Algorithm Engineering in Robust Optimization

Robust optimization is a young and emerging field of research having received a considerable increase of interest over the last decade. In this paper, we argue that the the algorithm engineering methodology fits very well to the field of robust optimization and yields a rewarding new perspective on both the current state of research and open research directions. To this end we go through the algorithm engineering cycle of design and analysis of concepts, development and implementation of algorithms, and theoretical and experimental evaluation. We show that many ideas of algorithm engineering have already been applied in publications on robust optimization. Most work on robust optimization is devoted to analysis of the concepts and the development of algorithms, some papers deal with the evaluation of a particular concept in case studies, and work on comparison of concepts just starts. What is still a drawback in many papers on robustness is the missing link to include the results of the experiments again in the design

Gluon scattering in N=4{\cal N}=4 Super Yang-Mills at finite temperature

We extend the AdS/CFT prescription of Alday and Maldacena to finite temperature $T$, defining the amplitude for gluon scattering in ${\cal N}=4$ Super Yang-Mills at strong coupling from string theory. It is defined by a lightlike ''Wilson loop'' living at the horizon of the T-dual to the black hole in AdS space. Unlike the zero temperature case, this is different from the Wilson loop contour defined at the boundary of the AdS black hole metric, thus at finite $T$ there is no relation between gluon scattering amplitudes and the Wilson loop. We calculate the amplitude at strong coupling for forward scattering of a low energy gluon ($E<T$) off a high energy gluon ($E\gg T$) in both cut-off and generalized dimensional regularization. The generalized dimensional regularization is defined in string theory as an IR modified dimensional reduction. For this calculation, the corresponding usual Wilson loop is related to the jet quenching parameter of the finite temperature ${\cal N}=4$ SYM plasma, while the gluon scattering amplitude is related to the viscosity coefficient.Comment: 33 pages, 9 figures; clarifications of some points added, reference adde

The Complexity of Flat Freeze LTL

We consider the model-checking problem for freeze LTL on one-counter automata (OCAs). Freeze LTL extends LTL with the freeze quantifier, which allows one to store different counter values of a run in registers so that they can be compared with one another. As the model-checking problem is undecidable in general, we focus on the flat fragment of freeze LTL, in which the usage of the freeze quantifier is restricted. Recently, Lechner et al. showed that model checking for flat freeze LTL on OCAs with binary encoding of counter updates is decidable and in 2NEXPTIME. In this paper, we prove that the problem is, in fact, NEXPTIME-complete no matter whether counter updates are encoded in unary or binary. Like Lechner et al., we rely on a reduction to the reachability problem in OCAs with parameterized tests (OCAPs). The new aspect is that we simulate OCAPs by alternating two-way automata over words. This implies an exponential upper bound on the parameter values that we exploit towards an NP algorithm for reachability in OCAPs with unary updates. We obtain our main result as a corollary

Global hybrids from the semiclassical atom theory satisfying the local density linear response

We propose global hybrid approximations of the exchange-correlation (XC) energy functional which reproduce well the modified fourth-order gradient expansion of the exchange energy in the semiclassical limit of many-electron neutral atoms and recover the full local density approximation (LDA) linear response. These XC functionals represent the hybrid versions of the APBE functional [Phys. Rev. Lett. 106, 186406, (2011)] yet employing an additional correlation functional which uses the localization concept of the correlation energy density to improve the compatibility with the Hartree-Fock exchange as well as the coupling-constant-resolved XC potential energy. Broad energetical and structural testings, including thermochemistry and geometry, transition metal complexes, non-covalent interactions, gold clusters and small gold-molecule interfaces, as well as an analysis of the hybrid parameters, show that our construction is quite robust. In particular, our testing shows that the resulting hybrid, including 20\% of Hartree-Fock exchange and named hAPBE, performs remarkably well for a broad palette of systems and properties, being generally better than popular hybrids (PBE0 and B3LYP). Semi-empirical dispersion corrections are also provided.Comment: 12 pages, 4 figure

Susceptibility of optimal train schedules to stochastic disturbances of process times

This work focuses on the stochastic evaluation of train schedules computed by a microscopic scheduler of railway operations based on deterministic information. The research question is to assess the degree of sensitivity of various rescheduling algorithms to variations in process times (running and dwell times). In fact, the objective of railway traffic management is to reduce delay propagation and to increase disturbance robustness of train schedules at a network scale. We present a quantitative study of traffic disturbances and their effects on the schedules computed by simple and advanced rescheduling algorithms. Computational results are based on a complex and densely occupied Dutch railway area; train delays are computed based on accepted statistical distributions, and dwell and running times of trains are subject to additional stochastic variations. From the results obtained on a real case study, an advanced branch and bound algorithm, on average, outperforms a First In First Out scheduling rule both in deterministic and stochastic traffic scenarios. However, the characteristic of the stochastic processes and the way a stochastic instance is handled turn out to have a serious impact on the scheduler performance

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set

Random-phase approximation and its applications in computational chemistry and materials science

The random-phase approximation (RPA) as an approach for computing the electronic correlation energy is reviewed. After a brief account of its basic concept and historical development, the paper is devoted to the theoretical formulations of RPA, and its applications to realistic systems. With several illustrating applications, we discuss the implications of RPA for computational chemistry and materials science. The computational cost of RPA is also addressed which is critical for its widespread use in future applications. In addition, current correction schemes going beyond RPA and directions of further development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals