Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis.

Phylogenetic analyses are increasingly used in attempts to clarify transmission patterns of human immunodeficiency virus type 1 (HIV-1), but there is a continuing discussion about their validity because convergent evolution and transmission of minor HIV variants may obscure epidemiological patterns. Here we have studied a unique HIV-1 transmission cluster consisting of nine infected individuals, for whom the time and direction of each virus transmission was exactly known. Most of the transmissions occurred between 1981 and 1983, and a total of 13 blood samples were obtained approximately 2-12 years later. The p17 gag and env V3 regions of the HIV-1 genome were directly sequenced from uncultured lymphocytes. A true phylogenetic tree was constructed based on the knowledge about when the transmissions had occurred and when the samples were obtained. This complex, known HIV-1 transmission history was compared with reconstructed molecular trees, which were calculated from the DNA sequences by several commonly used phylogenetic inference methods [Fitch-Margoliash, neighbor-joining, minimum-evolution, maximum-likelihood, maximum-parsimony, unweighted pair group method using arithmetic averages (UPGMA), and a Fitch-Margoliash method assuming a molecular clock (KITSCH)]. A majority of the reconstructed trees were good estimates of the true phylogeny; 12 of 13 taxa were correctly positioned in the most accurate trees. The choice of gene fragment was found to be more important than the choice of phylogenetic method and substitution model. However, methods that are sensitive to unequal rates of change performed more poorly (such as UPGMA and KITSCH, which assume a constant molecular clock). The rapidly evolving V3 fragment gave better reconstructions than p17, but a combined data set of both p17 and V3 performed best. The accuracy of the phylogenetic methods justifies their use in HIV-1 research and argues against convergent evolution and selective transmission of certain virus variants.

Determining RNA solution structure by segmental isotopic labeling and NMR: application to Caenorhabditis elegans spliced leader RNA 1.

Recent developments in multidimensional heteronuclear NMR spectroscopy and large-scale synthesis of uniformly 13C- and 15N-labeled oligonucleotides have greatly improved the prospects for determination of the solution structure of RNA. However, there are circumstances in which it may be advantageous to label only a segment of the entire RNA chain. For example, in a larger RNA molecule the structural question of interest may reside in a localized domain. Labeling only the corresponding nucleotides simplifies the spectrum and resonance assignments because one can filter proton spectra for coupling to 13C and 15N. Another example is in resolving alternative secondary structure models that are indistinguishable in imino proton connectivities. Here we report a general method for enzymatic synthesis of quantities of segmentally labeled RNA molecules required for NMR spectroscopy. We use the method to distinguish definitively two competing secondary structure models for the 5' half of Caenorhabditis elegans spliced leader RNA by comparison of the two-dimensional [15N] 1H heteronuclear multiple quantum correlation spectrum of the uniformly labeled sample with that of a segmentally labeled sample. The method requires relatively small samples; solutions in the 200-300 microM concentration range, with a total of 30 nmol or approximately 40 micrograms of RNA in approximately 150 microliters, give strong NMR signals in a short accumulation time. The method can be adapted to label an internal segment of a larger RNA chain for study of localized structural problems. This definitive approach provides an alternative to the more common enzymatic and chemical footprinting methods for determination of RNA secondary structure.

A method for distance determination in proteins using a designed metal ion binding site and site-directed spin labeling: evaluation with T4 lysozyme.

The use of molecular genetics to introduce both a metal ion binding site and a nitroxide spin label into the same protein opens the use of paramagnetic metalnitroxyl interactions to estimate intramolecular distances in a wide variety of proteins. In this report, a His-Xaa3-His metal ion binding motif was introduced at the N terminus of the long interdomain helix of T4 lysozyme (Lys-65 --> His/Gln-69 --> His) of three mutants, each containing a single nitroxide-labeled cysteine residue at position 71, 76, or 80. The results show that Cu(II)-induced relaxation effects on the nitroxide can be quantitatively analyzed in terms of interspin distance in the range of 10-25 A using Redfield theory, as first suggested by Leigh [Leigh, J.S. (1970) J. Chem. Phys. 52, 2608-2612]. Of particular interest is the observation that distances can be determined both under rigid lattice conditions in frozen solution and in the presence of motion of the spins at room temperature under physiological conditions. The method should be particularly attractive for investigating structure in membrane proteins that are difficult to crystallize. In the accompanying paper, the technique is applied to a polytopic membrane protein, lactose permease.

Thermodynamic parameters for the helix-coil transition of oligopeptides: molecular dynamics simulation with the peptide growth method.

The helix-coil transition equilibrium of polypeptides in aqueous solution was studied by molecular dynamics simulation. The peptide growth simulation method was introduced to generate dynamic models of polypeptide chains in a statistical (random) coil or an alpha-helical conformation. The key element of this method is to build up a polypeptide chain during the course of a molecular transformation simulation, successively adding whole amino acid residues to the chain in a predefined conformation state (e.g., alpha-helical or statistical coil). Thus, oligopeptides of the same length and composition, but having different conformations, can be incrementally grown from a common precursor, and their relative conformational free energies can be calculated as the difference between the free energies for growing the individual peptides. This affords a straightforward calculation of the Zimm-Bragg sigma and s parameters for helix initiation and helix growth. The calculated sigma and s parameters for the polyalanine alpha-helix are in reasonable agreement with the experimental measurements. The peptide growth simulation method is an effective way to study quantitatively the thermodynamics of local protein folding.

New method for designing distillation columns of multicomponent mixtures

This paper presents a series of calculation procedures for computer design of ternary distillation columns overcoming the iterative equilibrium calculations necessary in these kind of problems and, thus, reducing the calculation time. The proposed procedures include interpolation and intersection methods to solve the equilibrium equations and the mass and energy balances. The calculation programs proposed also include the possibility of rigorous solution of mass and energy balances and equilibrium relations.

Pitfalls on computing liquid-liquid phase equilibria using the k-value method

Poster presented in the 11th Mediterranean Congress of Chemical Engineering, Barcelona, October 21-24, 2008.

An improvement of a SLAM RGB-D method with movement prediction derived from a study of visual features

This paper presents a method for the fast calculation of a robot’s egomotion using visual features. The method is part of a complete system for automatic map building and Simultaneous Location and Mapping (SLAM). The method uses optical flow to determine whether the robot has undergone a movement. If so, some visual features that do not satisfy several criteria are deleted, and then egomotion is calculated. Thus, the proposed method improves the efficiency of the whole process because not all the data is processed. We use a state-of-the-art algorithm (TORO) to rectify the map and solve the SLAM problem. Additionally, a study of different visual detectors and descriptors has been conducted to identify which of them are more suitable for the SLAM problem. Finally, a navigation method is described using the map obtained from the SLAM solution.

3D numerical modelling of acoustic horns using the method of fundamental solutions

In the present work, a three-dimensional (3D) formulation based on the method of fundamental solutions (MFS) is applied to the study of acoustic horns. The implemented model follows and extends previous works that only considered two-dimensional and axisymmetric horn configurations. The more realistic case of 3D acoustic horns with symmetry regarding two orthogonal planes is addressed. The use of the domain decomposition technique with two interconnected sub-regions along a continuity boundary is proposed, allowing for the computation of the sound pressure generated by an acoustic horn installed on a rigid screen. In order to reduce the model discretization requirements for these cases, Green’s functions derived with the image source methodology are adopted, automatically accounting for the presence of symmetry conditions. A strategy for the calculation of an optimal position of the virtual sources used by the MFS to define the solution is also used, leading to improved reliability and flexibility of the proposed method. The responses obtained by the developed model are compared to reference solutions, computed by well-established models based on the boundary element method. Additionally, numerically calculated acoustic parameters, such as directivity and beamwidth, are compared with those evaluated experimentally.

Organic distributed feedback laser to monitor solvent extraction upon thermal annealing in solution-processed polymer films

Solution-processed polymer films are used in multiple technological applications. The presence of residual solvent in the film, as a consequence of the preparation method, affects the material properties, so films are typically subjected to post-deposition thermal annealing treatments aiming at its elimination. Monitoring the amount of solvent eliminated as a function of the annealing parameters is important to design a proper treatment to ensure complete solvent elimination, crucial to obtain reproducible and stable material properties and therefore, device performance. Here we demonstrate, for the first time to our knowledge, the use of an organic distributed feedback (DFB) laser to monitor with high precision the amount of solvent extracted from a spin-coated polymer film as a function of the thermal annealing time. The polymer film of interest, polystyrene in the present work, is doped with a small amount of a laser dye as to constitute the active layer of the laser device and deposited over a reusable DFB resonator. It is shown that solvent elimination translates into shifts in the DFB laser wavelength, as a consequence of changes in film thickness and refractive index. The proposed method is expected to be applicable to other types of annealing treatments, polymer-solvent combinations or film deposition methods, thus constituting a valuable tool to accurately control the quality and reproducibility of solution-processed polymer thin films.

Rapid solution of finite element equations on locally refined grids by multi-level methods /

"UILU-ENG 80 1712."

Methods in Monte Carlo solution of the radiation transport equation /

"UNC-5014 (Volume A) Final Report covering the period 20 March 1961 - 31 May 1962."

The planter's guide; or, A practical essay on the best method of giving immediate effect to wood, by the removal of large trees and underwood; being an attempt to place the art, and that of geneneral arboriculture, on fixed and phytological principles; interspersed with observations on general planting, and the improvement of real landscape. Originally intended for the climate of Scotland.

Mode of access: Internet.

A Kinetic Vlasov Model for Plasma Simulation Using Discontinuous Galerkin Method on Many-Core Architectures

Thesis (Ph.D.)--University of Washington, 2016-03

Analysis of the free vibration of rectangular plates with central cut-outs using the discrete Ritz method

We present an analysis of the free vibration of plates with internal discontinuities due to central cut-outs. A numerical formulation for a basic L-shaped element which is divided into appropriate sub-domains that are dependent upon the location of the cut-out is used as the basic building element. Trial functions formed to satisfy certain boundary conditions are employed to define the transverse deflection of each sub-domain. Mathematical treatments in terms of the continuities in displacement, slope, moment, and higher derivatives between the adjacent sub-domains are enforced at the interconnecting edges. The energy functional results, from the proper assembly of the coupled strain and kinetic energy contributions of each sub-domain, are minimized via the Ritz procedure to extract the vibration frequencies and. mode shapes of the plates. The procedures are demonstrated by considering plates with central cut-outs that are subjected to two types of boundary conditions. (C) 2003 Elsevier Ltd. All rights reserved.

A convergent solution-phase synthesis of the macrocycle Ac-Phe-[Orn-Pro-D-Cha-Trp-Arg], a potent new antiinflammatory drug

Relatively few cyclic peptides have reached the pharmaceutical marketplace during the past decade, most produced through fermentation rather than made synthetically. Generally, this class of compounds is synthesized for research purposes on milligram scales by solid-phase methods, but if the potential of macrocyclic peptidomimetics is to be realized, low-cost larger scale solution-phase syntheses need to be devised and optimized to provide sufficient quantities for preclinical, clinical, and commercial uses. Here, we describe a cheap, medium-scale, solution-phase synthesis of the first reported highly potent, selective, and orally active antagonist of the human C5a receptor. This compound, Ac-Phe[Orn-Pro-D-Cha-Trp-Arg], known as 3D53, is a macrocyclic peptidomimetic of the human plasma protein C5a and displays excellent antiinflammatory activity in numerous animal models of human disease. In a convergent approach, two tripeptide fragments Ac-Phe-Orn-(Boc)-Pro-OH and H-D-Cha-Trp(For)-Arg-OEt were first prepared by high-yielding solution-phase couplings using a mixed anhydride method before coupling them to give a linear hexapeptide which, after deprotection, was obtained in 38% overall yield from the commercially available amino acids. Cyclization in solution using BOP reagent gave the antagonist in 33% yield (13% overall) after HPLC purification. Significant features of the synthesis were that the Arg side chain was left unprotected throughout, the component Boe-D-Cha-OH was obtained very efficiently via hydrogenation Of D-Phe with PtO2 in TFA/water, the tripeptides were coupled at the Pro-Cha junction to minimize racemization via the oxazolone pathway, and the entire synthesis was carried out without purification of any intermediates. The target cyclic product was purified (>97%) by reversed-phase HPLC. This convergent synthesis with minimal use of protecting groups allowed batches of 50100 g to be prepared efficiently in high yield using standard laboratory equipment. This type of procedure should be useful for making even larger quantities of this and other macrocyclic peptidomimetic drugs.