IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Moho map of South America from receiver functions and surface waves

We estimate crustal structure and thickness of South America north of roughly 40 degrees S. To this end, we analyzed receiver functions from 20 relatively new temporary broadband seismic stations deployed across eastern Brazil. In the analysis we include teleseismic and some regional events, particularly for stations that recorded few suitable earthquakes. We first estimate crustal thickness and average Poisson`s ratio using two different stacking methods. We then combine the new crustal constraints with results from previous receiver function studies. To interpolate the crustal thickness between the station locations, we jointly invert these Moho point constraints, Rayleigh wave group velocities, and regional S and Rayleigh waveforms for a continuous map of Moho depth. The new tomographic Moho map suggests that Moho depth and Moho relief vary slightly with age within the Precambrian crust. Whether or not a positive correlation between crustal thickness and geologic age is derived from the pre-interpolation point constraints depends strongly on the selected subset of receiver functions. This implies that using only pre-interpolation point constraints (receiver functions) inadequately samples the spatial variation in geologic age. The new Moho map also reveals an anomalously deep Moho beneath the oldest core of the Amazonian Craton.

Continuous GRASP with a local active-set method for bound-constrained global optimization

Global optimization seeks a minimum or maximum of a multimodal function over a discrete or continuous domain. In this paper, we propose a hybrid heuristic-based on the CGRASP and GENCAN methods-for finding approximate solutions for continuous global optimization problems subject to box constraints. Experimental results illustrate the relative effectiveness of CGRASP-GENCAN on a set of benchmark multimodal test functions.

On E-functions of semisimple Lie groups

We develop and describe continuous and discrete transforms of class functions on a compact semisimple, but not simple, Lie group G as their expansions into series of special functions that are invariant under the action of the even subgroup of the Weyl group of G. We distinguish two cases of even Weyl groups-one is the direct product of even Weyl groups of simple components of G and the second is the full even Weyl group of G. The problem is rather simple in two dimensions. It is much richer in dimensions greater than two-we describe in detail E-transforms of semisimple Lie groups of rank 3.

Optimisation of a continuous flash fermentation for butanol production using the response surface methodology

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

Generalized squeezing operators, bipartite Wigner functions and entanglement via Wehrl's entropy functionals

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Interpolating EFGM for computing continuous and discontinuous electromagnetic fields

Purpose - This paper proposes an interpolating approach of the element-free Galerkin method (EFGM) coupled with a modified truncation scheme for solving Poisson's boundary value problems in domains involving material non-homogeneities. The suitability and efficiency of the proposed implementation are evaluated for a given set of test cases of electrostatic field in domains involving different material interfaces.Design/methodology/approach - the authors combined an interpolating approximation with a modified domain truncation scheme, which avoids additional techniques for enforcing the Dirichlet boundary conditions and for dealing with material interfaces usually employed in meshfree formulations.Findings - the local electric potential and field distributions were correctly described as well as the global quantities like the total potency and resistance. Since, the treatment of the material interfaces becomes practically the same for both the finite element method (FEM) and the proposed EFGM, FEM-oriented programs can, thus, be easily extended to provide EFGM approximations.Research limitations/implications - the robustness of the proposed formulation became evident from the error analyses of the local and global variables, including in the case of high-material discontinuity.Practical implications - the proposed approach has shown to be as robust as linear FEM. Thus, it becomes an attractive alternative, also because it avoids the use of additional techniques to deal with boundary/interface conditions commonly employed in meshfree formulations.Originality/value - This paper reintroduces the domain truncation in the EFGM context, but by using a set of interpolating shape functions the authors avoided the use of Lagrange multipliers as well Mathematics in Engineering high-material discontinuity.

Discrete approximations for strict convex continuous time problems and duality

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Optimization procedures in the design of continuous induction hardening and tempering installations for magnetic steel bars

An inverse problem concerning the industrial process of steel bars hardening and tempering is considered. The associated optimization problem is formulated in terms of membership functions and, for the sake of comparison, also in terms of quadratic residuals; both geometric and electromagnetic design variables have been considered. The numerical solution is achieved by coupling a finite difference procedure for the calculation of the electromagnetic and thermal fields to a deterministic strategy of minimization based on modified Flctcher and Reeves method. © 1998 IEEE.

Chaos induced by turbulent and erratic functions

Let (X, d) be a compact metric space and f: X → X a continuous function and consider the hyperspace (K(X), H) of all nonempty compact subsets of X endowed with the Hausdorff metric induced by d. Let f̄: K(X) → K (X) be defined by f̄(A) = {f(a)/a ∈ A} the natural extension of f to K(X), then the aim of this work is to study the dynamics of f when f is turbulent (erratic, respectively) and its relationships.

Improving the stability conditions of TS fuzzy systems with fuzzy Lyapunov functions

In this paper, the fuzzy Lyapunov function approach is considered for stabilizing continuous-time Takagi-Sugeno fuzzy systems. Previous linear matrix inequality (LMI) stability conditions are relaxed by exploring further the properties of the time derivatives of premise membership functions and by introducing a slack LMI variable into the problem formulation. The stability results are thus used in the state feedback design which is also solved in terms of LMIs. Numerical examples illustrate the efficiency of the new stabilizing conditions presented. © 2011 IFAC.

Advances on statistical/thermodynamical models for unpolarized structure functions

During the eights and nineties many statistical/thermodynamical models were proposed to describe the nucleons' structure functions and distribution of the quarks in the hadrons. Most of these models describe the compound quarks and gluons inside the nucleon as a Fermi / Bose gas respectively, confined in a MIT bag[1] with continuous energy levels. Another models considers discrete spectrum. Some interesting features of the nucleons are obtained by these models, like the sea asymmetries d̄/ū and d̄-ū. © 2013 American Institute of Physics.

A C2-continuous high-resolution upwind convection scheme

A bounded upwinding scheme for numerical solution of hyperbolic conservation laws and Navier-Stokes equations is presented. The scheme is based on convection boundedness criterion and total variation diminishing stability criteria and developed by employing continuously differentiable functions. The accuracy of the scheme is verified by assessing the error and observed convergence rate on 1-D benchmark test cases. A comparative study between the new scheme and conventional total variation diminishing/convection boundedness criterion-based upwind schemes to solve standard nonlinear hyperbolic conservation laws is also accomplished. The scheme is then examined in the simulation of Newtonian and non-Newtonian fluid flows of increasing complexity; a satisfactory agreement has been observed in terms of the overall behavior. Finally, the scheme is used to study the hydrodynamics of a gas-solid flow in a bubbling fluidized bed. © 2013 John Wiley & Sons, Ltd.

Reducing the conservatism of LMI-based stabilisation conditions for TS fuzzy systems using fuzzy Lyapunov functions

In this article, the fuzzy Lyapunov function approach is considered for stabilising continuous-time Takagi-Sugeno fuzzy systems. Previous linear matrix inequality (LMI) stability conditions are relaxed by exploring further the properties of the time derivatives of premise membership functions and by introducing slack LMI variables into the problem formulation. The relaxation conditions given can also be used with a class of fuzzy Lyapunov functions which also depends on the membership function first-order time-derivative. The stability results are thus extended to systems with large number of rules under membership function order relations and used to design parallel-distributed compensation (PDC) fuzzy controllers which are also solved in terms of LMIs. Numerical examples illustrate the efficiency of the new stabilising conditions presented. © 2013 Copyright Taylor and Francis Group, LLC.

Separation of satured and unsaturated fatty acids from palm fatty acids distillates in continuous multistage countercurrent columns with supercritical carbon dioxide as solvent: a process design methodology

In this work the separation of multicomponent mixtures in counter-current columns with supercritical carbon dioxide has been investigated using a process design methodology. First the separation task must be defined, then phase equilibria experiments are carried out, and the data obtained are correlated with thermodynamic models or empirical functions. Mutual solubilities, Ki-values, and separation factors aij are determined. Based on this data possible operating conditions for further extraction experiments can be determined. Separation analysis using graphical methods are performed to optimize the process parameters. Hydrodynamic experiments are carried out to determine the flow capacity diagram. Extraction experiments in laboratory scale are planned and carried out in order to determine HETP values, to validate the simulation results, and to provide new materials for additional phase equilibria experiments, needed to determine the dependence of separation factors on concetration. Numerical simulation of the separation process and auxiliary systems is carried out to optimize the number of stages, solvent-to-feed ratio, product purity, yield, and energy consumption. Scale-up and cost analysis close the process design. The separation of palmitic acid and (oleic+linoleic) acids from PFAD-Palm Fatty Acids Distillates was used as a case study.