FTIR difference spectroscopy is widely used to probe molecular bonding interactions of protein-bound electron transfer cofactors. The technique is particularly attractive because it provides information on both neutral and radical cofactor states. Such dual information is not easily obtainable using other techniques. Although FTIR difference spectroscopy has been used to study cofactors in biological protein complexes, in nearly all cases interpretation of the spectra has been purely qualitative. Virtually no computational work has been undertaken in an attempt to model the spectra. To address this problem we have developed the use of ONIOM (our own N-layered integrated molecular Orbital þ Molecular mechanics package) (quantum mechanical:molecular mechanics) methods to calculate FTIR difference spectra associated with protein-bound cofactors. As a specific example showing the utility of the approach we have calculated isotope edited FTIR difference spectra associated with unlabeled and labeled ubiquinones in the Q A binding site in Rhodobacter sphaeroides photosynthetic reaction centers. The calculated spectra are in remarkable agreement with experiment. Such agreement cannot be obtained by considering ubiquinone molecules in the gas phase or in solution. A calculation including the protein environment is required. The ONIOM calculated spectra agree well with experiment but indicate a very different interpretation of the experimental data compared to that proposed previously. In particular the calculations do not predict that one of the carbonyl groups of Q A is very strongly hydrogen bonded. We show that a computational-based interpretation of FTIR difference spectra associated with protein-bound cofactors is now possible. This approach will be applicable to FTIR studies of many cofactor-containing proteins.photosynthesis | vibration U biquinones play an important role in biological electron and proton transfer processes that occur in both respiration and photosynthesis (1). In photosynthetic reaction centers from purple bacteria, two ubiquinone (UQ) molecules, called Q A and Q B , act as terminal electron acceptors (2). In Rhodobacter (Rb.) sphaeroides purple bacterial reaction centers (PBRCs), Q A and Q B are both ubiquinone-10 (UQ 10 ) molecules. Q A and Q B have very different functions, however. Q A is an intermediary cofactor involved in transferring electrons from bacteriopheophytin to Q B , whereas Q B couples electron and proton transfer processes (3, 4). The very different redox functions of Q A and Q B is testimony to the flexibility of UQs in biological processes. Because Q A and Q B are both UQ 10 molecules, pigment-protein interactions must modulate their functional properties. Elucidation of how protein interactions modulate the functional properties of quinone cofactors is at the heart of much current research in photosynthesis (5, 6).FTIR difference spectroscopy is a sensitive molecular-level probe of pigment-protein interactions, and it is widely used to study both the neutral and radical stat...

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The coupling of presheath-sheath parameters is extended for the study of magnetized plasma sheath using the kinetic trajectory simulation (KTS) method, in which the final self-consistent states are obtained iteratively by solving the kinetic equations. In our case, it is assumed that the ion and electron velocity distribution functions are cut-off Maxwellians at the sheath entrance. The results show that the cut-off and Maxwellian maximum velocities have equal magnitudes at the sheath entrance and at wall. The presheath electron temperature has a considerable effect on the self-consistent potential profile which affects the Child sheath thickness. The latter increases from 3.8320 μm to 5.4190 μm when the presheath electron temperature increases from 10 eV to 20 eV. It is found that the number of ions reaching wall is higher than that of the electrons and hence the space charge density has its maximum value there. Furthermore, the temperature of ions in the sheath region increases with the increase in presheath ion temperature. Moreover, the cut-off distribution causes our simulation result to deviate from the theoretical result found for the Boltzmann distribution by about 3%. The coupling scheme presented here provides a basis for smooth transition of plasma parameters at the presheath-sheath interface. The proper understanding of the magnetized plasma-wall transition plays a vital role for further exploring the plasma sheath characteristics which has useful applications in fusion and industrial plasma devices.

FTIR microscopy has been used to collect spectra for uninfected (mock) Vero cells, and cells that have been infected with herpes simplex virus type 1 (HSV-1) and human adenovirus type 5 (Ad-5). Cells were infected at a multiplicity of infection of 10, and studied at 24 hours post exposure. The spectra for infected samples display many differences compared to the spectra for uninfected samples. To estimate how well the spectra for uninfected and infected samples could be discriminated, we used logistic and partial least squares regression methods. We show that the spectra for HSV-1 and mock infected samples are well differentiated and, for a sensitivity of 95%, we calculate a specificity of 0.999 using partial least squares regression. Spectra for Ad-5 and mock infected samples are also well differentiated. We find that applying our regression models constructed with one data set to a new validating data set still gives very high levels of specificity for a given sensitivity. Spectra for Ad-5 and HSV-1 infected samples are also differentiable. Applying our constructed regression models to new validating data, however, leads to a decrease in the discrimination capability in this instance. If one is simply interested in differentiating spectra associated with uninfected and infected cells, without distinguishing the type of infection, then we show that logistic regression models can break down whereas partial least squares regression models perform well.

Beat frequency and velocity variation of ions in a magnetized plasma sheath has been numerically investigated by using a kinetic trajectory simulation (KTS) model for varying obliqueness of the external magnetic field in presence of an electric field. Angular dependence of mean value, maximum amplitude, damping constant, frequency of oscillation and beat frequency have been studied. As the obliqueness of the field changes the mean values, beat frequency as well as the maximum amplitude of the velocity components also change but frequency of oscillation remains almost the same.