The COLUMBUS Standard Integral File Structure: A proposed interchange format

The integral file structure used in the COLUMBUS Program System is described. This file structure is proposed for use as an interchange format for the exchange of information between various electronic structure codes. Access to the integral and density matrix arrays stored in the file structure is simplified by a supporting subroutine library. This library is portable across various computers and is readily available to programmers from the COLUMBUS distribution files. This library provides for the efficient processing of individual records, including the use of asynchronous I/O and the vectorized processing of packed orbital labels. The individual arrays are identified in a self-defining and extensible manner, allowing for the addition of new integral types as demanded by the application. The format of the individual records is also self-defining, allowing for the use of various packing and data compression methods within each record without burdening the calling program with unnecessary complications.     

The Separation and Quantitation of Peptides with and without Oxidation of Methionine and Deamidation of Asparagine Using Hydrophilic Interaction Liquid Chromatography with Mass Spectrometry (HILIC-MS)

Peptides with deamidated asparagine residues and oxidized methionine residues are often not resolved sufficiently to allow quantitation of their native and modified forms using reversed phase (RP) chromatography. The accurate quantitation of these modifications is vital in protein biotherapeutic analysis because they can affect a protein’s function, activity, and stability. We demonstrate here that hydrophilic interaction liquid chromatography (HILIC) adequately and predictably separates peptides with these modifications from their native counterparts. Furthermore, coefficients describing the extent of the hydrophilicity of these modifications have been derived and were incorporated into a previously made peptide retention prediction model that is capable of predicting the retention times of peptides with and without these modifications.

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Constructing near spanning trees with few local inspections

Constructing a spanning tree of a graph is one of the most basic tasks in graph theory. Motivated by several recent studies of local graph algorithms, we consider the following variant of this problem. Let G be a connected bounded‐degree graph. Given an edge e in G we would like to decide whether e belongs to a connected subgraph consisting of edges (for a prespecified constant ), where the decision for different edges should be consistent with the same subgraph . Can this task be performed by inspecting only a constant number of edges in G ? Our main results are:

• We show that if every t‐vertex subgraph of G has expansion then one can (deterministically) construct a sparse spanning subgraph of G using few inspections. To this end we analyze a “local” version of a famous minimum‐weight spanning tree algorithm.
• We show that the above expansion requirement is sharp even when allowing randomization. To this end we construct a family of 3‐regular graphs of high girth, in which every t‐vertex subgraph has expansion . We prove that for this family of graphs, any local algorithm for the sparse spanning graph problem requires inspecting a number of edges which is proportional to the girth.

© 2016 Wiley Periodicals, Inc. Random Struct. Alg., 50, 183–200, 2017     

Evaluation of direct analysis in real time mass spectrometry for onsite monitoring of batch slurry reactions

Batch slurry reactions are widely used in the industrial manufacturing of chemicals, pharmaceuticals, petrochemicals and polymers. However, onsite monitoring of batch slurry reactions is still not feasible in production plants due to the challenge in analyzing heterogeneous samples without complicated sample preparation procedures. In this study, direct analysis in real time mass spectrometry (DART-MS) has been evaluated for the onsite monitoring of a model batch slurry reaction. The results suggested that automation of the sampling process of DART-MS is important to achieve quantitative results. With a sampling technique of manual sample deposition on melting point capillaries followed by automatic sample introduction across the helium beam, relative standard deviation (RSD) of the protonated molecule signals from the reaction product of the model batch slurry reaction ranged from 6 to 30%. This RSD range is improved greatly over a sampling technique of manual sample deposition followed by manual sample introduction where the RSDs are up to 110%. Furthermore, with the semi-automated sampling approach, semi-quantitative analysis of slurry samples has been achieved. Better quantification is expected with a fully automated sampling approach.     

The Max-Flow Min-Cut theorem for countable networks

We prove a strong version of the Max-Flow Min-Cut theorem for countable networks, namely that in every such network there exist a flow and a cut that are “orthogonal” to each other, in the sense that the flow saturates the cut and is zero on the reverse cut. If the network does not contain infinite trails then this flow can be chosen to be mundane, i.e. to be a sum of flows along finite paths. We show that in the presence of infinite trails there may be no orthogonal pair of a cut and a mundane flow. We finally show that for locally finite networks there is an orthogonal pair of a cut and a flow that satisfies Kirchhoff's first law also for ends.     

Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires

A systematic study of the amplified optical detection of DNA by Mg(2+)-dependent DNAzyme subunits is described. The use of two DNAzyme subunits and the respective fluorophore/quencher-modified substrate allows the detection of the target DNA with a sensitivity corresponding to 1 × 10(-9) M. The use of two functional hairpin structures that include the DNAzyme subunits in a caged, inactive configuration leads, in the presence of the target DNA, to the opening of one of the hairpins and to the activation of an autonomous cross-opening process of the two hairpins, which affords polymer DNA wires consisting of the Mg(2+)-dependent DNAzyme subunits. This amplification paradigm leads to the analysis of the target DNA with a sensitivity corresponding to 1 × 10(-14) M. The amplification mixture composed of the two hairpins can be implemented as a versatile sensing platform for analyzing any gene in the presence of the appropriate hairpin probe. This is exemplified with the detection of the BRCA1 oncogene.     

Tuning of switching properties and excited-state dynamics of fulgides by structural modifications

The ultrafast photo-induced dynamics of the E-isomers of four selected photochromic fulgides with distinct structural motifs have been elucidated by femtosecond broadband transient absorption spectroscopy in n-hexane as solvent. E→C and E→Z isomerisations, respectively, with time constants of ～0.12 ± 0.02 ps and ～0.34 ± 0.03 ps taking place in parallel were found for derivatives with a methyl substituent at the central hexatriene (HT) unit. In contrast, fulgides with increased steric constraints by an iso-propyl substituent or by intramolecular bridging displayed virtually zero E→Z isomerisation, but instead a desired accelerated and more efficient ring closure in a reaction time of only ～50 ± 10 fs. Both photoisomerisations appear to follow excited-state pathways with distinctive conical intersections. For the ring closure, direct barrierless pathways with steep downhill gradients are likely. Furthermore, the results indicate conformer-specific reactions, with ring closure exclusively by the E(α) conformer and E→Z isomerisation predominantly by the E(β) conformer, because the E(α)→Z channel is unfavoured by the faster and kinetically more competitive E(α)→C reaction. DFT calculations of the equilibrium structures showed that the sterically demanding groups at the HT unit shift the conformer equilibria towards the E(α) conformers. At the same time, they appear to cause a favourable pre-orientation of the furyl unit that accelerates the conrotatory ring closure in the E(α)→C reaction. Benzo-annulation of the furyl unit has little effect on the observed dynamics. Overall, the results demonstrate how the excited-state dynamics and thereby the photoswitching properties of fulgides can be successfully tuned and improved by structural modifications at the chromophores.     

Electronic and steric effects on the photo-induced C→E ring-opening of structurally modified furylfulgides

The ultrafast C→E ring-opening reactions of four selectively modified furylfulgides have been studied by means of ultrafast broadband transient absorption spectroscopy after femtosecond laser excitation at λ = 500 nm. A large difference in the dynamics was found in the case of benzannulation at the furyl moiety as an example for an electronic effect by extension of the conjugated π-electron system compared to furylfulgides carrying sterically different alkyl substituents at the central cyclohexadiene (CHD) ring. The measured very similar spectro-temporal absorption maps for the furylfulgides with a methyl or isopropyl group at the CHD ring or an intramolecular alkyl bridge from the CHD to the furyl moiety showed two distinctive excited-state absorptions with slightly different decay times. The first time constant (τ(1) = 0.39-0.57 ps) was assigned to the rapid departure of the excited wavepacket from the Franck-Condon region. The slightly longer second decay time of τ(2) = 0.66-0.92 ps, depending on the compound, was attributed to the electronic deactivation and ring-opening through a conical intersection to the S(0) state. In contrast, the benzannulation at the furyl moiety was found to lead to a bi-phasic excited-state decay with τ(2) = 4.7 ps and a much slower additional contribution of τ(3) = 17.4 ps, ≈25 times longer compared to the normal furylfulgides. The drastic change is attributed to a trapping of excited molecules in a local potential energy minimum en route to the conical intersection.