Application of the Mixed Time-averaging Semiclassical Initial Value Representation method to Complex Molecular Spectra

The recently introduced mixed time-averaging semiclassical initial value representation molecular dynamics method for spectroscopic calculations [M. Buchholz, F. Grossmann, and M. Ceotto, J. Chem. Phys. 144, 094102 (2016)] is applied to systems with up to 61 dimensions, ruled by a condensed phase Caldeira-Leggett model potential. By calculating the ground state as well as the first few excited states of the system Morse oscillator, changes of both the harmonic frequency and the anharmonicity are determined. The method faithfully reproduces blueshift and redshift effects and the importance of the counter term, as previously suggested by other methods. Differently from previous methods, the present semiclassical method does not take advantage of the specific form of the potential and it can represent a practical tool that opens the route to direct ab initio semiclassical simulation of condensed phase systems.Comment: 11 figure

Engineered DNA modifying enzymes: Components of a future strategy to cure HIV/AIDS

AbstractDespite phenomenal advances in AIDS therapy transforming the disease into a chronic illness for most patients, a routine cure for HIV infections remains a distant goal. However, a recent example of HIV eradication in a patient who had received CCR5-negative bone marrow cells after full-body irradiation has fuelled new hopes for a cure for AIDS. Here, we review new HIV treatment strategies that use sophisticated genome engineering to target HIV infections. These approaches offer new ways to tackle the infection, and alone or in conjunction with already established treatments, promise to transform HIV into a curable disease

Herman-Kluk propagator is free from zero-point energy leakage

Semiclassical techniques constitute a promising route to approximate quantum dynamics based on classical trajectories starting from a quantum-mechanically correct distribution. One of their main drawbacks is the so-called zero-point energy (ZPE) leakage, that is artificial redistribution of energy from the modes with high frequency and thus high ZPE to that with low frequency and ZPE due to classical equipartition. Here, we show that an elaborate semiclassical formalism based on the Herman-Kluk propagator is free from the ZPE leakage despite utilizing purely classical propagation. This finding opens the road to correct dynamical simulations of systems with a multitude of degrees of freedom that cannot be treated fully quantum-mechanically due to the exponential increase of the numerical effort.Comment: 6 pages 2 figure

Simplified Approach to the Mixed Time-averaging Semiclassical Initial Value Representation for the Calculation of Dense Vibrational Spectra

We present and test an approximate method for the semiclassical calculation of vibrational spectra. The approach is based on the mixed time-averaging semiclassical initial value representation method, which is simplified to a form that contains a filter to remove contributions from approximately harmonic environmental degrees of freedom. This filter comes at no additional numerical cost, and it has no negative effect on the accuracy of peaks from the anharmonic system of interest. The method is successfully tested for a model Hamiltonian, and then applied to the study of the frequency shift of iodine in a krypton matrix. Using a hierarchic model with up to 108 normal modes included in the calculation, we show how the dynamical interaction between iodine and krypton yields results for the lowest excited iodine peaks that reproduce experimental findings to a high degree of accuracy

Wirtschaftswachstum und Verkehr als siamesische Zwillinge?

Wirtschaftswachstum wird zumeist durch Infrastrukturförderungen unterstützt, die zusätzlichen Verkehr verursachen, oder zumindest begünstigen. Eine regionalisierte Wirtschaftsförderung erscheint als Mittel der Wahl, wenn Wirtschaftsförderung nicht mit verkehrsverursachenden Investitionen verbunden sein soll

Joint versus separate inpatient rehabilitation treatment for patients with alcohol use disorder or drug use disorder : an observational study

Background: In many national treatment systems, patients with alcohol use disorders (AUD) and those with drug use disorders (DUD) are treated separately, while other systems provide joint treatment for both kinds of substance use disorders (SUDs). Regarding long-term rehabilitation treatment of DUD and AUD patients, there is however a lack of empirical studies on the comparison between a separate versus joint treatment modality. Methods: Data were gathered from 2 rehabilitation units located in small towns from the same German region. One unit provided treatment to a mixed group of AUD and DUD patients, while the other unit treated the 2 groups separately. Staffing, funding, and treatment programs were otherwise similar between facilities. Data were gathered from standardized routine documentation and standardized interviews. In order to understand correlates of premature treatment termination, a logistic regression analysis was performed, with treatment modality and type of SUD as main predictors, and a range of patient characteristics as covariates. Results: Patients (N=319) were diagnosed with AUD (48%), DUD (34%), or AUD plus DUD (18%). Patients in joint treatment showed a higher prevalence of lapses during treatment than those in separate treatment (26% versus 12%; p=0.009), but there was no significant difference in the prevalence of premature terminations (38% versus 44%, p=0.26). Treatment modality and interaction between modality and type of SUD was not significantly associated with premature termination. Joint treatment completers showed higher satisfaction with treatment than separate treatment completers ( p<0.001). Conclusion: We found no evidence here for a difference between treatment modalities in terms of premature termination rate. Satisfaction level was higher in those who completed joint treatment compared to separate treatment.Peer reviewe

Ammonium excretion and oxygen respiration of tropical copepods and euphausiids exposed to oxygen minimum zone conditions

Calanoid copepods and euphausiids are key components of marine zooplankton communities worldwide. Most euphausiids and several copepod species perform diel vertical migrations (DVMs) that contribute to the export of particulate and dissolved matter to midwater depths. In vast areas of the global ocean, and in particular in the eastern tropical Atlantic and Pacific, the daytime distribution depth of many migrating organisms corresponds to the core of the oxygen minimum zone (OMZ). At depth, the animals experience reduced temperature and oxygen partial pressure (pO2) and an increased carbon dioxide partial pressure (pCO2) compared to their near-surface nighttime habitat. Although it is well known that low oxygen levels can inhibit respiratory activity, the respiration response of tropical copepods and euphausiids to relevant pCO2, pO2 and temperature conditions remains poorly parameterized. Further, the regulation of ammonium excretion at OMZ conditions is generally not well understood. It was recently estimated that DVM-mediated ammonium supply considerably fuels bacterial anaerobic ammonium oxidation – a major loss process for fixed nitrogen in the ocean. These estimates were based on the implicit assumption that hypoxia or anoxia in combination with hypercapnia (elevated pCO2) does not result in a downregulation of ammonium excretion. Here we show that exposure to OMZ conditions can result in strong depression of respiration and ammonium excretion in calanoid copepods and euphausiids from the Eastern Tropical North Atlantic and the Eastern Tropical South Pacific. These physiological responses need to be taken into account when estimating DVM-mediated fluxes of carbon and nitrogen into OMZs

Erfahrungen mit dem System TROSS beim DRK

Die Projektgruppe Transportoptimierung hat in einem Jahr (WS~97/98, SS~98) das System 'Transportorganisation für soziale Serviceanbieter' (TROSS) zur Disposition für die Fahrdienste des Deutschen Roten Kreuzes (DRK) Stuttgart erstellt. In den Fakultätsberichten Nr. 1998/10 und 1998/06 wird TROSS im Detail vorgestellt. Weil keine Wartung gewährleistet werden kann und das System auch noch einige Fehler hat, wird TROSS vom DRK nicht bei der täglichen Disposition benutzt. Trotzdem ist das Interesse vom DRK an einer computerunterstützten Planung und Optimierung bei der Organisation der Fahrdienste sehr groß. Aus diesem Grund hat man sich dort intensiv mit TROSS beschäftigt. Die dabei gesammelten Erfahrungen und daraufhin durchgeführten Korrekturen an TROSS werden in diesem Bericht zusammengefasst. Am Ende des Berichts werden dann mögliche Erweiterungen des Systems vorgestellt

SeLOX—a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems

Site-specific recombinases have become a resourceful tool for genome engineering, allowing sophisticated in vivo DNA modifications and rearrangements, including the precise removal of integrated retroviruses from host genomes. In a recent study, a mutant form of Cre recombinase has been used to excise the provirus of a specific HIV-1 strain from the human genome. To achieve provirus excision, the Cre recombinase had to be evolved to recombine an asymmetric locus of recombination (lox)-like sequence present in the long terminal repeat (LTR) regions of a HIV-1 strain. One pre-requisite for this type of work is the identification of degenerate lox-like sites in genomic sequences. Given their nature—two inverted repeats flanking a spacer of variable length—existing search tools like BLAST or RepeatMasker perform poorly. To address this lack of available algorithms, we have developed the web-server SeLOX, which can identify degenerate lox-like sites within genomic sequences. SeLOX calculates a position weight matrix based on lox-like sequences, which is used to search genomic sequences. For computational efficiency, we transform sequences into binary space, which allows us to use a bit-wise AND Boolean operator for comparisons. Next to finding lox-like sites for Cre type recombinases in HIV LTR sequences, we have used SeLOX to identify lox-like sites in HIV LTRs for six yeast recombinases. We finally demonstrate the general usefulness of SeLOX in identifying lox-like sequences in large genomes by searching Cre type recombination sites in the entire human genome. SeLOX is freely available at http://selox.mpi-cbg.de/cgi-bin/selox/index

Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering

Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. alpha B, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets