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Programmatic conversion of crystal structures into 3D printable files using Jmol

Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie, Jason E. Bara
2016 Journal of Cheminformatics  
Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results: A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the
more » ... ography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting. The resulting data file conversion of the 30,000 CIFs proceeded as expected, however some inconsistencies and unintended results were observed with co-crystallized structures, racemic mixtures, and structures with large counterions that led to 3D printable files not containing the desired chemical structure. Potential solutions to these challenges are considered and discussed. Further, a searchable Jmol 3D Print website was created that allows users to both discover the 3D file dataset created in this work and create custom 3D printable files for any structure in the COD. Conclusions: Over 30,000 crystal structures were programmatically converted into 3D printable files, allowing users to have quick access to a sizable collection of 3D printable crystal structures. Further, any crystal structure (>350,000) in the COD can now be conveniently converted into 3D printable file formats using the Jmol 3D Print website created in this work. The 3D Print website also allows users to convert their own CIFs into 3D printable files. 3D file data, scripts, and the Jmol 3D Print website are provided openly to the community in an effort to promote discovery and use of 3D printable crystal structures. The 3D file dataset and Jmol 3D Print website will find wide use with researchers and educators seeking to 3D print chemical structures, while the scripts will be useful for programmatically converting large database collections of crystal structures into 3D printable files.
doi:10.1186/s13321-016-0181-z pmid:27933103 pmcid:PMC5122160 fatcat:337gkomo2vgjzb7sc2l3ej4tnu

Identification of "Known Unknowns" Utilizing Accurate Mass Data and ChemSpider

James L. Little, Antony J. Williams, Alexey Pshenichnov, Valery Tkachenko
2011 Journal of the American Society for Mass Spectrometry  
In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource
more » ... to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.
doi:10.1007/s13361-011-0265-y pmid:22069037 fatcat:dkqpc2n4sbfp3jjbv74epgdfce

PET monitoring of cancer therapy with3He and12C beams: a study with the GEANT4 toolkit

Igor Pshenichnov, Alexei Larionov, Igor Mishustin, Walter Greiner
2007 Physics in Medicine and Biology  
In the present work we use a Monte Carlo model for Heavy-Ion Therapy (MCHIT) (Pshenichnov et al 2005 (Pshenichnov et al , 2006 based on the GEANT4 simulation toolkit (Agostinelli et al 2003 , Allison  ... 
doi:10.1088/0031-9155/52/24/007 pmid:18065840 fatcat:qzjlk4debzgffanb3lifr53qqa

Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data

Alena Kushniarevich, Olga Utevska, Marina Chuhryaeva, Anastasia Agdzhoyan, Khadizhat Dibirova, Ingrida Uktveryte, Märt Möls, Lejla Mulahasanovic, Andrey Pshenichnov, Svetlana Frolova, Andrey Shanko, Ene Metspalu (+28 others)
2015 PLoS ONE  
The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion-mainly to East Europe and the northern Balkans-resulted in the incorporation of genetic components from numerous autochthonous populations into the Slavic gene pools. Here, we characterize genetic variation in all extant ethnic groups speaking Balto-Slavic languages by
more » ... g mitochondrial DNA (n = 6,876), Y-chromosomes (n = 6,079) and genome-wide SNP profiles (n = 296), within PLOS ONE |
doi:10.1371/journal.pone.0135820 pmid:26332464 pmcid:PMC4558026 fatcat:so6kmn4ng5ebzhvc5r4x7orzmu

Measurement of Mutual Coulomb Dissociation insNN=130GeVAu+AuCollisions

Mickey Chiu, Alexei Denisov, Edmundo Garcia, Judith Katzy, Andrei Makeev, Michael Murray, Sebastian White
2002 Physical Review Letters  
We thank Tony Baltz and Igor Pshenichnov for many useful discussions. The U.S. Department of Energy and the Deutsche Forschungsgemeinschaft supported this work.  ... 
doi:10.1103/physrevlett.89.012302 pmid:12097036 fatcat:b36t5tfcvvg3xdxq2t4urmabme

Long-range angular correlations on the near and away side in p–Pb collisions at sNN=5.02 TeV

Betty Abelev, Jaroslav Adam, Dagmar Adamova, Andrew Marshall Adare, Madan Aggarwal, Gianluca Aglieri Rinella, Michelangelo Agnello, Andras Gabor Agocs, Andrea Agostinelli, Zubayer Ahammed, Nazeer Ahmad, Arshad Ahmad (+963 others)
2013 Physics Letters B  
Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < p_ T^ assoc < p_ T^ trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the
more » ... ar side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p_ T bins, and the widths show no significant evolution with event multiplicity or p_ T. These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge.
doi:10.1016/j.physletb.2013.01.012 fatcat:sk5oy2mp3fbd7frdwjeqq6od4a

Jet-associated deuteron production in pp collisions at $\sqrt{s}$ = 13 TeV

Shreyasi Acharya, Dagmar Adamova, Alexander Adler, Jonatan Adolfsson, Gianluca Aglieri Rinella, Michelangelo Agnello, Neelima Agrawal, Zubayer Ahammed, Shakeel Ahmad, Sang Un Ahn, Zaenal Akbar, Alexander Akindinov (+995 others)
2021 Physics letters / B 819  
Deuteron production in high-energy collisions is sensitive to the space–time evolution of the collision system, and is typically described by a coalescence mechanism. For the first time, we present results on jet-associated deuteron production in pp collisions at $\sqrt{s}$ = 13 TeV, providing an opportunity to test the established picture for deuteron production in events with a hard scattering. Using a trigger particle with high transverse-momentum ($p_T$ > 5 GeV/c) as a proxy for the
more » ... of a jet at midrapidity, we observe a measurable population of deuterons being produced around the jet proxy. The associated deuteron yield measured in a narrow angular range around the trigger particle differs by 2.4 – 4.8 standard deviations from the uncorrelated background. The data are described by PYTHIA model calculations featuring baryon coalescence.
doi:10.15120/gsi-2022-00104 fatcat:cfrnbhxokzbnflrftjnahpttqu

Soft-Dielectron Excess in Proton-Proton Collisions at $\sqrt{s}$ = 13 TeV

Shreyasi Acharya, Dagmar Adamova, Alexander Adler, Jonatan Adolfsson, Madan Mohan Aggarwal, Gianluca Aglieri Rinella, Michelangelo Agnello, Neelima Agrawal, Zubayer Ahammed, Shakeel Ahmad, Sang Un Ahn, Zaenal Akbar (+1020 others)
2021 Physical review letters 127(4)  
A measurement of dielectron production in proton-proton (pp) collisions at $\sqrt{s} = 13$ TeV, recorded with the ALICE detector at the CERN LHC, is presented in this Letter. The data set was recorded with a reduced magnetic solenoid field. This enables the investigation of a kinematic domain at low dielectron invariant mass $m_{\rm ee}$ and pair transverse momentum $p_{\rm T,ee}$ that was previously inaccessible at the LHC. The cross section for dielectron production is studied as a function
more » ... $m_{\rm ee}$, $p_{\rm T,ee}$, and event multiplicity ${\rm d} N_{\rm ch}/{\rm d} \eta$. The expected dielectron rate from hadron decays, called hadronic cocktail, utilizes a parametrization of the measured $\eta/\pi^0$ ratio in pp and proton-nucleus (p-A) collisions, assuming that this ratio shows no strong dependence on collision energy at low transverse momentum. Comparison of the measured dielectron yield to the hadronic cocktail at $0.15 < m_{\rm ee} < 0.6$ GeV/$c^2$ and for $p_{\rm T,ee} < 0.4$ GeV/$c$ indicates an enhancement of soft dielectrons, reminiscent of the 'anomalous' soft-photon and -dilepton excess in hadron-hadron collisions reported by several experiments under different experimental conditions. The enhancement factor over the hadronic cocktail amounts to $1.61\pm 0.13\,(\rm{stat.})\pm 0.17\,(\rm{syst., data}) \pm 0.34\,(\rm{syst., cocktail})$ in the ALICE acceptance. Acceptance-corrected excess spectra in $m_{\rm ee}$ and $p_{\rm T,ee}$ are extracted and compared with calculations of dielectron production from hadronic bremsstrahlung and thermal radiation within a hadronic many-body approach.
doi:10.15120/gsi-2022-00108 fatcat:rkami234kraedc7mivvgfkqo24

Multiharmonic Correlations of Different Flow Amplitudes in Pb-Pb Collisions at $\sqrt{s_{_{NN}}}=2.76$ TeV

Shreyasi Acharya, Dagmar Adamova, Alexander Adler, Jonatan Adolfsson, Gianluca Aglieri Rinella, Michelangelo Agnello, Neelima Agrawal, Zubayer Ahammed, Shakeel Ahmad, Sang Un Ahn, Zaenal Akbar, Alexander Akindinov (+999 others)
2021 Physical review letters 127(9)  
The event-by-event correlations between three flow amplitudes are measured for the first time in Pb-Pb collisions, using higher-order symmetric cumulants. We find that different three-harmonic correlations develop during the collective evolution of the medium when compared to correlations that exist in the initial state. These new results cannot be interpreted in terms of previous lower-order flow measurements since contributions from two-harmonic correlations are explicitly removed in the new
more » ... bservables. A comparison to Monte Carlo simulations provides new and independent constraints for the initial conditions and system properties of nuclear matter created in heavy-ion collisions.
doi:10.15120/gsi-2022-00103 fatcat:pilqekqmbnadtonzcfa6llm5um

$\Lambda^+_c$ Production and Baryon-to-Meson Ratios in pp and p-Pb Collisions at $\sqrt {s_{NN}}$=5.02 TeV at the LHC

Shreyasi Acharya, Dagmar Adamova, Alexander Adler, Jonatan Adolfsson, Gianluca Aglieri Rinella, Michelangelo Agnello, Neelima Agrawal, Zubayer Ahammed, Shakeel Ahmad, Sang Un Ahn, Zaenal Akbar, Alexander Akindinov (+1003 others)
2021 Physical review letters 127(20)  
The prompt production of the charm baryon Λ$_c^+$ and the Λ$_c^+$/D$^0$ production ratios were measured at midrapidity with the ALICE detector in pp and p-Pb collisions at $\sqrt {s_{NN}}$ = 5.02 TeV. These new measurements show a clear decrease of the Λ$_c^+$/D$^0$ ratio with increasing transverse momentum ($p_T$) in both collision systems in the range 2 < $p_T$ < 12 GeV/c, exhibiting similarities with the light-flavor baryon-to-meson ratios p/π and Λ/K$_S^0$. At low $p_T$, predictions that
more » ... lude additional color-reconnection mechanisms beyond the leading-color approximation, assume the existence of additional higher-mass charm-baryon states, or include hadronization via coalescence can describe the data, while predictions driven by charm-quark fragmentation processes measured in e$^+$e$^-$ and e-p collisions significantly underestimate the data. The results presented in this Letter provide significant evidence that the established assumption of universality (colliding-system independence) of parton-to-hadron fragmentation is not sufficient to describe charm-baryon production in hadronic collisions at LHC energies.
doi:10.15120/gsi-2022-00081 fatcat:363db6nhxbbbla3gtlzry6uyvy

Measurement of prompt J/ψ and beauty hadron production cross sections at mid-rapidity in pp collisions at $ \sqrt{s}=7 $ TeV

Betty Abelev, Jaroslav Adam, Dagmar Adamova, Andrew Marshall Adare, Madan Aggarwal, Gianluca Aglieri Rinella, Andras Gabor Agocs, Andrea Agostinelli, Saul Aguilar Salazar, Zubayer Ahammed, Arshad Ahmad, Nazeer Ahmad (+981 others)
2012 Journal of High Energy Physics  
The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at sqrts=7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L_int = 5.6nb-1. The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p_t>1.3 GeV/c and rapidity |y|<0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states
more » ... uch as the Psi(2S) and Csi_c resonances, is sigma_prompt-J/psi(pt > 1.3 GeV/c, |y| < 0.9) = 8.3 +- 0.8(stat.) +- 1.1(syst.) + 1.5 - 1.4(syst. pol.) micro barn. The cross section for the production of b-hadrons decaying to J/psi with p_t>1.3 GeV/c and |y|<0.9 is sigma_J/psi<-h_B = 1.46 +- 0.38(stat.) + 0.26 -0.32(syst.) micro barn. The results are compared to QCD model predictions. The shape of the p_t and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b-bbar pair total cross section and dsigma/dy at mid-rapidity.
doi:10.1007/jhep11(2012)065 fatcat:6izxv2xevnektcusqldvol4xzu

A Study of Scientific output of the Russian Academy of Medical Sciences in 2011 and its Qualitative and Quantitative Growth Prospects (in Concordance with Official Indicators and Policy Targets)
Анализ публикационного потока РАМН за 2011 г. и перспективы увеличения его объемов и авторитетности в соответствии с индикаторами «Программы фундаментальных научных исследований госакадемий на 2013–2020 гг.»

N.G. Kurakova, V.I. Starodubov, S.L. Kuznetsov, L.A. Tsvetkova, P.G. Aref'ev, O.A. Eremchenko, A.V. Ivanov, S.K. Kolin
2013 Rossiiskaya Akademiya Meditsinskikh Nauk. Vestnik  
Golimbet V. 23 Kutuev Ildus Pshenichnov Andrey Balanovsky Oleg Balanovska Elena European journal of human genetics 22 Tiganov Alexander S. Pantelejeva Galina Abramova Lilia I.  ...  .: (495) 553-74-89; e-mail: Ivanov Alexey Viktorovich, PhD, Chief Specialist of Federal Research Institute for Health Organization and Informatics of Ministry of Health of the Russian Federation  ... 
doi:10.15690/vramn.v68i4.604 fatcat:vvkrqg7ixbal7dx7ow7zx44pxa

Experimental Evidence for an Attractive p-$\phi$ Interaction

Shreyasi Acharya, Dagmar Adamova, Alexander Adler, Jonatan Adolfsson, Gianluca Aglieri Rinella, Michelangelo Agnello, Neelima Agrawal, Zubayer Ahammed, Shakeel Ahmad, Sang Un Ahn, Ishaan Ahuja, Zaenal Akbar (+1027 others)
2021 Physical review letters 127(17)  
This Letter presents the first experimental evidence of the attractive strong interaction between a proton and a ϕ meson. The result is obtained from two-particle correlations of combined $p$-ϕ⊕ $\bar{p}$-ϕ pairs measured in high-multiplicity pp collisions at $\sqrt{s}$ = 13 TeV by the ALICE Collaboration. The spin-averaged scattering length and effective range of the p-ϕ interaction are extracted from the fully corrected correlation function employing the Lednický-Lyuboshits approach. In
more » ... ular, the imaginary part of the scattering length vanishes within uncertainties, indicating that inelastic processes do not play a prominent role for the p-ϕ interaction. These data demonstrate that the interaction is dominated by elastic p-ϕ scattering. Furthermore, an analysis employing phenomenological Gaussian- and Yukawa-type potentials is conducted. Under the assumption of the latter, the N-ϕ coupling constant is found to be $g_{N-ϕ}$ = 0.14 ± 0.03(stat) ± 0.02(syst). This work provides valuable experimental input to accomplish a self-consistent description of the N-ϕ interaction, which is particularly relevant for the more fundamental studies on partial restoration of chiral symmetry in nuclear medium.
doi:10.15120/gsi-2022-00095 fatcat:4d3yvh2h3va5zdlphbkzy77ocy

Energy dependence of $\phi $ meson production at forward rapidity in pp collisions at the LHC

Shreyasi Acharya, Dagmar Adamova, Alexander Adler, Jonatan Adolfsson, Gianluca Aglieri Rinella, Michelangelo Agnello, Neelima Agrawal, Zubayer Ahammed, Shakeel Ahmad, Sang Un Ahn, Ishaan Ahuja, Zaenal Akbar (+1009 others)
2021 The European physical journal / C 81(8)  
The production of $\phi $ mesons has been studied in pp collisions at LHC energies with the ALICE detector via the dimuon decay channel in the rapidity region $2.5< y < 4$. Measurements of the differential cross section $\mathrm{d}^2\sigma /\mathrm{d}y \mathrm{d}p_{\mathrm {T}}$ are presented as a function of the transverse momentum ($p_{\mathrm {T}}$) at the center-of-mass energies $\sqrt{s}=5.02$, 8 and 13 TeV and compared with the ALICE results at midrapidity. The differential cross sections
more » ... at $\sqrt{s}=5.02$ and 13 TeV are also studied in several rapidity intervals as a function of $p_{\mathrm {T}}$, and as a function of rapidity in three $p_{\mathrm {T}}$ intervals. A hardening of the $p_{\mathrm {T}}$-differential cross section with the collision energy is observed, while, for a given energy, $p_{\mathrm {T}}$ spectra soften with increasing rapidity and, conversely, rapidity distributions get slightly narrower at increasing $p_{\mathrm {T}}$. The new results, complementing the published measurements at $\sqrt{s}=2.76$ and 7 TeV, allow one to establish the energy dependence of $\phi $ meson production and to compare the measured cross sections with phenomenological models. None of the considered models manages to describe the evolution of the cross section with $p_{\mathrm {T}}$ and rapidity at all the energies.
doi:10.15120/gsi-2022-00106 fatcat:hprul6ovojfyzdd7eebdwonzw4

Underlying Event measurements in pp collisions at $ \sqrt {s} = 0.9 $ and 7 TeV with the ALICE experiment at the LHC

Betty Abelev, Arian Abrahantes Quintana, Dagmar Adamova, Andrew Marshall Adare, Madan Aggarwal, Gianluca Aglieri Rinella, Andras Gabor Agocs, Andrea Agostinelli, Saul Aguilar Salazar, Zubayer Ahammed, Nazeer Ahmad, Arshad Ahmad (+958 others)
2012 Journal of High Energy Physics  
We present measurements of Underlying Event observables in pp collisions at √(s) = 0.9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p_ T, LT in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected
more » ... be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p_ T thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p) T threshold considered. Data are compared to Pythia 6.4, Pythia 8.1 and Phojet. On average, all models considered underestimate the multiplicity and summed p_ T in the Transverse region by about 10-30
doi:10.1007/jhep07(2012)116 fatcat:ih3oo5lvg5b57inmz46n6yjqw4
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