Aerodynamic evaluation of the empty nose syndrome by means of computational fluid dynamics

The potential outcome of a surgical enlargement of internal nasal channels may be a complication of nasal breathing termed the Empty Nose Syndrome (ENS). ENS pathophysiology is not entirely understood because the expansion of air pathways would in theory ease inhalation. The present contribution is aimed at defining the biophysical markers responsible for ENS. Our study, conducted in silico, compares nasal aerodynamics in pre- and post-operative geometries acquired by means of computer tomography from the same individual. In this article, we elucidate and analyse the deviation of airflow patterns and nasal microclimate from the healthy benchmarks. The analysis reveals 53% reduction in flow resistance, radical re-distribution of nasal airflow, as well as dryer and colder nasal microclimate for the post-operative case.     

Photophysical properties, X-ray structures, electrochemistry, and DFT computational chemistry of osmium complexes

We report the synthesis of phosphorescent divalent osmium complexes of the form [Os(N-N)₂(L-L) or Os(L-L)₂(N-N)]²⁺ (PF₆)₂ where N-N is a derivative of 1,10-phenanthroline, and L-L is a diarsine or diphosphine ligand: 1,2-bis(dimethylphosphino)ethane, 1,2-bis(dicyclohexylphosphino)ethane, or 1,2-bis(dimethylarseno)benzene. X-ray structures have been determined, luminescent and electrochemical properties have been measured and DFT calculations have been performed on the complexes. The emission lifetime of complexes of structure Os(II)(L-L)₂(N-N) are longer than the those of Os(II)(N-N)₂(L-L). The DFT calculations show that there is significant mixing of the π−π^∗ into the dπ−π^∗ charge-transfer state for the complexes of the form Os(II)(L-L)₂(N-N) resulting in a longer lived excited state. Through DFT calculations we were able to conclude that the HOMO of the complexes is a d orbital on the osmium while the LUMO is the b₁(ψ) π^∗ system of the phenanthroline. However, we found that the HOMO did not have the correct symmetry to enable strong charge transfer to the phenanthroline to be observed, and the strong MLCT transition observed in the spectra is the metal d HOMO(−1) to the b1 π^∗ LUMO of the phenanthroline.     

Tropomyosin position on F-actin revealed by EM reconstruction and computational chemistry

Electron microscopy and fiber diffraction studies of reconstituted F-actin-tropomyosin filaments reveal the azimuthal position of end-to-end linked tropomyosin molecules on the surface of actin. However, the longitudinal z-position of tropomyosin along F-actin is still uncertain. Without this information, atomic models of F-actin-tropomyosin filaments, free of constraints imposed by troponin or other actin-binding proteins, cannot be formulated, and thus optimal interfacial contacts between actin and tropomyosin remain unknown. Here, a computational search assessing electrostatic interactions for multiple azimuthal locations, z-positions, and pseudo-rotations of tropomyosin on F-actin was performed. The information gleaned was used to localize tropomyosin on F-actin, yielding an atomic model characterized by protein-protein contacts that primarily involve clusters of basic amino acids on actin subdomains 1 and 3 juxtaposed against acidic residues on the successive quasi-repeating units of tropomyosin. A virtually identical model generated by docking F-actin and tropomyosin atomic structures into electron microscopy reconstructions of F-actin-tropomyosin validated the above solution. Here, the z-position of tropomyosin alongside F-actin was defined by matching the seven broad and narrow motifs that typify tropomyosin's twisting superhelical coiled-coil to the wide and tapering tropomyosin densities seen in surface views of F-actin-tropomyosin reconstructions. The functional implications of the F-actin-tropomyosin models determined in this work are discussed.     

Reduction of biological properties by means of functional sub-types

The general aim of this paper is to propose a reductionist strategy to higher-level property types. Starting from a common ground in the philosophy of science, I shall elaborate on possible realizer differences of higher-level property types. Because of the realizer types' causal heterogeneity, an introduction of functional subtypes of higher-level properties will be suggested. Each higher-level functional sub-type corresponds to one realizer type. This means that there is the theoretical possibility to reach some kind of type-identity and this opens up the way for theory reduction in a more complete manner. This kind of type-identity will go beyond the common ground of the identity of tokens and their reductive explanation. In the second part of the paper, this reductionist strategy will be applied to a specific debate in the philosophy of biology--the reductionist approach to classical genetics from a molecular point of view.     

Towards validation of computational analyses of peri-implant displacements by means of experimentally obtained displacement maps

Micro-finite element (μFE) analysis has recently been introduced for the detailed quantification of the mechanical interaction between bone and implant. The technique has been validated at an apparent level. The aim of this study was to address the accuracy of μFE analysis at the trabecular level. Experimental displacement fields were obtained by deformable image registration, also known as strain mapping (SM), of dynamic hip screws implanted in three human femoral heads. In addition, displacement fields were calculated using μFE analysis. On a voxel-by-voxel basis, the coefficients of determination (R(2)) between experimental and μFE-calculated displacements ranged from 0.67 to 0.92. Linear regression of the mean displacements over nine volumes of interest yielded R(2) between 0.81 and 0.84. The lowest R(2) values were found in regions of very small displacements. In conclusion, we found that peri-implant bone displacements calculated with μFE analysis correlated well with displacements obtained from experimental SM.     

On the radiation chemistry of thymine in aqueous solution

The reactions of thymine in aqueous solution with radiation-induced radicals OH, H, and e-aq were studied under various conditions. Competition studies using scavengers of OH radicals (methanol, ethanol, iodide) or of e-aq and/or H atoms (N2O, H+, O2) led to the conclusion that OH and H radicals destroy the chromophoric group of thymine, but e-aq does not. A trace of O2 proved to be necessary to obtain maximal destruction. Removal of the last traces of O2 resulted in a decrease of the destruction yield, possibly through restitution reactions. It was found that (1) alcohol radicals destroy thymine, even in the presence of O2; (2) the rate constant, k(OH + thymine) = 4.3 X 10(9) M(-1) sec(-1) (from competition with iodide); and (3) k(H + thymine) = 8 X 10(8) M(-1) sec(-1) (from competition with O2 in acid solution).     

A conformational study in solution of pro-somatostatin fragments by NMR and computational methods

The results of a conformational study by nuclear magnetic spectroscopy and computational methods on a series of point-mutated synthetic peptides, containing 14 amino acid residues and mimicking the region containing the Arg-Lys dibasic cleavage site of pro-somatostatin, have confirmed the possible role of a well defined secondary structure in the recognition phenomenon by processing enzymes. The importance of the residues located near the Arg-Lys dibasic site in the C-terminal region of the pro-hormone for the cleavage of the precursor into somatostatin-14 has been confirmed. The present structural analysis indicates the occurrence of two β-turns in the 4–7 and 11–14 regions, flanking the cleavage site, for all the peptides recognized as substrates by the processing enzyme. Interestingly, in the point-mutated analogue not processed by the enzyme and containing the replacement of proline by alanine in position 5 the first β-turn is displaced by one residue and involves the Ala⁵-Arg⁸ segment. This observation may explain the lack of recognition by the maturation enzyme. © 1998 European Peptide Society and John Wiley & Sons, Ltd.     

Rationalizing the design of polymeric biomaterials.

Polymers are a promising class of biomaterials that can be engineered to meet specific end-use requirements. They can be selected according to key 'device' characteristics such as mechanical resistance, degradability, permeability, solubility and transparency, but the currently available polymers need to be improved by altering their surface and bulk properties. The design of macromolecules must therefore be carefully tailored in order to provide the combination of chemical, interfacial, mechanical and biological functions necessary for the manufacture of new and improved biomaterials.     

Some considerations on the proper use of computational tools in transition metal chemistry

The current understanding of transition metal chemistry is reviewed placing the attention at the applications and applicability of computational quantum chemistry to the calculation and prediction of spectroscopic properties of transition metal complexes and molecular magnets.     

Bugs in computational chemistry software and their consequences: the importance of the source code

The increase in computer power and the development of new mathematical concepts implemented in software have allowed computational chemistry to emerge as a new research field. Although programs were freely distributed during the "golden age" of this discipline, today they are usually copyrighted and have become easier and easier to use through sophisticated graphical interfaces. This "democratization" is a vector of success for this discipline. Nowadays, non-theoreticians can use such programs more easily and solve chemistry-related problems with the computer. The number of program offerings has rapidly grown and private companies specialized in molecular modeling have appeared and compete to sell their products. Thus, numerous software packages, often presenting similar capabilities, are now available on the market. Within this context, the availability of the program source code remains, in our opinion, an important criterion for program selection.     

An approach to the evaluation of RNA solution structure and metal coordination chemistry by titration calorimetry

 Binding of divalent magnesium to RNA homopolymers was evaluated by titration calorimetry and analyzed in terms of the McGhee and von Hippel model of a one-dimensional infinite lattice. Examination of Mg²⁺ binding data for ds poly(A)×poly(U), ss poly(A), and ss poly(U) revealed that the sign of the enthalpy term relates to the mode of metal binding (inner or outer sphere), which in turn is directly related to the structural ordering of the polynucleotide in solution. This approach provides details of the thermodynamics of metal binding, stoichiometry, and coordination chemistry that underlie the structural and catalytic chemistry of RNA and offers a potential new probe of the solution structure of nucleic acids.     

The solution conformations of ferrichrome and deferriferrichrome determined by 1H-NMR spectroscopy and computational modeling

We have applied computational procedures that utilize nmr data to model the solution conformation of ferrichrome, a rigid microbial iron transport cyclohexapeptide of known x-ray crystallographic structure [D. van der Helm et al. (1980) J. Am. Chem. Soc. 102, 4224-4231]. The Al3+ and Ga3+ diamagnetic analogues, alumichrome and gallichrome, dissolved in d6-dimethylsulfoxide (d6-DMSO), were investigated via one- and two-dimensional 1H-nmr spectroscopy at 300, 600, and 620 MHz. Interproton distance constraints derived from proton Overhauser experiments were input to a distance geometry algorithm [T. F. Havel and K. Wüthrich (1984) Bull. Math. Biol. 46, 673-691] in order to generate a family of ferrichrome structures consistent with the experimental data. These models were subsequently optimized through restrained molecular dynamics/energy minimization [B. R. Brooks et al. (1983) J. Comp. Chem. 4, 187-217]. The resulting structures were characterized in terms of relative energies and conformational properties. Computations based on integration of the generalized Bloch equations for the complete molecule, which include the 14N-1H dipolar interaction, demonstrate that the x-ray coordinates reproduce the experimental nuclear Overhauser effect time courses very well, and indicate that there are no significant differences between the crystalline and solution conformations of ferrichrome. A similar study of the metal free peptide, deferriferrichrome, suggests that at least two conformers are present in d6-DMSO at 23 degrees C. Both are different from the ferrichrome structure and explain, through conformational averaging, the observed amide NH and CH alpha multiplet splittings. The occurrence of interconverting peptide backbone conformations yields an increased number of sequential NH-CH alpha and NH-NH Overhauser connectivities, which reflects the mean value of r-6 dependence of the dipolar interaction. Our results support the idea that, in the case of structurally rigid peptides, moderately accurate distance constraints define a conformational subspace encompassing the "true" structure, and that energy considerations reduce the size of this subspace. For flexible peptides, however, the straight-forward approach can be misleading since the nmr parameters are averaged over substantially different conformational states.     

Enzyme active sites: Identification and prediction of function using computational chemistry

Understanding the biochemically active amino acids in proteins is a key factor to improve the knowledge of how enzymes work, to predict the function of newly discovered protein structures of unknown function, and to establish design principles for enzyme engineering. Here, we explore recently reported computational chemistry-based methods for the prediction of active amino acids in protein 3D structures, including biochemically important distal residues, and their implications for functional genomics, for enzyme design, and for enhancing understanding of the function of enzymes.