Two-Photon Polymerization for Fabricating Structures Containing the Biopolymer Chitosan

Two-photon polymerization is a powerful tool for fabricating three-dimensional micro/nano structures for applications ranging from nanophotonics to biology. To tailor such structure for specific purposes it is often important to dope them. In this paper we report on the fabrication of structures, with nanometric surface features (resolution of approximately 700 nm), using two-photon polymerization of an acrylic resin doped with the biocompatible polymer chitosan using a guest-host scheme. The fluorescence background in the Raman spectrum indicates the presence of chitosan throughout the structure. Mechanical characterization reveals that chitosan does not affect the mechanical properties of the host acrylic resin and, consequently, the structures exhibit excellent integrity. The approach presented in this work can be used in the fabrication of micro- and nanostructures containing biopolymers for biomedical applications.

Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Fragment-Based QSAR and Molecular Modeling Studies on a Series of Discodermolide Analogs as Microtubule-Stabilizing Anticancer Agents

Inhibition of microtubule function is an attractive rational approach to anticancer therapy. Although taxanes are the most prominent among the microtubule-stabilizers, their clinical toxicity, poor pharmacokinetic properties, and resistance have stimulated the search for new antitumor agents having the same mechanism of action. Discodermolide is an example of nontaxane natural product that has the same mechanism of action, demonstrating superior antitumor efficacy and therapeutic index. The extraordinary chemical and biological properties have qualified discodermolide as a lead structure for the design of novel anticancer agents with optimized therapeutic properties. In the present work, we have employed a specialized fragment-based method to develop robust quantitative structure - activity relationship models for a series of synthetic discodermolide analogs. The generated molecular recognition patterns were combined with three-dimensional molecular modeling studies as a fundamental step on the path to understanding the molecular basis of drug-receptor interactions within this important series of potent antitumoral agents.

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Design of novel antituberculosis compounds using graph-theoretical and substructural approaches

The increasing resistance of Mycobacterium tuberculosis to the existing drugs has alarmed the worldwide scientific community. In an attempt to overcome this problem, two models for the design and prediction of new antituberculosis agents were obtained. The first used a mixed approach, containing descriptors based on fragments and the topological substructural molecular design approach (TOPS-MODE) descriptors. The other model used a combination of two-dimensional (2D) and three-dimensional (3D) descriptors. A data set of 167 compounds with great structural variability, 72 of them antituberculosis agents and 95 compounds belonging to other pharmaceutical categories, was analyzed. The first model showed sensitivity, specificity, and accuracy values above 80% and the second one showed values higher than 75% for these statistical indices. Subsequently, 12 structures of imidazoles not included in this study were designed, taking into account the two models. In both cases accuracy was 100%, showing that the methodology in silico developed by us is promising for the rational design of antituberculosis drugs.

Crystal and molecular structures of three 2-sulphur-substituted cyclohexanones studied by X-ray crystallography and by ab initio molecular orbital calculations

The conformational features of three 2-sulphur-substituted cyclohexanone derivatives, which differ in the number of sulphur-bound oxygen atoms, i.e. zero (I), one (II) and two (III), were investigated by single crystal X-ray crystallography and geometry optimized structures determined using Hartree-Fock method. In each of (I)-(III) an intramolecular S center dot center dot center dot O(carbonyl) interaction is found with the magnitude correlated with the oxidation state of the sulphur atom, i.e. 2.838(3) angstrom in (I) to 2.924(2) angstrom in (II) to 3.0973(18) angstrom in (III). There is an inverse relationship between the strength of this interaction and the magnitude of the carbonyl bond. The supramolecular aggregation patterns are primarily determined by C-H center dot center dot center dot O contacts and are similarly influenced by the number of oxygen atoms in the molecular structures. Thus, a supramolecular chain is found in the crystal structure of (I). With an additional oxygen atom available to participate in C-H center dot center dot center dot O interactions, as in (II), a two-dimensional array is found. Finally, a three-dimensional network is found for (III). Despite there being differences in conformations between the experimental structures and those calculated in the gas-phase, the S center dot center dot center dot O interactions persist. The presence of intermolecular C-H center dot center dot center dot O interactions involving the cyclohexanone-carbonyl group in the solid-state, disrupts the stabilising intramolecular C-H center dot center dot center dot O interaction in the energetically-favoured conformation. (I): C(12)H(13)NO(3)S, triclinic space group P (1) over bar with a = 5.392(3) angstrom b = 10.731(6) angstrom, c = 11.075(6) angstrom, alpha = 113.424(4)degrees, beta = 94.167(9)degrees, gamma = 98.444(6)degrees, V = 575.5(6) angstrom(3), Z = 2, R(1) = 0.052; (II): C(12)H(13)NO(4)S, monoclinic P2(1)/n, a = 7.3506(15) angstrom, b = 6.7814(14) angstrom, c = 23.479(5) angstrom, beta = 92.94(3)degrees, V = 1168.8(4) angstrom(3), Z = 4, R(1) = 0.046; (III): C(12)H(13)NO(5)S, monoclinic P2(1)/c, a = 5.5491(11) angstrom, b = 24.146(3) angstrom, c = 11.124(3) angstrom, beta = 114.590(10)degrees, V = 1355.3(5) angstrom(3), Z = 4, R(1) = 0.051.

Temperature Dynamics Investigation At Small And Shallow Lakes Using Hydrodynamic Model

A three-dimensional time-dependent hydrodynamic and heat transport model of Lake Binaba, a shallow and small dam reservoir in Ghana, emphasizing the simulation of dynamics and thermal structure has been developed. Most numerical studies of temperature dynamics in reservoirs are based on one- or two-dimensional models. These models are not applicable for reservoirs characterized with complex flow pattern and unsteady heat exchange between the atmosphere and water surface. Continuity, momentum and temperature transport equations have been solved. Proper assignment of boundary conditions, especially surface heat fluxes, has been found crucial in simulating the lake’s hydrothermal dynamics. This model is based on the Reynolds Average Navier-Stokes equations, using a Boussinesq approach, with a standard k − ε turbulence closure to solve the flow field. The thermal model includes a heat source term, which takes into account the short wave radiation and also heat convection at the free surface, which is function of air temperatures, wind velocity and stability conditions of atmospheric boundary layer over the water surface. The governing equations of the model have been solved by OpenFOAM; an open source, freely available CFD toolbox. As its core, OpenFOAM has a set of efficient C++ modules that are used to build solvers. It uses collocated, polyhedral numerics that can be applied on unstructured meshes and can be easily extended to run in parallel. A new solver has been developed to solve the hydrothermal model of lake. The simulated temperature was compared against a 15 days field data set. Simulated and measured temperature profiles in the probe locations show reasonable agreement. The model might be able to compute total heat storage of water bodies to estimate evaporation from water surface.

Finding a maximum skewness portfolio - A general solution to three-moments portfolio choice

Considering the three first moments and allowing short sales, the efficient portfolios set for n risky assets and a riskless one is found, supposing that agents like odd moments and dislike even ones. Analytical formulas for the solution surface are obtained and important geometric properties provide insights on its shape in the three dimensional space defined by the moments. A special duality result is needed and proved. The methodology is general, comprising situations in which, for instance, the investor trades a negative skewness for a higher expected return. Computation of the optimum portfolio weights is feasible in most cases.

Simulação computacional de medidas estereológicas em estruturas de metal duro (WC-Co)

This work focuses on the creation and applications of a dynamic simulation software in order to study the hard metal structure (WC-Co). The technological ground used to increase the GPU hardware capacity was Geforce 9600 GT along with the PhysX chip created to make games more realistic. The software simulates the three-dimensional carbide structure to the shape of a cubic box where tungsten carbide (WC) are modeled as triangular prisms and truncated triangular prisms. The program was proven effective regarding checking testes, ranging from calculations of parameter measures such as the capacity to increase the number of particles simulated dynamically. It was possible to make an investigation of both the mean parameters and distributions stereological parameters used to characterize the carbide structure through cutting plans. Grounded on the cutting plans concerning the analyzed structures, we have investigated the linear intercepts, the intercepts to the area, and the perimeter section of the intercepted grains as well as the binder phase to the structure by calculating the mean value and distribution of the free path. As literature shows almost consensually that the distribution of the linear intercepts is lognormal, this suggests that the grain distribution is also lognormal. Thus, a routine was developed regarding the program which made possible a more detailed research on this issue. We have observed that it is possible, under certain values for the parameters which define the shape and size of the Prismatic grain to find out the distribution to the linear intercepts that approach the lognormal shape. Regarding a number of developed simulations, we have observed that the distribution curves of the linear and area intercepts as well as the perimeter section are consistent with studies on static computer simulation to these parameters.

Mapeamento robótico 2,5-D com representação em grade de ocupação-elevação

This work introduces a new method for environment mapping with three-dimensional information from visual information for robotic accurate navigation. Many approaches of 3D mapping using occupancy grid typically requires high computacional effort to both build and store the map. We introduce an 2.5-D occupancy-elevation grid mapping, which is a discrete mapping approach, where each cell stores the occupancy probability, the height of the terrain at current place in the environment and the variance of this height. This 2.5-dimensional representation allows that a mobile robot to know whether a place in the environment is occupied by an obstacle and the height of this obstacle, thus, it can decide if is possible to traverse the obstacle. Sensorial informations necessary to construct the map is provided by a stereo vision system, which has been modeled with a robust probabilistic approach, considering the noise present in the stereo processing. The resulting maps favors the execution of tasks like decision making in the autonomous navigation, exploration, localization and path planning. Experiments carried out with a real mobile robots demonstrates that this proposed approach yields useful maps for robot autonomous navigation

Evidence for conformational changes in the yeast deoxyhypusine hydroxylase Lia1 upon iron displacement from its active site

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Dirac-like monopoles in three dimensions and their possible influences on the dynamics of particles

Dirac-like monopoles are studied in three-dimensional Abelian Maxwell and Maxwell-Chern-Simons models. Their scalar nature is highlighted and discussed through a dimensional reduction of four-dimensional electrodynamics with electric and magnetic sources. Some general properties and similarities whether considered in Minkowski or Euclidean space are mentioned. However, by virtue of the structure of the space-time in which they are studied, a number of differences among them occur. Furthermore, we pay attention to some consequences of these objects when they act upon the usual particles. Among other subjects, special attention is given to the study of a Lorentz-violating nonminimal coupling between neutral fermions and the field generated by a monopole alone. In addition, an analogue of the Aharonov-Casher effect is discussed in this framework.

Molecular models of NS3 protease variants of the Hepatitis C virus

Background: Hepatitis C virus (HCV) currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed.Results: the atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures.Conclusions: This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure-based drug design of a new generation of NS3 protease variants inhibitors. All models in the database are publicly accessible via our interactive website, providing us with large amount of structural models for use in protein-ligand docking analysis.

Dynamics of bright matter-wave solitons in a Bose-Einstein condensate with inhomogeneous scattering length

We investigate dynamical effects of a bright soliton in Bose-Einstein condensed (BEC) systems with local and smooth space variations of the two-body atomic scattering length. It includes a discussion about the possible observation of a new type of standing nonlinear atomic matter wave in cigar-type traps. A rich dynamics is observed in the interaction between the soliton and an inhomogeneity. By considering an analytical time-dependent variational approach and also full numerical simulation of one-dimensional and three-dimensional Gross-Pitaevskii equations, we study processes such as trapping, reflection and transmission of the bright matter soliton due to the impurity. We also derive conditions for the collapse of the bright solitary wave, considering a quasi-one-dimensional BEC with attractive local inhomogeneity.

Relaxation algorithm to hyperbolic states in Gross-Pitaevskii equation

A new version of the relaxation algorithm is proposed in order to obtain the stationary ground-state solutions of nonlinear Schrodinger-type equations, including the hyperbolic solutions. In a first example, the method is applied to the three-dimensional Gross-Pitaevskii equation, describing a condensed atomic system with attractive two-body interaction in a non-symmetrical trap, to obtain results for the unstable branch. Next, the approach is also shown to be very reliable and easy to be implemented in a non-symmetrical case that we have bifurcation, with nonlinear cubic and quintic terms. (c) 2006 Elsevier B.V. All rights reserved.