Kleber C. Mundim

GEOMETRY OPTIMIZATION AND CONFORMATIONAL ANALYSIS THROUGH GENERALIZED SIMULATED ANNEALING

On statistical-mechanical grounds, a stochastic optimization technique (generalized simulated annealing) has been recently proposed which contains both classical simulated annealing (Kirkpatrick et al., 1983) and fast simulated annealing (Szu, 1986) as particular cases. This technique can be faster than both in detecting global (and also local) minima. Its utility in quantum chemistry is here illustrated, through the use of a semiempirical quantum method, on molecules of the series CH3-R (C2H6, CH3COH, CH3OH), H2X2 (H2O2, H2S2), X2Y4 (N2H4, P2H4, N2F4), for double bonds (C2H4 and CH2NH), and finally for H2O3.

Stochastic molecular optimization using generalized simulated annealing

We propose a stochastic optimization technique based on a generalized simulated annealing (GSA) method for mapping minima points of molecular conformational energy surfaces. The energy maps are obtained by coupling a classical molecular force field (THOR package) with a GSA procedure. Unlike the usual molecular dynamics (MD) method, the method proposed in this study is force independent; that is, we obtain the optimized conformation without calculating the force, and only potential energy is involved. Therefore, we do not need to know the conformational energy gradient to arrive at equilibrium conformations. Its utility in molecular mechanics is illustrated by applying it to examples of simple molecules (H2O and H2O3) and to polypeptides. The results obtained for H2O and H2O3 using Tsallis thermostatistics suggest that the GSA approach is faster than the other two conventional methods (Boltzmann and Cauchy machines). The results for polypeptides show that pentalanine does not form a stable α‐helix structure, probably because the number of hydrogen bonds is insufficient to maintain the helical array. On the contrary, the icoalanine molecule forms an α‐helix structure. We obtain this structure simulating all Φ, Ψ pairs using only a few steps, as compared with conventional methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 647–657, 1998

Atomistic study of interaction zone at copper-carbon interfaces

Abstract Formation of Cu–C composite is a difficult technological problem: carbon is practically insoluble in copper. We show that the heat treatment of the Cu–C composite leads to the formation of thin (approximately 50 nm) interface, which provides the bonding between fiber and matrix. The high-resolution scanning electron microscopy (HR SEM) study displays the formation of the interaction zone. Monte Carlo simulations with repulsive Cu–C interatomic potentials study this zone on the interface.

New stochastic strategy to analyze helix folding.

We propose an alternative stochastic strategy to search secondary structures based on the generalized simulated annealing (GSA) algorithm, by using conformational preferences based on the Ramachandran map. We optimize the search for polypeptide conformational space and apply to peptides considered to be good alpha-helix promoters above a critical number of residues. Our strategy to obtain conformational energies consist in coupling a classical force field (THOR package) with the GSA procedure, biasing the Phi x Psi backbone angles to the allowed regions in the Ramachandran map. For polyalanines we obtained stable alpha-helix structures when the number of residues were equal or exceeded 13 amino acids residues. We also observed that the energy gap between the global minimum and the first local minimum tends to increase with the polypeptide size. These conformations were generated by performing 2880 stochastic molecular optimizations with a continuum medium approach. When compared with molecular dynamics or Monte Carlo methods, GSA can be considered the fastest.

Microstructure of Cu–C interface in Cu-based metal matrix composite

Abstract Existence of dilute copper–carbon solid solutions is one of the characteristic features of the interfaces of the metal matrix composites widely used in the electrical applications. Experimental high-resolution SEM study allows to visualize the formation of the interaction zone on carbon fibre. We model interstitial solid solutions formed in this interaction zone non-empirically within the embedded-cluster and supercell approaches. Atomistic approach allows selection of the geometry of the solid solution. Electronic structure studies show that the most favourable position of the carbon atom is shifted along the [110] direction from the centre of the octahedral position. Investigation of this physical phenomenon allows us to understand the nature of the chemical bonding in copper-based solid solutions with carbon.

Optimization of non-linear gravity models through generalized simulated annealing

In this paper we apply the generalized simulated annealing (GSA) approach to the inversion of gravity data for 2-D and 3-D density distributions. We consider a modeling process where the input is the vector of model parameters m (that can be density contrast, mass or some coordinates) and the output is described by the transformation h(m)=d, where d is the vector of data parameters, we generally have access in practical problems. If the vector d describes the observed actual output of the system, the problem is to “choose”, or estimate, the parameters mest in order to minimize, in some sense, in our case in the least-squares sense, the difference between the observed vector d and the prescribed output of the system h(mest). The tests with synthetic data show the promising application of GSA in gravity inversion. The results obtained suggest us that the GSA approach enables to find quickest optimization machines than the two conventional approaches (Boltzmann and Cauchy machines).

Formation of nano-crystalline structure at the interface in Cu–C composite

Abstract Formation of Cu–C composite is a difficult technological problem: carbon is practically insoluble in copper. We show that the heat treatment of the Cu–C composite leads to the formation of a thin (approximately 50 nm) interface which provides the bonding between fiber and matrix. The HR SEM study displays the formation of small copper nano-crystals in the interaction zone. This structure of the interface is predicted by molecular dynamic and Monte Carlo simulations with semi-empirical repulsive Cu–C interatomic potentials. We show that inclusion of a small amount of carbon in fcc copper leads to strong deformation of the copper host matrix in the vicinity of carbon. Decrease of stresses in the lattice may be reached by the formation of the developed surface in nano-crystalline structure.

Interstitial carbon in copper: Electronic and mechanical properties

The effects of interstitial carbon on the electronic and mechanical properties of copper are studied theoretically. Semiempirical methodology, atomistic simulations and first-principles density-functional embedded-cluster schemes are combined to extract some understanding of the diffusion process and related degradation of Cu-C composite materials under extremes of temperature and stress. High-resolution scanning electron microscopy results are presented, which demonstrate the existence of a solid solution zone at the Cu-C interface.

Carbon in copper and silver: Diffusion and mechanical properties

Abstract The effects of interstitial carbon on the diffusion and mechanical properties of copper and silver are studied theoretically. Semiempirical methodology, atomistic simulations, and first-principles density functional schemes are combined to extract some understanding of the diffusion process and lattice reconstruction in extremely dilute interstitial Cu–C and Ag–C alloys. It is demonstrated that carbon inclusion in the host matrix leads to sufficient non-uniform dilatation of the lattice. We also show that an account of static displacements is important in the calculations of the activation energy for the diffusion of the interstitial atoms. The “embedded” cluster scheme is suggested to simulate the relaxation in extremely dilute alloys. High-resolution scanning electron microscopy results are presented, which demonstrate the existence of a solid solution zone at the Cu–C interface.

Polarization effects on peptide conformations at water–membrane interface by molecular dynamics simulation

The electrostatic image method was applied to investigate the conformation of peptides characterized by different hydrophobicities in a water–membrane interface model. The interface was represented by a surface of discontinuity between two media with different dielectric constants, taking into account the difference between the polarizabilities of the aqueous medium and the hydrocarbon one. The method consists of a substitution of the real problem, which involves the charges and the induced polarization at the surface of discontinuity, by a simpler problem formed with charges and their images. The electric field due to the polarization induced at the surface by charge q was calculated using a hypothetical charge q′ (image of q), symmetrically located on the opposite side of the surface. The value of q′ was determined using the appropriate electrostatic boundary conditions at the surface. By means of this procedure, the effect of the interface can be introduced easily in the usual force field. We included this extension in the computational package that we are developing for molecular dynamics simulations (Thor). The peptides studied included hydrophilic tetraaspartic acid (Asp–Asp–Asp–Asp), tetralysine (Lys–Lys–Lys–Lys), hydrophobic tetrapeptide (His–Phe–Arg–Trp), an amphiphilic fragment of β‐endorphin, and the signal sequence of the E. coli λ‐receptor. The simulation results are in agreement with known experimental data regarding the behavior of peptides at the water–membrane interface. An analysis of the conformational dynamics of the signal sequence peptide at the interface was performed over the course of a few nanoseconds. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 971–982, 1999