Evolutionary dynamics on rugged fitness landscapes: Exact dynamics and information theoretical aspects

The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the random energy model (REM) and by a ferromagnetic version of the REM. The solution method uses the mapping of the evolutionary dynamics into a quantum Ising chain in a transverse field and the Suzuki-Trotter formalism to calculate the transition probabilities between configurations at different times. We find that in the case of the REM landscape the dynamics can exhibit three distinct regimes: pure diffusion or stasis for short times, depending on the fitness of the initial configuration, and a spin-glass regime for large times. The dynamic transition between these dynamical regimes is marked by discontinuities in the mean-fitness as well as in the overlap with the initial reference sequence. The relaxation to equilibrium is described by an inverse time decay. In the ferromagnetic REM, we find in addition to these three regimes, a ferromagnetic regime where the overlap and the mean-fitness are frozen. In this case, the system relaxes to equilibrium in a finite time. The relevance of our results to information processing aspects of evolution is discussed.

Density functional theory investigation of 3d, 4d, and 5d 13-atom metal clusters

The knowledge of the atomic structure of clusters composed by few atoms is a basic prerequisite to obtain insights into the mechanisms that determine their chemical and physical properties as a function of diameter, shape, surface termination, as well as to understand the mechanism of bulk formation. Due to the wide use of metal systems in our modern life, the accurate determination of the properties of 3d, 4d, and 5d metal clusters poses a huge problem for nanoscience. In this work, we report a density functional theory study of the atomic structure, binding energies, effective coordination numbers, average bond lengths, and magnetic properties of the 3d, 4d, and 5d metal (30 elements) clusters containing 13 atoms, M(13). First, a set of lowest-energy local minimum structures (as supported by vibrational analysis) were obtained by combining high-temperature first- principles molecular-dynamics simulation, structure crossover, and the selection of five well-known M(13) structures. Several new lower energy configurations were identified, e. g., Pd(13), W(13), Pt(13), etc., and previous known structures were confirmed by our calculations. Furthermore, the following trends were identified: (i) compact icosahedral-like forms at the beginning of each metal series, more opened structures such as hexagonal bilayerlike and double simple-cubic layers at the middle of each metal series, and structures with an increasing effective coordination number occur for large d states occupation. (ii) For Au(13), we found that spin-orbit coupling favors the three-dimensional (3D) structures, i.e., a 3D structure is about 0.10 eV lower in energy than the lowest energy known two-dimensional configuration. (iii) The magnetic exchange interactions play an important role for particular systems such as Fe, Cr, and Mn. (iv) The analysis of the binding energy and average bond lengths show a paraboliclike shape as a function of the occupation of the d states and hence, most of the properties can be explained by the chemistry picture of occupation of the bonding and antibonding states.

Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale

This paper describes a new and simple method to determine the molecular weight of proteins in dilute solution, with an error smaller than similar to 10%, by using the experimental data of a single small-angle X-ray scattering (SAXS) curve measured on a relative scale. This procedure does not require the measurement of SAXS intensity on an absolute scale and does not involve a comparison with another SAXS curve determined from a known standard protein. The proposed procedure can be applied to monodisperse systems of proteins in dilute solution, either in monomeric or multimeric state, and it has been successfully tested on SAXS data experimentally determined for proteins with known molecular weights. It is shown here that the molecular weights determined by this procedure deviate from the known values by less than 10% in each case and the average error for the test set of 21 proteins was 5.3%. Importantly, this method allows for an unambiguous determination of the multimeric state of proteins with known molecular weights.

ON GENERIC ROTATIONLESS DIFFEOMORPHISMS OF THE ANNULUS

Let f be a C(r)-diffeomorphism of the closed annulus A that preserves the orientation, the boundary components and the Lebesgue measure. Suppose that f has a lift (f) over tilde to the infinite strip (A) over tilde which has zero Lebesgue measure rotation number. If the rotation number of f restricted to both boundary components of (f) over tilde is positive, then for such a generic f (r >= 16), zero is an interior point of its rotation set. This is a partial solution to a conjecture of P. Boyland.

Solution structure of the human signaling protein RACK1

Background: The adaptor protein RACK1 (receptor of activated kinase 1) was originally identified as an anchoring protein for protein kinase C. RACK1 is a 36 kDa protein, and is composed of seven WD repeats which mediate its protein-protein interactions. RACK1 is ubiquitously expressed and has been implicated in diverse cellular processes involving: protein translation regulation, neuropathological processes, cellular stress, and tissue development. Results: In this study we performed a biophysical analysis of human RACK1 with the aim of obtaining low resolution structural information. Small angle X-ray scattering (SAXS) experiments demonstrated that human RACK1 is globular and monomeric in solution and its low resolution structure is strikingly similar to that of an homology model previously calculated by us and to the crystallographic structure of RACK1 isoform A from Arabidopsis thaliana. Both sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation techniques showed that RACK1 is predominantly a monomer of around 37 kDa in solution, but also presents small amounts of oligomeric species. Moreover, hydrodynamic data suggested that RACK1 has a slightly asymmetric shape. The interaction of RACK1 and Ki1/57 was tested by sedimentation equilibrium. The results suggested that the association between RACK1 and Ki-1/57(122-413) follows a stoichiometry of 1:1. The binding constant (KB) observed for RACK1-Ki-1/57(122-413) interaction was of around (1.5 +/- 0.2) x 10(6) M(-1) and resulted in a dissociation constant (KD) of (0.7 +/- 0.1) x 10(-6) M. Moreover, the fluorescence data also suggests that the interaction may occur in a cooperative fashion. Conclusion: Our SAXS and analytical ultracentrifugation experiments indicated that RACK1 is predominantly a monomer in solution. RACK1 and Ki-1/57(122-413) interact strongly under the tested conditions.

Coconut coir as biosorbent for Cr(VI) removal from laboratory wastewater

A high cost-effective treatment of sulphochromic waste is proposed employing a raw coconut coir as biosorbent for Cr(VI) removal. The ideal pH and sorption kinetic, sorption capacities, and sorption sites were the studied biosorbent parameters. After testing five different isotherm models with standard solutions, Redlich-Peterson and Toth best fitted the experimental data, obtaining a theoretical Cr(VI) sorption capacity (SC) of 6.3 mg g(-1). Acid-base potentiometric titration indicated around of 73% of sorption sites were from phenolic compounds, probably lignin. Differences between sorption sites in the coconut coir before and after Cr adsorption identified from Fourier transform infrared spectra suggested a modification of sorption sites after sulphochromic waste treatment, indicating that the sorption mechanism involves organic matter oxidation and chromium uptake. For sulphocromic waste treatment, the SC was improved to 26.8 +/- 0.2 mg g(-1), and no adsorbed Cr(VI) was reduced, remaining only Cr(III) in the final solution. The adsorbed material was calcinated to obtain Cr2O3, with a reduction of more than 60% of the original mass. (c) 2008 Elsevier B.V. All rights reserved.

Kinetics of the xylitol crystallization in hydro-alcoholic solution

Nyvlt method Was used to determine the kinetic parameters of commercial xylitol in ethanol:water (50:50 %w/w) Solution by batch cooling crystallization. The kinetic exponents (n, g and in) and the system kinetic constant (B(N)) were determined. Model experiments were carried Out in order to verify the combined effects of saturation temperatures (40, 50 and 60 degrees C) and cooling rates (0.10, 0.25 and 0.50 degrees C/min) on these parameters. The fitting between experimental and Calculated crystal sizes has 11.30% mean deviation. (C) 2007 Elsevier B.V. All rights reserved.

Extending the kinetic solution of the classic Michaelis-Menten model of enzyme action

The principal aim of studies of enzyme-mediated reactions has been to provide comparative and quantitative information on enzyme-catalyzed reactions under distinct conditions. The classic Michaelis-Menten model (Biochem Zeit 49:333, 1913) for enzyme kinetic has been widely used to determine important parameters involved in enzyme catalysis, particularly the Michaelis-Menten constant (K (M) ) and the maximum velocity of reaction (V (max) ). Subsequently, a detailed treatment of the mechanisms of enzyme catalysis was undertaken by Briggs-Haldane (Biochem J 19:338, 1925). These authors proposed the steady-state treatment, since its applicability was constrained to this condition. The present work describes an extending solution of the Michaelis-Menten model without the need for such a steady-state restriction. We provide the first analysis of all of the individual reaction constants calculated analytically. Using this approach, it is possible to accurately predict the results under new experimental conditions and to characterize and optimize industrial processes in the fields of chemical and food engineering, pharmaceuticals and biotechnology.

Solution Polymerization of N-vinylcaprolactam in 1,4-dioxane. Kinetic Dependence on Temperature, Monomer, and Initiator Concentrations

The kinetics of the solution free radical polymerization of N-vinylcaprolactam, in 1,4-dioxane and under various polymerization conditions was studied. Azobisisobutyronitrile and 3-mercaptopropionic acid were used as initiator and as chain transfer agent (CTA), respectively. The influence of monomer and initiator concentrations and polymerization temperature on the rate of polymerizations (R(p)) was investigated. In general, high conversions were obtained. The order with respect to initiator was consistent with the classical kinetic rate equation, while the order with respect to the monomer was greater than unity. The overall activation energy of 53.6 kJ mol(-1) was obtained in the temperature range 60-80 degrees C. The decreasing of the absolute molecular weights when increasing the CIA concentration was confirmed by GPC/SEC/LALS analyses. It was confirmed by UV-visible analyses the effect of molecular weights on the lower critical solution temperature of the polymers. It was also verified that the addition of the CTA influenced the kinetic of the polymerizations. (C) 2010 Wiley Periodicals, Inc. J Appl Polym Sci 118: 229-240, 2010

Adsorption of Cr(VI) from aqueous solution by hydrous zirconium oxide

A type of ZrO(2)center dot nH(2)O Was synthesized and its Cr(VI) removal potential was investigated in this study. The kinetic study, adsorption isotherm, pH effect, thermodynamic study and desorption were examined in batch experiments. The kinetic process was described by a pseudo-second-order rate model very well. The Cr(VI) adsorption tended to increase with a decrease of pH. The adsorption data fitted well to the Langmuir model. The adsorption capacity increased from 61 to 66 mg g(-1) when the temperature was increased from 298 to 338 K. The positive values of both Delta H degrees and Delta S degrees suggest an endothermic reaction and increase in randomness at the solid-liquid interface during the adsorption. Delta G degrees values obtained were negative indicating a spontaneous adsorption process. The effective desorption of Cr(VI) on ZrO(2)center dot nH(2)O could be achieved using distilled water at pH 12. (C) 2009 Elsevier B.V. All rights reserved.

Corrosion behavior of Ti-xNb-13Zr alloys in Ringer`s solution

Ti-6Al-4V alloy has been widely used in restorative surgery due to its high corrosion resistance and biocompatibility. Nevertheless, some studies showed that V and Al release in the organism might induce cytotoxic effects and neurological disorders, which led to the development of V-free alloys and both V- and Al-free alloys containing Nb, Zr, Ta, or Mo. Among these alloys, Ti-13Nb-13Zr alloy is promising due to its better biomechanical compatibility than Ti-6Al-4V. In this work, the corrosion behavior of Ti, Ti-6Al-4V, and Ti-xNb-13Zr alloys (x=5, 13, and 20) was evaluated in Ringer`s solution (pH 7.5) at 37 degrees C through open-circuit potential measurements, potentiodynamic polarization, and electrochemical impedance spectroscopy. Spontaneous passivity was observed for all materials in this medium. Low corrosion current densities (in the order of 10(-7) A/cm(2)) and high impedance values (in the order of 10(5) Omega cm(2) at low frequencies) indicated their high corrosion resistance. EIS results showed that the passivating films were constituted of an outer porous layer (very low resistance) and an inner compact layer (high resistance), the latter providing the corrosion resistance of the materials. There was evidence that the Ti-xNb-13Zr alloys were more corrosion resistant than both Ti and Ti-6Al-4V in Ringer`s solution.

Combined solution for fault location in three-terminal lines based on wavelet transforms

This work presents the study and development of a combined fault location scheme for three-terminal transmission lines using wavelet transforms (WTs). The methodology is based on the low- and high-frequency components of the transient signals originated from fault situations registered in the terminals of a system. By processing these signals and using the WT, it is possible to determine the time of travelling waves of voltages and/or currents from the fault point to the terminals, as well as estimate the fundamental frequency components. A new approach presents a reliable and accurate fault location scheme combining some different solutions. The main idea is to have a decision routine in order to select which method should be used in each situation presented to the algorithm. The combined algorithm was tested for different fault conditions by simulations using the ATP (Alternative Transients Program) software. The results obtained are promising and demonstrate a highly satisfactory degree of accuracy and reliability of the proposed method.

H(infinity) filtering for rectangular discrete-time descriptor systems

This paper deals with the H(infinity) recursive estimation problem for general rectangular time-variant descriptor systems in discrete time. Riccati-equation based recursions for filtered and predicted estimates are developed based on a data fitting approach and game theory. In this approach, the nature determines a state sequence seeking to maximize the estimation cost, whereas the estimator tries to find an estimate that brings the estimation cost to a minimum. A solution exists for a specified gamma-level if the resulting cost is positive. In order to present some computational alternatives to the H(infinity) filters developed, they are rewritten in information form along with the respective array algorithms. (C) 2009 Elsevier Ltd. All rights reserved.

Experimental results on the nonlinear H(infinity) control via quasi-LPV representation and game theory for wheeled mobile robots

In this paper, nonlinear dynamic equations of a wheeled mobile robot are described in the state-space form where the parameters are part of the state (angular velocities of the wheels). This representation, known as quasi-linear parameter varying, is useful for control designs based on nonlinear H(infinity) approaches. Two nonlinear H(infinity) controllers that guarantee induced L(2)-norm, between input (disturbances) and output signals, bounded by an attenuation level gamma, are used to control a wheeled mobile robot. These controllers are solved via linear matrix inequalities and algebraic Riccati equation. Experimental results are presented, with a comparative study among these robust control strategies and the standard computed torque, plus proportional-derivative, controller.