Computational studies of the reversible domain swapping of p13suc1

A minimalist representation of protein structures using a Go- like potential for interactions is implemented to investigate the mechanisms of the domain swapping of p13suc1, a protein that exists in two native conformations: a monomer and a domain- swapped dimer formed by the exchange of a beta- strand. Inspired by experimental studies which showed a similarity of the transition states for folding of the monomer and the dimer, in this study we justify this similarity in molecular descriptions. When intermediates are populated in the simulations, formation of a domain- swapped dimer initiates from the ensemble of unfolded monomers, given by the fact that the dimer formation occurs at the folding/ unfolding temperature of the monomer ( T-f). It is also shown that transitions, leading to a dimer, involve the presence of two intermediates, one of them has a dimeric form and the other is monomeric; the latter is much more populated than the former. However, at temperatures lower than T-f, the population of intermediates decreases. It is argued that the two folded forms may coexist in absence of intermediates at a temperature much lower than T-f. Computational simulations enable us to find a mechanism, `` lock- and- dock'', for domain swapping of p13suc1. To explore the route toward dimer formation, the folding of unstructured monomers must be retarded by first locking one of the free ends of each chain. Then, the other free termini could follow and dock at particular regions, where most intrachain contacts are formed, and thus de. ne the transition states of the dimer. The simulations also showed that a decrease in the maximum distance between monomers increased their stability, which is explained based on confinement arguments. Although the simulations are based on models extracted from the native structure of the monomer and the dimer of p13suc1, the mechanism of the domain- swapping process could be general, not only for p13suc1.

Computational Aspects of the Calculation of Isometry Groups in General Relativity

We describe the ideas behind the package 'isometry', implemented in Maple to calculate isometry groups of dimensions 2, 3 and 4 in General Relativity. The package extends the functionality of previous programs written to perform invariant classification of space-times in General Relativity. Programming solutions used to surmount problems encountered with the calculation of eigenvectors and the determination of the signs of expressions are described. We also show how the package can be used to find the Killing vectors of a space-time.

Study of plasma immersion ion implantation into silicon substrate using magnetic mirror geometry

The effect of magnetic field enhanced plasma immersion ion implantation (PIII) in silicon substrate has been investigated at low and high pulsed bias voltages. The magnetic field in magnetic bottle configuration was generated by two magnetic coils installed outside the vacuum chamber. The presence of both, electric and magnetic field in PIII creates a system of crossed E x B fields, promoting plasma rotation around the target. The magnetized electrons drifting in crossed E x B fields provide electron-neutral collision. Consequently, the efficient background gas ionization augments the plasma density around the target where a magnetic confinement is achieved. As a result, the ion current density increases, promoting changes in the samples surface properties, especially in the surface roughness and wettability and also an increase of implantation dose and depth. (C) 2012 Elsevier B. V. All rights reserved.

A joint computational and experimental study of a novel dioxomolybdenum(VI) complex bearing chiral N,N-dimethyllactamide ligand

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

Exact dynamics of single-qubit-gate fidelities under the measurement-based quantum computation scheme

Measurement-based quantum computation is an efficient model to perform universal computation. Nevertheless, theoretical questions have been raised, mainly with respect to realistic noise conditions. In order to shed some light on this issue, we evaluate the exact dynamics of some single-qubit-gate fidelities using the measurement-based quantum computation scheme when the qubits which are used as a resource interact with a common dephasing environment. We report a necessary condition for the fidelity dynamics of a general pure N-qubit state, interacting with this type of error channel, to present an oscillatory behavior, and we show that for the initial canonical cluster state, the fidelity oscillates as a function of time. This state fidelity oscillatory behavior brings significant variations to the values of the computational results of a generic gate acting on that state depending on the instants we choose to apply our set of projective measurements. As we shall see, considering some specific gates that are frequently found in the literature, the fast application of the set of projective measurements does not necessarily imply high gate fidelity, and likewise the slow application thereof does not necessarily imply low gate fidelity. Our condition for the occurrence of the fidelity oscillatory behavior shows that the oscillation presented by the cluster state is due exclusively to its initial geometry. Other states that can be used as resources for measurement-based quantum computation can present the same initial geometrical condition. Therefore, it is very important for the present scheme to know when the fidelity of a particular resource state will oscillate in time and, if this is the case, what are the best times to perform the measurements.

Quantum geometry of chiral bosons on a circle

We extend the geometric treatment done for the Majorana-Weyl fermions in two dimensions by Sanielevici and Semenoff to chiral bosons on a circle. For this case we obtain a generalized Floreanini-Jackiw Lagrangian density, and the corresponding gravitational (or Virasoro) anomalies are found as expected. © 1989 The American Physical Society.

On the geometry of non-classical curves

In this paper we relate the numerical invariants attached to a projective curve, called the order sequence of the curve, to the geometry of the varieties of tangent linear spaces to the curve and to the Gauss maps of the curve. © 1992 Sociedade Brasileira de Matemática.

Modelling of the influence of the layer pollution thickness in high voltage polluted insulators

An experimental model and a mathematical model with the introduction of a ramp in the channel of Obenaus model are presented. The aim is to present a better reproduction of the real layer pollution deposited on the HV insulators. This better reproduction is obtained from two types of thickness variation: the introduction of a ramp (soft variation) and the introduction of a step (sudden variation). The computational simulations and the experimental data suggest that the introduction of the ramp is the better reproduction of the layer pollution. The ramp approximates to the real layer pollution more than the step.

Combining genetic algorithm and simulated annealing: A molecular geometry optimization study

We introduce a new hybrid approach to determine the ground state geometry of molecular systems. Firstly, we compared the ability of genetic algorithm (GA) and simulated annealing (SA) to find the lowest energy geometry of silicon clusters with six and 10 atoms. This comparison showed that GA exhibits fast initial convergence, but its performance deteriorates as it approaches the desired global extreme. Interestingly, SA showed a complementary convergence pattern, in addition to high accuracy. Our new procedure combines selected features from GA and SA to achieve weak dependence on initial parameters, parallel search strategy, fast convergence and high accuracy. This hybrid algorithm outperforms GA and SA by one order of magnitude for small silicon clusters (Si6 and Si10). Next, we applied the hybrid method to study the geometry of a 20-atom silicon cluster. It was able to find an original geometry, apparently lower in energy than those previously described in literature. In principle, our procedure can be applied successfully to any molecular system. © 1998 Elsevier Science B.V.

Case-based system: Indexing and retrieval with fuzzy hypercube

In some applications with case-based system, the attributes available for indexing are better described as linguistic variables instead of receiving numerical treatment. In these applications, the concept of fuzzy hypercube can be applied to give a geometrical interpretation of similarities among cases. This paper presents an approach that uses geometrical properties of fuzzy hypercube space to make indexing and retrieval processes of cases.

Energy and angular momentum of the gravitational field in the teleparallel geometry

The Hamiltonian formulation of the teleparallel equivalent of general relativity is considered. Definitions of energy, momentum and angular momentum of the gravitational field arise from the integral form of the constraint equations of the theory. In particular, the gravitational energy-momentum is given by the integral of scalar densities over a three-dimensional spacelike hypersurface. The definition for the gravitational energy is investigated in the context of the Kerr black hole. In the evaluation of the energy contained within the external event horizon of the Kerr black hole, we obtain a value strikingly close to the irreducible mass of the latter. The gravitational angular momentum is evaluated for the gravitational field of a thin, slowly rotating mass shell. © 2002 The American Physical Society.

Sensitivity of AMPA receptor channel to calcium oscillations: A computational study

We used a computational model of biochemical pathways that are involved in the phosphorylation/dephosphorylation of AMPA receptor to study the receptor responses to calcium oscillations. In the model, the biochemical pathways are assumed to be located immediately under the postsynaptic membrane and we included three states of AMPA receptor: dephosphorylated, and phosphorylated in one or in two sites. To characterize the effects of calcium oscillations on the AMPA receptor, we exposed the model to stimuli with three varying parameters, namely frequency, number of pulses and calcium spike duration. Our model showed sensitivity to all of these three parameters. © 2002 Elsevier Science B.V. All rights reserved.

Gravitational energy of Kerr and Kerr anti-de Sitter space-times in the teleparallel geometry

In the context of the hamiltonian formulation of the teleparallel equivalent of general relativity we compute the gravitational energy of Kerr and Kerr Anti-de Sitter (Kerr-AdS) space-times. The present calculation is carried out by means of an expression for the energy of the gravitational field that naturally arises from the integral form of the constraint equations of the formalism. In each case, the energy is exactly computed for finite and arbitrary spacelike two-spheres, without any restriction on the metric parameters. In particular, we evaluate the energy at the outer event horizon of the black holes. © SISSA/ISAS 2003.

Behavioural Analysis of a Nonlinear Mechanical System Using Transient Trajectories

This work aims at a better comprehension of the features of the solution surface of a dynamical system presenting a numerical procedure based on transient trajectories. For a given set of initial conditions an analysis is made, similar to that of a return map, looking for the new configuration of this set in the first Poincaré sections. The mentioned set of I.C. will result in a curve that can be fitted by a polynomial, i.e. an analytical expression that will be called initial function in the undamped case and transient function in the damped situation. Thus, it is possible to identify using analytical methods the main stable regions of the phase portrait without a long computational time, making easier a global comprehension of the nonlinear dynamics and the corresponding stability analysis of its solutions. This strategy allows foreseeing the dynamic behavior of the system close to the region of fundamental resonance, providing a better visualization of the structure of its phase portrait. The application chosen to present this methodology is a mechanical pendulum driven through a crankshaft that moves horizontally its suspension point.