Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002

NP-hardness of the cluster minimization problem revisited

The computational complexity of the "cluster minimization problem" is revisited [L. T. Wille and J. Vennik, J. Phys. A 18, L419 (1985)]. It is argued that the original NP-hardness proof does not apply to pairwise potentials of physical interest, such as those that depend on the geometric distance between the particles. A geometric analog of the original problem is formulated, and a new proof for such potentials is provided by polynomial time transformation from the independent set problem for unit disk graphs. Limitations of this formulation are pointed out, and new subproblems that bear more direct consequences to the numerical study of clusters are suggested.Comment: 8 pages, 2 figures, accepted to J. Phys. A: Math. and Ge

Continuous extremal optimization for Lennard-Jones Clusters

In this paper, we explore a general-purpose heuristic algorithm for finding high-quality solutions to continuous optimization problems. The method, called continuous extremal optimization(CEO), can be considered as an extension of extremal optimization(EO) and is consisted of two components, one is with responsibility for global searching and the other is with responsibility for local searching. With only one adjustable parameter, the CEO's performance proves competitive with more elaborate stochastic optimization procedures. We demonstrate it on a well known continuous optimization problem: the Lennerd-Jones clusters optimization problem.Comment: 5 pages and 3 figure

Molecular geometry optimization with a genetic algorithm

We present a method for reliably determining the lowest energy structure of an atomic cluster in an arbitrary model potential. The method is based on a genetic algorithm, which operates on a population of candidate structures to produce new candidates with lower energies. Our method dramatically outperforms simulated annealing, which we demonstrate by applying the genetic algorithm to a tight-binding model potential for carbon. With this potential, the algorithm efficiently finds fullerene cluster structures up to ${\rm C}_{60}$ starting from random atomic coordinates.Comment: 4 pages REVTeX 3.0 plus 3 postscript figures; to appear in Physical Review Letters. Additional information available under "genetic algorithms" at http://www.public.iastate.edu/~deaven

Simulation of Multicomponent Thin Film Deposition and Growth

Results from a multicomponent Monte Carlo simulation of the deposition and growth of YBa{sub 2}Cu{sub 3}0{sub 7} are presented and discussed. In particular, a detailed examination of the growth modes active during different morphological growth conditions is performed. At higher deposition rates, both (001) and (100) epitaxial variants (`c` and `a` type growth, respectively) are observed to grow by modes attributed to the classic Volmer-Weber mechanism. At very low deposition rates, the film is observed to grow in a distinct, cyclic, multi-stage process. Small islands of (0011) epitaxy nucleate and grow to one unit cell height followed by primarily horizontal growth or ``ledge extension`` until one unit cell layer has formed. This process then repeats. Simulated RHEED amplitude data from this growth process compares favorably to experimentally obtained data

Hydrogen molecule in a magnetic field: The lowest states of the Pi manifold and the global ground state of the parallel configuration

The electronic structure of the hydrogen molecule in a magnetic field is investigated for parallel internuclear and magnetic field axes. The lowest states of the $\Pi$ manifold are studied for spin singlet and triplet$(M_s = -1)$ as well as gerade and ungerade parity for a broad range of field strengths $0 \leq B \leq 100 a.u.$ For both states with gerade parity we observe a monotonous decrease in the dissociation energy with increasing field strength up to $B = 0.1 a.u.$ and metastable states with respect to the dissociation into two H atoms occur for a certain range of field strengths. For both states with ungerade parity we observe a strong increase in the dissociation energy with increasing field strength above some critical field strength $B_c$. As a major result we determine the transition field strengths for the crossings among the lowest $^1\Sigma_g$, $^3\Sigma_u$ and $^3\Pi_u$ states. The global ground state for $B \lesssim 0.18 a.u.$ is the strongly bound $^1\Sigma_g$ state. The crossings of the $^1\Sigma_g$ with the $^3\Sigma_u$ and $^3\Pi_u$ state occur at $B \approx 0.18$ and $B \approx0.39 a.u.$, respectively. The transition between the $^3\Sigma_u$ and $^3\Pi_u$ state occurs at $B \approx 12.3 a.u.$ Therefore, the global ground state of the hydrogen molecule for the parallel configuration is the unbound $^3\Sigma_u$ state for $0.18 \lesssim B \lesssim 12.3 a.u.$ The ground state for $B \gtrsim 12.3 a.u.$ is the strongly bound $^3\Pi_u$ state. This result is of great relevance to the chemistry in the atmospheres of magnetic white dwarfs and neutron stars.Comment: submitted to Physical Review

New Tetrahedral Global Minimum for the 98-atom Lennard-Jones Cluster

A new atomic cluster structure corresponding to the global minimum of the 98-atom Lennard-Jones cluster has been found using a variant of the basin-hopping global optimization algorithm. The new structure has an unusual tetrahedral symmetry with an energy of -543.665361, which is 0.022404 lower than the previous putative global minimum. The new LJ_98 structure is of particular interest because its tetrahedral symmetry establishes it as one of only three types of exceptions to the general pattern of icosahedral structural motifs for optimal LJ microclusters. Similar to the other exceptions the global minimum is difficult to find because it is at the bottom of a narrow funnel which only becomes thermodynamically most stable at low temperature.Comment: 3 pages, 2 figures, revte

Unbiased Global Optimization of Lennard-Jones Clusters for N <= 201 by Conformational Space Annealing Method

We apply the conformational space annealing (CSA) method to the Lennard-Jones clusters and find all known lowest energy configurations up to 201 atoms, without using extra information of the problem such as the structures of the known global energy minima. In addition, the robustness of the algorithm with respect to the randomness of initial conditions of the problem is demonstrated by ten successful independent runs up to 183 atoms. Our results indicate that the CSA method is a general and yet efficient global optimization algorithm applicable to many systems.Comment: revtex, 4 pages, 2 figures. Physical Review Letters, in pres

Bulk partitioning the growing season net ecosystem exchange of CO&lt;sub&gt;2&lt;/sub&gt; in Siberian tundra reveals the seasonality of its carbon sequestration strength

This paper evaluates the relative contribution of light and temperature on net ecosystem CO2 uptake during the 2006 growing season in a polygonal tundra ecosystem in the Lena River Delta in Northern Siberia (72°22´ N, 126°30´ E). The occurrence and frequency of warm periods may be an important determinant of the magnitude of the ecosystem's carbon sink function, as they drive temperature-induced changes in respiration. Hot spells during the early portion of the growing season, when the photosynthetic apparatus of vascular plants is not fully developed, are shown to be more influential in creating positive mid-day surface-to-atmosphere net ecosystem CO2 exchange fluxes than those occurring later in the season. In this work we also develop and present a multi-step bulk flux partition model to better account for tundra plant physiology and the specific light conditions of the arctic region. These conditions preclude the successful use of traditional partition methods that derive a respiration–temperature relationship from all nighttime data or from other bulk approaches that are insensitive to temperature or light stress. Nighttime growing season measurements are rare during the arctic summer, however, so the new method allows for temporal variation in the parameters describing both ecosystem respiration and gross uptake by fitting both processes at the same time. Much of the apparent temperature sensitivity of respiration seen in the traditional partition method is revealed in the new method to reflect seasonal changes in basal respiration rates. Understanding and quantifying the flux partition is an essential precursor to describing links between assimilation and respiration at different timescales, as it allows a more confident evaluation of measured net exchange over a broader range of environmental conditions. The growing season CO2 sink estimated by this study is similar to those reported previously for this site, and is substantial enough to withstand the long, low-level respiratory CO2 release during the rest of the year to maintain the site's CO2 sink function on an annual basis