Development of polyphosphate parameters for use with the AMBER force field

Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1016–1025, 2003Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34696/1/10262_ftp.pd

Laying the groundwork at the AGS: Recent results from experiment E895

The E895 Collaboration at the Brookhaven AGS has performed a systematic investigation of Au+Au collisions at 2-8 AGeV, using a large-acceptance Time Projection Chamber. In addition to extensive measurements of particle flow, spectra, two-particle interferometry, and strangeness production, we have performed novel hybrid analyses, including azimuthally-sensitive pion HBT, extraction of the six-dimensional pion phasespace density, and a first measurement of the Lambda-proton correlation function.Comment: Presented at Quark Matter 2001, 8 pages, 5 figure

Near-threshold production of the multi-strange Ξ−\Xi^- hyperon

The yield for the multi-strange $\Xi^{-}$ hyperon has been measured in 6 AGeV Au+Au collisions via reconstruction of its decay products $\pi^{-}$ and $\Lambda$, the latter also being reconstructed from its daughter tracks of $\pi^{-}$ and p. The measurement is rather close to the threshold for $\Xi^{-}$ production and therefore provides an important test of model predictions. The measured yield for $\Xi^{-}$ and $\Lambda$ are compared for several centralities. In central collisions the $\Xi^{-}$ yield is found to be in excellent agreement with statistical and transport model predictions, suggesting that multi-strange hadron production approaches chemical equilibrium in high baryon density nuclear matter.Comment: Submitted to PR

Comparison of Source Images for protons, π−\pi^-'s and Λ\Lambda's in 6 AGeV Au+Au collisions

Source images are extracted from two-particle correlations constructed from strange and non-strange hadrons produced in 6 AGeV Au + Au collisions. Very different source images result from pp vs p$\Lambda$ vs $\pi^-\pi^-$ correlations. These observations suggest important differences in the space-time emission histories for protons, pions and neutral strange baryons produced in the same events

Longitudinal Flow of Protons from 2-8 AGeV Central Au+Au Collisions

Rapidity distributions of protons from central $^{197}$Au + $^{197}$Au collisions measured by the E895 Collaboration in the energy range from 2 to 8 AGeV at the Brookhaven AGS are presented. Longitudinal flow parameters derived using a thermal model including collective longitudinal expansion are extracted from these distributions. The results show an approximately linear increase in the longitudinal flow velocity, $_{L}$, as a function of the logarithm of beam energy.Comment: 5 Pages, including 3 figures, 1 tabl

Non-homologous end-joining pathway associated with occurrence of myocardial infarction: gene set analysis of genome-wide association study data

<p>Purpose: DNA repair deficiencies have been postulated to play a role in the development and progression of cardiovascular disease (CVD). The hypothesis is that DNA damage accumulating with age may induce cell death, which promotes formation of unstable plaques. Defects in DNA repair mechanisms may therefore increase the risk of CVD events. We examined whether the joints effect of common genetic variants in 5 DNA repair pathways may influence the risk of CVD events.</p> <p>Methods: The PLINK set-based test was used to examine the association to myocardial infarction (MI) of the DNA repair pathway in GWAS data of 866 subjects of the GENetic DEterminants of Restenosis (GENDER) study and 5,244 subjects of the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER) study. We included the main DNA repair pathways (base excision repair, nucleotide excision repair, mismatch repair, homologous recombination and non-homologous end-joining (NHEJ)) in the analysis.</p> <p>Results: The NHEJ pathway was associated with the occurrence of MI in both GENDER (P = 0.0083) and PROSPER (P = 0.014). This association was mainly driven by genetic variation in the MRE11A gene (PGENDER = 0.0001 and PPROSPER = 0.002). The homologous recombination pathway was associated with MI in GENDER only (P = 0.011), for the other pathways no associations were observed.</p> <p>Conclusion: This is the first study analyzing the joint effect of common genetic variation in DNA repair pathways and the risk of CVD events, demonstrating an association between the NHEJ pathway and MI in 2 different cohorts.</p&gt

Charged Pion Production in 2 to 8 AGeV Central Au+Au Collisions

Momentum spectra of charged pions over nearly full rapidity coverage from target to beam rapidity have been measured in the 0-5% most central Au+Au collisions in the beam energy range from 2 to 8 AGeV by the E895 Experiment. Using a thermal parameterization to fit the transverse mass spectra, rapidity density distributions are extracted. The observed spectra are compared with predictions from the RQMD v2.3 cascade model and also to a thermal model including longitudinal flow. The total 4$\pi$ yields of the charged pions are used to infer an initial state entropy produced in the collisions.Comment: 13 pgs, 19 figs, accepted by Phys. Rev. C. Data tables available at http://nuclear.ucdavis.edu/~e895/published_spectra.htm

Climbing Bloom’s taxonomy pyramid: Lessons from a graduate histology course

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138235/1/ase1685_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138235/2/ase1685.pd