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Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry

Abstract

Not specified

Authors: Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz

Date Published: 27th Jul 2020

Publication Type: Journal

Towards standardization guidelines for in silico approaches in personalized medicine

Abstract (Expand)

Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind … its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.

Authors: Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath

Date Published: 24th Jul 2020

Publication Type: Journal

PSIXAS : A Psi4 plugin for efficient simulations of X‐ray absorption spectra based on the transition‐potential and Δ‐Kohn–Sham method

Abstract (Expand)

Near edge X‐ray absorption fine structure (NEXAFS) spectra and their pump‐probe extension (PP‐NEXAFS) offer insights into valence‐ and core‐excited states. We present PSIXAS, a recent implementation … for simulating NEXAFS and PP‐NEXAFS spectra by means of the transition‐potential and the Δ‐Kohn–Sham method. The approach is implemented in form of a software plugin for the Psi4 code, which provides access to a wide selection of basis sets as well as density functionals. We briefly outline the theoretical foundation and the key aspects of the plugin. Then, we use the plugin to simulate PP‐NEXAFS spectra of thymine, a system already investigated by others and us. It is found that larger, extended basis sets are needed to obtain more accurate absolute resonance positions. We further demonstrate that, in contrast to ordinary NEXAFS simulations, where the choice of the density functional plays a minor role for the shape of the spectrum, for PP‐NEXAFS simulations the choice of the density functional is important. Especially hybrid functionals (which could not be used straightforwardly before to simulate PP‐NEXAFS spectra) and their amount of “Hartree‐Fock like” exact exchange affects relative resonance positions in the spectrum.

Authors: Christopher Ehlert, Tillmann Klamroth

Date Published: 15th Jul 2020

Publication Type: Journal

Polluting the Pair-instability Mass Gap for Binary Black Holes through Super-Eddington Accretion in Isolated Binaries

Abstract (Expand)

The theory for single stellar evolution predicts a gap in the mass distribution of black holes (BHs) between approximately 45 and 130 $\,{M}_{\odot }$, the so-called "pair-instability mass gap." … We examine whether BHs can pollute the gap after accreting from a stellar companion. To this end, we simulate the evolution of isolated binaries using a population synthesis code, where we allow for super-Eddington accretion. Under our most extreme assumptions, we find that at most about 2% of all merging binary BH systems contains a BH with a mass in the pair-instability mass gap, and we find that less than 0.5% of the merging systems has a total mass larger than 90 $\,{M}_{\odot }$. We find no merging binary BH systems with a total mass exceeding 100 $\,{M}_{\odot }$. We compare our results to predictions from several dynamical pathways to pair-instability mass gap events and discuss the distinguishable features. We conclude that the classical isolated binary formation scenario will not significantly contribute to the pollution of the pair-instability mass gap. The robustness of the predicted mass gap for the isolated binary channel is promising for the prospective of placing constraints on (i) the relative contribution of different formation channels, (ii) the physics of the progenitors including nuclear reaction rates, and, tentatively, (iii) the Hubble parameter.

Authors: L. A. C. van Son, S. E. De Mink, F. S. Broekgaarden, M. Renzo, S. Justham, E. Laplace, J. Morán-Fraile, D. D. Hendriks, R. Farmer

Date Published: 1st Jul 2020

Publication Type: Journal

The Spectacular Ultraviolet Flash from the Peculiar Type Ia Supernova 2019yvq

Abstract

Not specified

Authors: A. A. Miller, M. R. Magee, A. Polin, K. Maguire, E. Zimmerman, Y. Yao, J. Sollerman, S. Schulze, D. A. Perley, M. Kromer, S. Dhawan, M. Bulla, I. Andreoni, E. C. Bellm, K. De, R. Dekany, A. Delacroix, C. Fremling, A. Gal-Yam, D. A. Goldstein, V. Z. Golkhou, A. Goobar, M. J. Graham, I. Irani, M. M. Kasliwal, S. Kaye, Y. -L. Kim, R. R. Laher, A. A. Mahabal, F. J. Masci, P. E. Nugent, E. Ofek, E. S. Phinney, S. J. Prentice, R. Riddle, M. Rigault, B. Rusholme, T. Schweyer, D. L. Shupe, M. T. Soumagnac, G. Terreran, R. Walters, L. Yan, J. Zolkower, S. R. Kulkarni

Date Published: 1st Jul 2020

Publication Type: Journal

Specifications of standards in systems and synthetic biology: status and developments in 2020

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology. …Not specified

Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 29th Jun 2020

Publication Type: Journal

Au 21 cage structures and their magic number tri‐cations

Abstract (Expand)

We examine the stability and properties of three Au21 cage structures, one with D3 symmetry and denoted as Au21 (D3), which is novel, and the other two with C2v symmetry. One, denoted as Au21 (C2v-1), … has been previously reported but the other, denoted as Au21 (C2v-2), is novel. As reference Au21 structures, we also examine a sheet isomer and a compact isomer, Au21 (Cs-Tetra), formed by adsorbing an Au atom on Au20 (Td). For all structures, we consider charge ranging from −1 to +4. For the Au21 cage structures, a primary property of interest is their spherical aromaticity, as measured by their nucleus independent chemical shift. Our focus is on charge +3 since each gold atom is assumed to contribute one (6s) valence electron, and 18 is a magic number for shell closing. We find that, although Au21 (D3)+3 has the largest aromaticity, it is not the most stable urn:x-wiley:00207608:media:qua26191:qua26191-math-0001 cage species. Surprisingly, Au21 (C2v-2), which is not even stable as a neutral cage species, is the most stable tri-cation cage species. We also examine the stability of (neutral) Au21Xn cage structures relative to Au21Xn structures derived from Au21 (Cs-Tetra) (with X = F, Cl, Br, I and n = 1, 3, 5). We find that, although Au21F3 derived from Au21 (D3) has the largest aromaticity, it is not the most stable Au21F3 cage structure. Nonetheless, all cage structures are stabilized relative to Au21 (Cs-Tetra) and, remarkably, for the trichlorinated, tribrominated, and triiodineated clusters, at least one cage structure is more stable than its Au21 (Cs-Tetra) counterpart.

Authors: Christopher Ehlert, Xiaojing J. Liu, Ian P. Hamilton

Date Published: 5th Jun 2020

Publication Type: Journal

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