Conformational effects on the Circular Dichroism of Human Carbonic Anhydrase II: a multilevel computational study

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions

Hydrodynamics of bubble flow through a porous medium with applications to packed bed reactors

Gas-liquid flows through packed bed reactors (PBRs) are challenging to predict due to the tortuous flow paths that fluid interfaces must traverse. Experiments at the International Space Station showed that bubble and pulse flows are predominately observed under microgravity conditions, while trickle and spray flows observed under terrestrial conditions, are not present in microgravity. Toward understanding the physics behind the latter experiments, we simulate bubble flow through a PBR for different packing-particle-diameter-based Weber numbers and under different gravity conditions. We demonstrate different pore-scale mechanisms such as capillary entrapment, buoyancy entrapment, and inertia-induced bubble displacement. Then, we perform a quantitative analysis by introducing a new dynamic length scale, dependent upon the evolving gas-liquid interfacial area, to understand the dynamic trade-offs between the inertia, capillary, and buoyancy forces on a bubble passing through a PBR. This analysis leads us to define new dimensionless Weber-like numbers that delineate bubble entrapment from bubble displacement.Comment: 12 pages, 9 figure

Attosecond time-scale intra-atomic phase matching of high harmonic generation

Includes bibliographical references (page 5461).Using a model of high-harmonic generation that couples a fully quantum calculation with a semi-classical electron trajectory picture, we show that a new type of phase matching is possible when an atom is driven by an optimal optical waveform. For an optimized laser pulse shape, strong constructive interference is obtained in the frequency domain between emissions from different electron trajectories, thereby selectively enhancing a particular harmonic order. This work demonstrates that coherent control in the strong-field regime is possible by adjusting the peaks of a laser field on an attosecond time scale

Self-Consistent Pushing and Cranking Corrections to the Meson Fields of the Chiral Quark-Loop Soliton

We study translational and spin-isospin symmetry restoration for the two-flavor chiral quark-loop soliton. Instead of a static soliton at rest we consider a boosted and rotating hedgehog soliton. Corrected classical meson fields are obtained by minimizing a corrected energy functional which has been derived by semi-classical methods ('variation after projection'). We evaluate corrected meson fields in the region 300 MeV \le M \le 600 MeV of constituent quark masses M and compare them with the uncorrected fields. We study the effect of the corrections on various expectation values of nuclear observables such as the root-mean square radius, the axial-vector coupling constant, magnetic moments and the delta-nucleon mass splitting.Comment: 19 pages, LaTeX, 7 postscript figures included using 'psfig.sty', to appear in Int.J.Mod.Phys.

The phase diagram and bulk thermodynamical quantities in the NJL model at finite temperature and density

We reexamine the recent instanton motivated studies of Alford, Rajagopal and Wilczek, and Berges and Rajagopal in the framework of the standard SU(2) Nambu-Jona-Lasinio model. The chiral phase diagram is calculated in the temperature--density plane, and the pressure is evaluated as the function of the density. Obtaining simple approximate relations describing the $T$-$\mu$ and $T$-$p_F$ phase transition lines we find that the results of the instanton based model and that of the NJL model are identical. The diquark transition line is also given.Comment: 11 pages LaTeX plus 7 PS figures. One figure has been added and there are some changes in the text describing thi