Biomedical subjects
Publications and source records attributed to M G Rockley.
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The reaction dynamics of vibrationally excited vinyl bromide have been investigated using classical trajectory methods on a neural network potential surface that is fitted to an ab initio database of 12 122 configuration energies obtained from electronic structure calculations conducted at the MP4(SDQ) level of theory using a 6-31G(d,p) basis set for the carbon and hydrogen atoms and Huzinaga's (43334334) basis set augmented with split outer s and p orbitals (4332143214) and a polarization f orbital with an exponent of 0.5 for the bromine atom. The sampling of the 12-dimensional configuration hyperspace of vinyl bromide prior to execution of the electronic structure calculations is accomplished by combining novelty-sampling methods, chemical intuition, and trajectory sampling on empirical and neural network surfaces. The final potential is obtained using a two-layer feed-forward neural network comprising 38 and 1 neurons, respectively, with hyperbolic tangent sigmoid and linear transfer functions in the hidden and output layers, respectively. The fitting is accomplished using the Levenberg-Marquardt algorithm with early stopping and Bayesian regularization methods to avoid overfitting. The interpolated potentials have a standard deviation from the ab initio results of 0.0578 eV, which is within the range generally regarded as "chemical accuracy" for the purposes of electronic structure calculations. It is shown that the potential surface may be easily and conveniently transferred from one research group to another. The files required for transfer of the vinyl bromide surface can be obtained from the Electronic Physics Auxiliary Publication Service. Total dissociation rate coefficients for vinyl bromide are obtained at five different excitation energies between 4.50 and 6.44 eV. Branching ratios into each of the six open reaction channels are computed at 24 vibrational energies in the range between 4.00 and 6.44 eV. The distribution of vibrational energies in HBr formed via three-center dissociation from vinyl bromide is determined and compared with previous theoretical and experimental results. It is concluded that the combination of ab initio electronic structure calculations, novelty sampling with chemical intuition and trajectories on empirical analytic surfaces, and feed-forward neural networks provides a viable framework in which to execute purely ab initio molecular-dynamics studies on complex systems with multiple open reaction channels.
A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.
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The Fourier transform infrared spectra of 15 purified retinoids were compared. Retinoids with conjugated C = O groups revealed the presence of a band between 1730 and 1630 cm-1 X A characteristic of retinoids is the presence of a band between 1650 and 1620 cm-1 due to C = C stretching where three to four conjugated C = O and C = C bonds were present or between 1610 and 1555 cm-1 where more conjugated unsaturations were present. The presence of cis double bonds was confirmed by a band at 1380 cm-1 while unsubstituted trans double bonds gave absorbances at 990 to 955 cm-1. Epoxy rings, which are present in some retinoids, resulted in bands at 1250, 880, and 790 cm-1 while a furan structure was confirmed by bands at 1175, 1083, and 1065 cm-1.
Time dependence of fluorescence enhancement of probes after addition to lipid vesicles has been used to investigate the position of chromophores in the lipid bilayer. Incorporation studies of a series of n-(9-anthroyloxy) fatty acids (n = 2, 2, 12 and 16) and 1,6-diphenylhexatriene in dipalmitoyl phosphatidylcholine vesicles are described. The activation energies for incorporation of these several lipid-mimic type fluorescent probes have been measured. Results show that the activation energy is a function of the distance of the anthracene moiety (chromophore) from the polar end of the probe and the length of the acyl portion of the probe. An average insertion energy of 0.6 kcal/carbon is seen for these fatty acid probes. The activation energy of 1,6-diphenylhexatriene, a factor of 2 greater than that of 16-(9-anthroyloxy)palmitic acid, is consistent with locating 1,6-diphenylhexatriene in the middle of the bilayer.
A new technique for measuring the infrared spectra of solids has been developed. The photoacoustic spectra of hemin, hemoglobin, protoporphyrin IX, and horseradish peroxidase show how this technique can be used to obtain structural information about biological materials which cannot readily be studied by normal transmission infrared spectroscopy. The method requires milligram quantities of material and involves no sample preparation.
An extremely rapid technique for deconvolving single exponential luminescence decay data is described that involves essentially no mathematical manipulation of the experimental data. The method permits "real time" measurement of deconvolved luminescence lifetimes with conventional pulsed, lifetime-fluorometers and phosphorimeters. The method assumes that the true luminescence decay of the chromophore is accurately represented by a single exponential decay function.
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Preparations of photosynthetic reaction centers from Rhodopseudomonas sphaeroides were excited with flashes lasting approximately 8 psec. Immediately after the excitation, there appeared a transient state which was characterized by new absorption bands near 500 and 680 nm, by a bleaching of bands near 540, 600, 760, and 870 nm, and by a blue shift of a band near 800 nm. The transient state decayed with an exponential decay time,t, of 246 plus or minus 16 psec after the flash. As the transient state decayed, the radical cation of the reaction center bacteriochlorophyll complex appeared. This indicates that the transient state is an intermediate in the photooxidation of the bacteriochlorophyll. The absorpiton spectrum of the transient state shows the state to be identical with a state (P-F) which has been detected previously in reaction centers that are prevented from completing the photooxidation, because of chemical reduction of the electron acceptor. Analysis of the spectrum suggests that the formation of P-F involves electron transfer from one bacteriochlorophyll molecule to another within the reaction center, or possibly from bacteriochlorophyll to the bacteriopheophytin of the complex. The initial absorbance changes after flash excitation also include a bleaching of an absorption band at 800 nm. The bleaching decays with tau approximately equal to 30 pse. The bleaching appers not to be a secondary effect, but rather to revael another early step in the primary photochemical reaction.