Algorithms for detecting optimal hereditary structures in graphs, with application to clique relaxations

Given a simple undirected graph, the problem of finding a maximum subset of vertices satisfying a nontrivial, interesting property Π that is hereditary on induced subgraphs, is known to be NP-hard. Many well-known graph properties meet the above conditions, making the problem widely applicable. This paper proposes a general purpose exact algorithmic framework to solve this problem and investigates key algorithm design and implementation issues that are helpful in tailoring the general framework for specific graph properties. The performance of the algorithms so derived for the maximum s-plex and the maximum s-defective clique problems, which arise in network-based data mining applications, is assessed through a computational study.     

A cationic cysteine-hydrazide as an enrichment tool for the mass spectrometric characterization of bacterial free oligosaccharides

In Campylobacterales and related ε-proteobacteria with N-linked glycosylation (NLG) pathways, free oligosaccharides (fOS) are released into the periplasmic space from lipid-linked precursors by the bacterial oligosaccharyltransferase (PglB). This hydrolysis results in the same molecular structure as the oligosaccharide that is transferred to a protein to be glycosylated. This allowed for the general elucidation of the fOS-branched structures and monosaccharides from a number of species using standard enrichment and mass spectrometry methods. To aid characterization of fOS, hydrazide chemistry has often been used for chemical modification of the reducing part of oligosaccharides resulting in better selectivity and sensitivity in mass spectrometry; however, the removal of the unreacted reagents used for the modification often causes the loss of the sample. Here, we develop a more robust method for fOS purification and characterize glycostructures using complementary tandem mass spectrometry (MS/MS) analysis. A cationic cysteine hydrazide derivative was synthesized to selectively isolate fOS from periplasmic fractions of bacteria. The cysteine hydrazide nicotinamide (Cyhn) probe possesses both thiol and cationic moieties. The former enables reversible conjugation to a thiol-activated solid support, while the latter improves the ionization signal during MS analysis. This enrichment was validated on the well-studied Campylobacter jejuni by identifying fOS from the periplasmic extracts. Using complementary MS/MS analysis, we approximated data of a known structure of the fOS from Campylobacter concisus. This versatile enrichment technique allows for the exploration of a diversity of protein glycosylation pathways.     

On imposing connectivity constraints in integer programs

We study an extension of the classical graph cut problem, wherein we replace the modular (sum of edge weights) cost function by a submodular set function defined over graph edges. Special cases of this problem have appeared in different applications in signal processing, machine learning, and computer vision. In this paper, we connect these applications via the generic formulation of “cooperative graph cuts”, for which we study complexity, algorithms, and connections to polymatroidal network flows. Finally, we compare the proposed algorithms empirically.     

Intermediate carbene formation in the reaction of thioamides with phosphorus (III) derivatives: Quantum chemical investigation

The reactions of perfluoroalkyl thioamides with trimethyl phosphine, trimethyl phosphite, and tris(dimethylamino)phosphine have been analyzed by means of quantum chemical (DFT and MP2) calculations. The reaction seems to proceed via the nucleophilic attack of the electrophilic carbon atom by the phosphorus lone pair with the formation of cyclic or acyclic adducts. The latter releases the thiophosphate molecule forming perfluoroalkylaminocarbene as the short‐lived intermediate. The reaction of the carbene with the second molecule of trialkyl phosphite yields phosphorus ylide. The ylide undergoes a migration of fluorine from carbon to phosphorus. The reactions of perfluoroalkyl thioamides with phosphines and tris(dimethylamino)phosphine probably proceeds differently. Using alkyl thioamides or amides instead of perfluoroalkyl thioamides also makes the reaction less favorable. The only combination of perfluoroalkyl thioamides with trialkyl phosphite fulfills both the kinetic requirements (moderate activation energies and relative energies for intermediates) and the thermodynamic aspects (higher stabilities of the reaction products compared with the starting materials). © 2013 Wiley Periodicals, Inc.     

Accurate non-Born-Oppenheimer calculations of the complete pure vibrational spectrum of D2 with including relativistic corrections

In this work we report very accurate variational calculations of the complete pure vibrational spectrum of the D(2) molecule performed within the framework where the Born-Oppenheimer (BO) approximation is not assumed. After the elimination of the center-of-mass motion, D(2) becomes a three-particle problem in this framework. As the considered states correspond to the zero total angular momentum, their wave functions are expanded in terms of all-particle, one-center, spherically symmetric explicitly correlated Gaussian functions multiplied by even non-negative powers of the internuclear distance. The nonrelativistic energies of the states obtained in the non-BO calculations are corrected for the relativistic effects of the order of α(2) (where α = 1/c is the fine structure constant) calculated as expectation values of the operators representing these effects.     

An algorithm for calculating atomic D states with explicitly correlated gaussian functions

An algorithm for the variational calculation of atomic D states employing n-electron explicitly correlated gaussians is developed and implemented. The algorithm includes formulas for the first derivatives of the hamiltonian and overlap matrix elements determined with respect to the gaussian nonlinear exponential parameters. The derivatives are used to form the energy gradient which is employed in the variational energy minimization. The algorithm is tested in the calculations of the two lowest D states of the lithium and beryllium atoms. For the lowest D state of Li the present result is lower than the best previously reported result.     

Optimal Security Liquidation Algorithms

This paper develops trading strategies for liquidation of a financial security, which maximize the expected return. The problem is formulated as a stochastic programming problem that utilizes the scenario representation of possible returns. Two cases are considered, a case with no constraint on risk and a case when the risk of losses associated with trading strategy is constrained by Conditional Value-at-Risk (CVaR) measure. In the first case, two algorithms are proposed; one is based on linear programming techniques, and the other uses dynamic programming to solve the formulated stochastic program. The third proposed algorithm is obtained by adding the risk constraints to the linear program. The algorithms provide path-dependent strategies, i.e., the fraction of security sold depends upon price sample-path of the security up to the current moment. The performance of the considered approaches is tested using a set of historical sample-paths of prices.     

Charge asymmetry in HD+

Expanding the wave functions of the ground and excited states of HD(+) (or pde) in terms of spherically symmetric explicitly correlated Gaussian functions with preexponential multipliers consisting of powers of the internuclear distance, and using the variational method, we performed very accurate nonadiabatic calculations of all bound states of this system corresponding to the zero total angular momentum quantum number (vibrational states; v=0-22). The total and the transition energies obtained agree with the best available calculations. For each state we computed the expectation values of the d-p, d-e, and p-e interparticle distances. This is the first time these quantities were computed for HD(+) using rigorous nonadiabatic wave functions. While up to the v=20 state some asymmetry is showing in the d-e and p-e distances, for v=21 and v=22 we observe a complete breakdown of the Born-Oppenheimer approximation and localization of the electron almost entirely at the deuteron.