measured 73% of the calculated dose in the point of the diode. The maximum of the calculated doses of diodes was 60% of the calculated maximal dose. The in vivo measured dose was 35% of the calculated maximal dose.ConclusionsUnder treatment conditions, the semiconductor diode does not provide reliable measured data. The probe pushes the rectal wall closer to the high dose areas and underestimates the dose of it. Semiconductor probe is not recommended for in vivo dosimetry of the rectum in image-guided brachytherapy of cervical cancer.     

Androsterone. The structure by force-field calculations.

The structure of androsterone was calculated by the force-field (molecular mechanics) method. Plots of the calculated structure are compared with those of the X-ray structure, and found to have all of the atoms in the same positions to within 0.1 A. The regular Dreiding model structure differs substantially from these calculated and experimental structures, atomic positions being up to 0.9 A removed from where they should be.     

Natural convection from leaves at realistic Grashof numbers

Abstract. The boundary layer resistance of model leaves was measured in still air, at a range of leaf-to-air temperature differences. The results were compared to those calculated from standard formulae for natural convection. The agreement between observed and calculated was only satisfactory when Grashof numbers exceeded about 105. At the lower Grashof numbers, which often prevail in nature, the observed rates of heat transfer considerably exceeded those calculated.     

Agreement between single crystal X-ray and molecular mechanical sugar ring conformations

We have calculated the deoxyribose sugar energy for a wide range of puckering parameters, (q, W), using different force fields. The intra-ring bond lengths, bond angles, and dihedral angles are calculated for every energy minimized structure and compared with 224 sugar ring structures available from DNA single crystal x-ray data. A modified Weiner's force field yields an excellent agreement with x-ray data. The calculated energy surface shows a variable amplitude repuckering path, with an average distortion of 0.42 A. Most of the experimental values of (q, W) fall within 1.0 Kcal/mol from the calculated minimum.     

Relationships between squamation chronology of the bluegill, Lepomis macrochims Rafinesque, and age-growth methods

Scales first developed on 13 mm juvenile bluegills along the midlateral line anterior to the caudal fin in the area of the caudal peduncle, squamation chronology continued anteriorly, and was completed in the dorsal area of the nape of 25 mm bluegills. Body-scale relationships calculated from scales taken from three distinct body regions of adult fish were compared using both the Dahl-Lea and the Fraser-Lee methods. The calculated body length intercepts followed the chronology of the squamation and compared closely with the observed fish length at scalation of each area. The body length intercepts were different from one another and from the origin. There was little difference among the Dahl-Lea and Fraser-Lee calculated lengths beyond annulus one for the three distinct body regions. In all cases, however, results from the Dahl-Lea method produced lower lengths than their corresponding values calculated by the Fraser-Lee method. Selected size classes which omitted the smaller fish resulted in body length intercepts higher than those calculated from the total sample regression.     

A telemetry-based velocometer to measure wheelchair velocity

The purpose of this paper is to present a telemetry-based velocometer that has the ability to measure wheelchair velocity. Five studies are described which provide measurements of the validity, dynamic response, reliability and resistance of the velocometer. Validity: a linear relationship was found when velocity calculated from the velocometer was plotted against three test velocities. The average root mean square deviation (ARMSD) was used to compare velocity calculated from the velocometer with velocity calculated by manual digitising at 200Hz. The ARMSD calculated for each test speed from three trials were 0.06+/-0.01, 0.27+/-0.05 and 0.48+/-0.16 ms(-1) at 1, 5 and 9 ms(-1), respectively. Dynamic response: expressed as a percentage of the average mean trial velocity, the ARMSD for the five acceleration and five deceleration trials were 6.5+/-1.8% and 6.9+/-1.2%, respectively. Reliability was assessed from a comparison between mean trial velocity calculated from velocometer output and the speed of the motor used to spin the wheels. Expressed as a percentage of the mean trial velocity, the mean+/-SD of the differences were 0.00+/-0.17%, for the ten disc wheel trials and 0.00+/-0.41%, for the ten spoke wheel trials. Velocometer resistance calculated as a factor of the mechanical resistance of the wheelchair rear wheel spinning in air were -0.50 and -0.91 N, for the disc and spoke wheel, respectively. Velocometer resistance calculated as a factor of the total mechanical resistance of the wheelchair-wheelchair user system were -1.37 and -1.82 N, for the disc and spoke wheel, respectively.     

Acoustic modes and nonbonded interactions of the double helix

Observations of acoustic velocities in DNA fibers have been used to refine nonbonded force constants for the DNA double helix. Long-range forces are found to be needed for A conformation and are likely to dominate in B conformation as well. The acoustic dispersion curves are described and calculated. A correction due to the effects of water is calculated. The effect of nonbonded interaction on other vibrational modes is calculated.     

Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles

Melting profiles were calculated for restriction fragments of ?X174 and fd phage DNAs and compared with experimental profiles. The algorithm of Fixman and Freire was slightly modified so that a stability parameter was assigned not to a base pair but to each nearest-neighbor doublet. Stabilities of the 10 kinds of nearest-neighbor doublets were estimated by fitting the calculated profiles to the observed ones. Agreement of the calculated and observed profiles was much improved by this modification. The most interesting finding was that purine (3′-5′) pyrimidine stackings are much more stable than their respective reverses. The order of nearest-neighbor stabilities is in excellent agreement with that of negative stacking energies calculated by Rein and coworkers by a quantum-chemical method.     

Phytochrome photoequilibria in green leaves under polychromatic radiation: a theoretical approach

Abstract Phytochrome photoequilibria within a model green leaf have been calculated. The results show a gradient in photoequilibria within the leaf lamina due to selective attenuation of incident light by the leaf tissue. Large differences were observed between photoequilibria calculated for a leaf under natural daylight and photoequilibria calculated for a leaf receiving daylight filtered through a vegetation canopy.     

Electrostatic calculations of amino acid titration and electron transfer, Q-AQB-->QAQ-B, in the reaction center.

The titration of amino acids and the energetics of electron transfer from the primary electron acceptor (QA) to the secondary electron acceptor (QB) in the photosynthetic reaction center of Rhodobacter sphaeroides are calculated using a continuum electrostatic model. Strong electrostatic interactions between titrating sites give rise to complex titration curves. Glu L212 is calculated to have an anomalously broad titration curve, which explains the seemingly contradictory experimental results concerning its pKa. The electrostatic field following electron transfer shifts the average protonation of amino acids near the quinones. The pH dependence of the free energy between Q-AQB and QAQ-B calculated from these shifts is in good agreement with experiment. However, the calculated absolute free energy difference is in severe disagreement (by approximately 230 meV) with the observed experimental value, i.e., electron transfer from Q-A to QB is calculated to be unfavorable. The large stabilization energy of the Q-A state arises from the predominantly positively charged residues in the vicinity of QA in contrast to the predominantly negatively charged residues near QB. The discrepancy between calculated and experimental values for delta G(Q-AQB-->QAQ-B) points to limitations of the continuum electrostatic model. Inclusion of other contributions to the energetics (e.g., protein motion following quinone reduction) that may improve the agreement between theory and experiment are discussed.     

Molecular weight and hydrodynamic properties of a proteinase A inhibitor from baker's yeast.

The molecular weight of the proteinase A inhibitor IA3 from baker's yeast was determined by different methods. From gel-filtration experiments, a molecular weight of 19 000 was calculated for the native inhibitor, while under denaturing conditions a molecular weight of 7400 was found. From electrophoretic experiments with the native protein, a molecular weight of 9000 was calculated. A similar value was obtained from the analytical ultracentrifuge, even at a protein concentration of 12 mg/ml. The diffusion coefficient and the partial specific volume were measured and from these data the frictional ratio and the Stokes radius were calculated. These parameters indicate that the relatively high apparent molecular weight calculated from the gel-filtration experiments is caused by the assymetric shape of the inhibitor molecule rather than by an aggregation of subunits.     

成虫期长于幼期的昆虫实验种群生殖力表参数估计模型的改进

针对昆虫的某些类群成虫期长于幼期的实际情况,利用矩阵建立了内禀增长力估计的改进型模型,使得因成虫期过长而引起的世代重叠情况下,子孙后代在母代成虫存活期内的繁殖量得到表达.对成虫期远长于幼期而引发的当代成虫生殖期间,出现的世代重叠和生殖量进行估计,使得内禀增长力rm的计算与实际较为吻合.经rm的精确值估计模型的验算,证明新模型比原模型在估计rm值时,更加接近精确值.     

Calculation of the thermodynamic quantities of solvation for lysozyme and β-lactoglobulin a in guanidinium chloride

The thermodynamic quantities of solvation, that is, Gibbs free energy, enthalpy, and entropy for the transfer of lysozyme and β-lactoglobulin A from water to 6M guanidinium chloride solution, were calculated from the respective contributions of constituent groups. Comparison of the calculated values with the experimental ones reveals satisfactory agreement for lysozyme, whereas for β-lactoglobulin A, it is semiquantitative. Thus the method of calculation appears to be fundamentally sound. The reasons for the differences in calculated and experimental value are briefly discussed.     

Dipole moment, enthalpy, and entropy changes of Hodgkin-Huxley type kinetic units.

Dipole moment, enthalpy, and entropy changes were calculated for hypothetical structural units which control the opening and closing of ionic channels in axon membranes. The changes of these thermodynamic functions were calculated both for activation (transition to intermediate complex) and for the structural transformation as a whole. The calculations are based on the experimentally determined Q10 values and the empirical formulae for the rate constants (alpha's and beta's) as functions of membrane potentials in Hodgkin-Huxley type models. From the calculated thermodynamic functions we suggest that the specific structural units of the axon membranes are probably of macromolecular (possible protein-like) dimensions with large dipole moments (hundreds of debyes). The calculated dipole moment changes of a single structural unit indicate that in many cases these dipole moments saturate at strong depolarizations or hyperpolarizations. The transitions in structural units show substantial activation enthalpies and entropies but the net enthalpy and entropy changes are practically negligible for the transition as a whole, i.e. the structural units presumably undergo displacements. While the calculated dipole moment changes associated with structural transformations in Loligo and Myxicola show similar potential dependencies, those for Rana usually show a different behavior. The relevance of the dipole moment changes to gating currents is discussed.     

Spatial structure of angiotensin in an aqueous solution

The spatial structure of spin-labeled angiotensin in aqueous solution wa investigated with the combined use of NMR, fluorescence spectroscopy and energy calculation including Monte-Carlo techniques. The calculated mean values of molecular parameters were compared with the experimental ones. The calculated and experimental mean values were regarded as statistically indistinguishable when the corresponding mean values occurred within the 95% confidence limit. The experimental parameters were shown to be adequately described by calculated conformers only with the assumption of the existence of dynamic equilibrium of conformers in solution. The mean values of statistical weights and their limits providing the agreement between the calculated and experimental data were determined. Two geometrically different forms of backbone structure for C-terminal hexapeptide in aqueous solution were revealed using the discussed approach; the N-terminal part of the molecule appeared to be much more conformationally labile. The model of molecule spatial structure is consistent with available literature data upon angiotensin titration experiments, its complexing with heavy metal ions etc.     

Agreement between Single Crystal X-Ray and Molecular Mechanical Sugar Ring Conformations

Abstract

We have calculated the deoxyribose sugar energy for a wide range of puckering parameters, (q, W), using different force fields. The intra-ring bond lengths, bond angles, and dihedral angles are calculated for every energy minimized structure and compared with 224 sugar ring structures available from DNA single crystal x-ray data. A modified Weiner's force field yields an excellent agreement with x-ray data.

The calculated energy surface shows a variable amplitude repuckering path, with an average distortion of 0.42 Å. Most of the experimental values of (q, W) fall within 1.0 Kcal/mol from the calculated minimum.     

Frontal plane moments do not accurately reflect ankle dynamics during running

The ankle joint has typically been treated as a universal joint with moments calculated about orthogonal axes and the frontal plane moment generally used to represent the net muscle action about the subtalar joint. However, this joint acts about an oblique axis. The purpose of this study was to examine the differences between joint moments calculated about the orthogonal frontal plane axis and an estimated subtalar joint axis. Three-dimensional data were collected on 10 participants running at 3.6 m/s. Joint moments, power, and work were calculated about the orthogonal frontal plane axis of the foot and about an oblique axis representing the subtalar joint. Selected parameters were compared with a paired t-test (alpha = 0.05). The results indicated that the joint moments calculated about the two axes were characteristically different. A moment calculated about an orthogonal frontal plane axis of the foot resulted in a joint moment that was invertor in nature during the first half of stance, but evertor during the second half of stance. The subtalar joint axis moment, however, was invertor during most of the stance. These two patterns may result in qualitatively different interpretations of the muscular contributions at the ankle during the stance phase of running.