Initial state nuclear effects for jet production measured in sNN=200GeV\sqrt{s_\mathrm{NN}} = 200 \mathrm{GeV} d+Au collisions by STAR

Full jet reconstruction in heavy-ion collisions is a promising tool for quantitative study of properties of the dense medium produced at RHIC. Measurements of d+Au collisions are important to disentangle initial state nuclear effects from medium-induced $k_\mathrm{T}$ broadening and jet quenching. We report measurements of mid-rapidity ($|\eta_{jet}| < 0.4|$) di-jet correlations in d+Au using high-statistics run 8 RHIC data at $\sqrt{s_\mathrm{NN}} = 200 \mathrm{GeV}$.Comment: 2 pages, 2 figures - To appear in the conference proceedings for Quark Matter 2009, March 30 - April 4, Knoxville, Tennesse

Jets in 200 GeV p+p and d+Au collisions from the STAR experiment at RHIC

Full jet reconstruction in heavy-ion collisions is a promising tool for the quantitative study of properties of the dense medium produced at RHIC. Measurements of d+Au collisions are important to disentangle initial state nuclear effects from medium-induced kT broadening and jet quenching. Study of jet production and properties in d+Au in combination with similar studies in p+p is an important baseline measurement needed to better understand heavy-ion results. We present mid-rapidity inclusive jet pT spectra and di-jet correlations (kT) in 200 GeV p+p and d+Au collisions from the 2007-2008 RHIC run. We discuss the methods used to correct the data for detector effects and for background in d+Au collisions.Comment: 4 pages, 5 figures. To appear in Hot Quarks 2010 conference proceeding

Setting up a STAR Tier 2 Site at Golias/Prague Farm

High Energy Nuclear Physics (HENP) collaborations' experience show that the computing resources available at a single site are often neither sufficient nor satisfy the need of remote collaborators. From latencies in the network connectivity to the lack of interactivity, work at distant computing centers is often inefficient. Having fully functional software stack on local resources is a strong enabler of science opportunities for any local group who can afford the time investment. Prague's heavy-ions group participating in STAR experiment at RHIC has been a strong advocate of local computing as the most efficient means of data processing and physics analyses. Tier 2 computing center was set up at a Regional Computing Center for Particle Physics called "Golias". We report on our experience in setting up a fully functional Tier 2 center and discuss the solutions chosen to address storage space and analysis issues and the impact on the farms overall functionality. This includes a locally built STAR analysis framework, integration with a local DPM system (a cost effective storage solution), the influence of the availability and quality of the network connection to Tier 0 via a dedicated CESNET/ESnet link and the development of light-weight yet fully automated data transfer tools allowing the movement of entire datasets from BNL (Tier 0) to Golias (Tier 2).Comment: To appear in proceedings of Computing in High Energy and Nuclear Physics 200

STAR inner tracking upgrade - A performance study

Anisotropic flow measurements have demonstrated development of partonic collectivity in $200\mathrm{GeV}$ Au+Au collisions at RHIC. To understand the partonic EOS, thermalization must be addressed. Collective motion of heavy-flavor (c,b) quarks can be used to indicate the degree of thermalization of the light-flavor quarks (u,d,s). Measurement of heavy-flavor quark collectivity requires direct reconstruction of heavy-flavor hadrons in the low \pt region. Measurement of open charm spectra to high \pt can be used to investigate heavy-quark energy loss and medium properties. The Heavy Flavor Tracker (HFT), a proposed upgrade to the STAR experiment at midrapidity, will measure $v_{2}$ of open-charm hadrons to very low \pt by reconstructing their displaced decay vertices. The innermost part of the HFT is the PIXEL detector (made of two low mass monolithic active pixel sensor layers), which delivers a high precision position measurement close to the collision vertex. The Intermediate Silicon Tracker (IST), a 1-layer strip detector, is essential to improve hit identification in the PIXEL detector when running at full RHIC-II luminosity. Using a full GEANT simulation, open charm measurement capabilities of STAR with the HFT will be shown. Its performance in a broad \pt range will be demonstrated on $v_{2}$ (\pt > 0.5\mathrm{GeV}/c) and $R_\mathrm{CP}$ (\pt < 10\mathrm{GeV}/c) measurements of \D meson. Results of reconstruction of \Lc baryon in heavy-ion collisions are presented.Comment: to appear in EPJ C (Hot Quarks 2008 conference volume

A Proline-Based Neuraminidase Inhibitor: DFT Studies on the Zwitterion Conformation, Stability and Formation

The designs of potent neuraminidase (NA) inhibitors are an efficient way to deal with the recent “2009 H1N1” influenza epidemic. In this work, density functional calculations were employed to study the conformation, stability and formation of the zwitterions of 5-[(1R,2S)-1-(acetylamino)-2-methoxy-2-methylpentyl]-4-[(1Z)-1-propenyl]-(4S,5R)-d-proline (BL), a proline-based NA inhibitor. Compared to proline, the zwitterion stability of BL is enhanced by 1.76 kcal mol−1 due to the introduction of functional groups. However, the zwitterion of BL will not represent a local minimum on the potential energy surface until the number of water molecules increases up to two (n = 2). With the addition of two and three water molecules, the energy differences between the zwitterions and corresponding canonical isomers were calculated at 3.13 and −1.54 kcal mol−1, respectively. The zwitterions of BL are mainly stabilized by the H-bonds with the water molecules, especially in the case of three water molecules where the carboxyl-O atoms are largely coordination-saturated by three H-bonds of medium strengths, causing the zwitterion stability even superior to the canonical isomer. With the presence of two and three water molecules, the energy barriers for the conversion processes from the canonical isomers to the zwitterions are equal to 4.96 and 3.13 kcal mol−1, respectively. It indicated that the zwitterion formation is facile to take place with addition of two molecules and further facilitated by more water molecules. Besides, the zwitterion formation of BL is finished in a single step, different from other NA inhibitors. Owing to the above advantages, BL is a good NA inhibitor candidate and more attention should be paid to explorations of BL-based drugs

An empirical force field for the simulation of the vibrational spectroscopy of carbon nanomaterials

An empirical force field for carbon based upon the Murrell-Mottram potential is developed for the calculation of the vibrational frequencies of carbon nanomaterials. The potential is reparameterised using data from density functional theory calculations through a Monte-Carlo hessian-matching approach, and when used in conjunction with the empirical bond polarisability model provides an accurate description of the non-resonant Raman spectroscopy of carbon nanotubes and graphene. With the availability of analytical first and second derivatives, the computational cost of evaluating harmonic vibrational frequencies is a fraction of the cost of corresponding quantum chemical calculations, and makes the accurate atomistic vibrational analysis of systems with thousands of atoms possible. Subsequently, the non-resonant Raman spectroscopy of carbon nanotubes and graphene, including the role of defects and carbon nanotube junctions is explored

The Raman optical activity of β-D-xylose: where experiment and theory meet

Besides its applications in bioenergy and biosynthesis, β-D-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure–spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved