Molecular dynamics simulations reveal how graphene oxide stabilizes and activates lipase in an anhydrous gas

The interaction between Candida antarctica lipase B (CALB) and graphene oxide (GO) in an anhydrous gas was studied using molecular dynamics (MD) simulations augmented with a simulated annealing procedure to accelerate relaxation towards equilibrium.

Determination of stacking ordering in disordered close-packed structures from pairwise correlation functions

It is shown how to reconstruct the stacking sequence from the pairwise correlation functions between layers in close-packed structures. First, of theoretical interest, the analytical formulation and solution of the problem are presented when the exact pairwise correlation counts are known. In the second part, the practical problem is approached. A simulated annealing procedure is developed to solve the problem using as initial guess approximate solutions from previous treatments. The robustness of the procedure is tested with synthetic data, followed by an experimental example. The developed approach performs robustly over different synthetic and experimental data, comparing favorably with the reported methods.

Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements

Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites.

A hybrid genetic algorithm for ROADEF'05-like complex production problems

In this work, we present a hybrid technique that combines a Genetic Algorithm with meta-heuristics to solve a problem in RENAULT France’s production plants. The method starts with an initial solution obtained by means of a GRASP (Greedy Randomized Adaptive Search Procedure) used as an input for a Genetic Algorithm complemented by a Simulated Annealing procedure of population improvement. We establish a comparison point among the different techniques used in the method. Their performances are evaluated as well as that of the entire method. The conclusion is that hybrid methods have clear advantages for the treatment of production planning problems.

Delineating conservation areas on the Oak Ridges Moraine using a systematic conservation planning approach

Protected lands form an essential component of landscape planning, and often extend beyond protection of existing natural areas to consider enhancement through restoration to improve existing conditions. We tested an automated conservation science-based methodology and systematic approach to delineate conservation and restoration priority areas on the Oak Ridges Moraine (ORM). The methodology comprised: a) preparing and assembling existing spatial (GIS) information and tessellating the study area to 5-ha hexagon planning units; b) conducting a gap analysis to provide a basis for setting conservation targets that protect, or that through future restoration activities might enhance, under-represented biodiversity elements; and c) applying a simulated annealing procedure (i.e., mathematical algorithm) to find solutions that optimize the set biodiversity targets. The final output of our work is a map of conservation priority area that enables the more than 50 conservation partners in this landscape to coordinate various conservation, stewardship and restoration activities by focusing on those areas that have the highest conservation value. Key words: restoration, settled landscapes, conservation planning, mathematical algorithm

Doping high Tc superconductors with oxygen and metallic atoms: A molecular dynamics study

Using classical molecular dynamics based on Lennard–Jones-like potentials, a mechanically stable YBa2Cu3O7 high Tc superconductor structure is generated. This process is controlled via interactive computer graphics. After doping atoms into or removing atoms from the sample using a recently implemented picking mechanism, the lattice oscillation energy is annihilated with a simulated annealing procedure. The remaining minimum ground state energy allows marking of the preferred doping location. Information on the doping mechanism is important because the magnetic and superconducting properties of these compounds depend very strongly on their oxygen content.