Melanin is a ubiquitous pigment in living organisms with multiple important functions, yet its structure is not well understood. We propose a structural model for eumelanin protomolecules, consisting of 4 or 5 of the basic molecular units (hydroquinone, indolequinone, and its tautomers), in arrangements that contain an inner porphyrin ring. We use time-dependent density functional theory to calculate the optical absorption spectrum of the structural model, which reproduces convincingly the main features of the experimental spectrum of eumelanin. Our model also reproduces accurately other important properties of eumelanin, including x-ray scattering data, its ability to capture and release metal ions, and the characteristic size of the protomolecules.

We present a new method for studying melanin in vivo based on diffuse reflectance spectroscopy of human skin. We find that the optical absorption spectrum of in vivo melanin exhibits an exponential dependence on wavelength, consistent with, but with a higher decay slope than, in vitro results. We offer theoretical justification for this exponential dependence on the basis of a recently proposed model for the structure of eumelanin protomolecules. Moreover, we report on a new method for analysis of diffuse reflectance spectra, which identifies intrinsic differences in absorption spectra between malignant melanoma and dysplastic nevi in vivo. These preliminary results are confirmed both by analysis of our own clinical data as well as by analysis of data from three independent, previously published studies. In particular, we find evidence that the histologic transition from dysplastic nevi to melanoma in situ and then to malignant melanoma is reflected in the melanin absorption spectra. Our results are very promising for the development of techniques for the noninvasive detection of melanoma and, more generally, for the study and characterization of pigmented skin lesions. It is also a promising approach for a better understanding of the biological role, structure, and function of melanin.

We report on a general method for the calculation of the frequency-dependent optical response of clusters based upon time-dependent density functional theory (TDDFT). The implementation is done using explicit propagation in the time domain and a self-consistent program that uses a linear combination of atomic orbitals (LCAO). Our actual calculations employ the SIESTA program, which is designed to be fast and accurate for large clusters. We use the adiabatic local density approximation to account for exchange and correlation effects. Results are presented for the imaginary part of the linear polarizability, ℑα(ω), and the dipole strength function, S(ω), of C60 and Na8, compared to previous calculations and to experiment. We also show how to calculate the integrated frequency-dependent second order non-linear polarizability for the case of a step function electric field,γstep(ω), and present results for C60. I. INTRODUCTIONAlthough density functional theory (DFT) 1,2 is a very successful theory for the ground state properties, the excited states calculated within the Kohn-Sham scheme often are much less successful in describing the optical response and the excitation spectra. The solution to this problem, in principle, is the extension of DFT to the time-dependent systems. It is interesting to note that the first calculation 3 using TDDFT preceded any formal development and it relied heavily on the analogy with the time-dependent Hartree-Fock method. The first steps towards the formulation of TDDFT were done by Deb and Gosh 4,5 who focused on potentials periodic in time, and by Bartolotti 6,7 who focused on adiabatic processes. Runge and Gross 8 established the foundations of TDDFT for a generic form of the time-dependent potential. TDDFT was further developed 9,10 to acquire a structure that is very similar to that of the conventional DFT. A very interesting feature of TDDFT, that does not appear in DFT, is the dependence of the density functionals on the initial state. For more information about TDDFT the reader is advised to read the authoritative reviews of Gross, Ullrich, and Gossmann, 11 and Gross, Dobson, and Petersilka. 12The polarizability describes the distortion of the charge cloud caused by the application of an external field. It is one of the most important response functions because it is directly related to electron-electron interactions, and correlations. In addition, it determines the response to charged particles, and optical properties. A quantity of particular interest is the dipole strength function, S(ω), which is directly related to the frequency-dependent linear polarizability, α(ω), byBy taking the imaginary part of Eq. (1) we obtainThe dipole strength function, S(ω), is proportional to the photoabsorption cross section, σ(ω), measured by most experiments and, therefore, allows direct comparison with experiment. In addition, the integration of S over energy gives the number of electrons, N e , (f-sum rule ) i.e.where f i are the oscillator strengths. This sum rule is very important becaus...

We present calculations of the optical response of the DNA bases and base pairs both in their normal and tautomeric forms in the gas phase, using time-dependent density functional theory (TDDFT). These calculations are performed in real time within the adiabatic approximation with a basis of local orbitals. Our results for the individual bases are in good agreement with experiment and computationally more demanding calculations of chemical accuracy. The optical response of base pairs indicates that the differences between normal and tautomeric forms in certain cases are significant enough to provide a means of identification.

We dispersed bulk crystalline Si into identical hydrogenated nanoparticles with negligible impurities and defects, which provide the opportunity for detailed comparison between measurement and theory. The UV photoluminescence of a dispersion of 1 nm silicon particles was studied. Distinct bands appear in the emission spectra with the lowest peaks in wavelength identified to be at 400, 360, and 310 nm with optimal excitation at 3.7, 4.0, and 4.6 eV, respectively. The multiple photoluminescence bands are analyzed in terms of the molecularlike energy levels of one bulklike and two nonbulklike reconstruction configurations of the filled fullerene single-core Si 29 H 24 , calculated by quantum Monte Carlo calculations and by time-dependent density functional theory. The measured bands are in close agreement with the excited states of the ideal bulklike configuration. However, there is a possibility that some of the observed bands might originate from the nonbulklike reconstructions. The Stokes shifts are discussed in terms of radiative relaxation via the molecularlike states versus charge carrier relaxation via the underlying continuum states.

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High Pressure Air Injection (HPAI) is a potentially attractive enhanced oil recovery method for deep, high-pressure light oil reservoirs after waterflooding. The advantage of air over other injectants, like hydrocarbon gas, carbon dioxide, nitrogen, or flue gas, is its availability at any location. HPAI has been successfully applied in the Williston Basin for more than twenty years and is currently being considered by many operators for application in their assets.Evaluation of the applicability of HPAI requires conducting laboratory experiments under reservoir temperature and pressure conditions to confirm crude auto-ignition and to assess the burn characteristics of the crude/reservoir rock system. The ensuing estimation of the potential incremental recovery from the application of HPAI in the reservoir under consideration requires fit-for-purpose numerical modeling. Typically, the flue gas generated in-situ by combustion leads to in an immiscible gas drive, where the stripping of volatile components is a key recovery mechanism. HPAI has therefore, in some instances, been modeled as an isothermal flue gas drive, employing an Equation of State (EOS) methodology. This approach, however, neglects combustion and its effects on both displacement and sweep. Furthermore, the EOS approach cannot predict if, and when, oxygen breakthrough at producers occurs. Combustion can be included in a limited fashion in simulations at the expense of extra computational time and complexity. In the available literature, combustion is taken generally into account under quite simplified conditions. This paper addresses the role that combustion plays on the incremental recovery of HPAI. Numerical simulations were conducted in a 3D model with real geological features. In order to capture more realistically the physics of the combustion front, a reservoir simulator with dynamic gridding capabilities was used. Kinetic parameters were based on the combustion tube laboratory experiments. The impact of combustion on residual oil, sweep efficiency and predicted project lifetime is presented by comparing isothermal EOS-simulations and multi-component combustion runs.

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