| 1. |
- Jung, Minyong, et al.
(author)
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The AGORA High-resolution Galaxy Simulations Comparison Project. V. Satellite Galaxy Populations in a Cosmological Zoom-in Simulation of a Milky Way-Mass Halo
- 2024
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In: Astrophysical Journal. - 0004-637X. ; 964:2
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Journal article (peer-reviewed)abstract
- We analyze and compare the satellite halo populations at z ∼ 2 in the high-resolution cosmological zoom-in simulations of a 1012 M ⊙ target halo (z = 0 mass) carried out on eight widely used astrophysical simulation codes (Art-I, Enzo, Ramses, Changa, Gadget-3, Gear, Arepo-t, and Gizmo) for the AGORA High-resolution Galaxy Simulations Comparison Project. We use slightly different redshift epochs near z = 2 for each code (hereafter “z ∼ 2”) at which the eight simulations are in the same stage in the target halo’s merger history. After identifying the matched pairs of halos between the CosmoRun simulations and the DMO simulations, we discover that each CosmoRun halo tends to be less massive than its DMO counterpart. When we consider only the halos containing stellar particles at z ∼ 2, the number of satellite galaxies is significantly fewer than that of dark matter halos in all participating AGORA simulations and is comparable to the number of present-day satellites near the Milky Way or M31. The so-called “missing satellite problem” is fully resolved across all participating codes simply by implementing the common baryonic physics adopted in AGORA and the stellar feedback prescription commonly used in each code, with sufficient numerical resolution (≲100 proper pc at z = 2). We also compare other properties such as the stellar mass-halo mass relation and the mass-metallicity relation. Our work highlights the value of comparison studies such as AGORA, where outstanding problems in galaxy formation theory are studied simultaneously on multiple numerical platforms.
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| 2. |
- Kovalevsky, Andrey, et al.
(author)
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"To Be or Not to Be" Protonated : Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation
- 2018
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In: Structure. - : Elsevier BV. - 0969-2126. ; 26:3, s. 3-390
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Journal article (peer-reviewed)abstract
- Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site. All sulfonamide inhibitors studied bind to the Zn metal center in the deprotonated, anionic, form. Other chemical groups of the drugs can remain neutral or be protonated when bound to hCA II. MD simulations have shown that flexible functional groups of the inhibitors may alter their conformations at room temperature and occupy different sub-sites. This study offers insights into the design of specific drugs to target cancer-related hCA isoform IX. Kovalevsky et al. used macromolecular neutron crystallography and molecular dynamics simulations to obtain a detailed picture of clinical inhibitors binding to human carbonic anhydrase II. The study visualized hydrogen atom positions, revealing protonation/deprotonation events and intricate hydrogen-bonding networks, providing insights for drug design.
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| 3. |
- Magaña, Ilse, et al.
(author)
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Fully Bio-Based Elastomer Nanocomposites Comprising Polyfarnesene Reinforced with Plasma-Modified Cellulose Nanocrystals
- 2021
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In: Polymers. - : MDPI AG. - 2073-4360. ; 13:16
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Journal article (peer-reviewed)abstract
- This article proposes a process to prepare fully bio-based elastomer nanocomposites based on polyfarnesene and cellulose nanocrystals (CNC). To improve the compatibility of cellulose with the hydrophobic matrix of polyfarnesene, the surface of CNC was modified via plasma-induced polymerization, at different powers of the plasma generator, using a trans-beta-farnesene monomer in the plasma reactor. The characteristic features of plasma surface-modified CNC have been corroborated by spectroscopic (XPS) and microscopic (AFM) analyses. Moreover, the cellulose nanocrystals modified at 150 W have been selected to reinforce polyfarnesene-based nanocomposites, synthesized via an in-situ coordination polymerization using a neodymium-based catalytic system. The effect of the different loading content of nanocrystals on the polymerization behavior, as well as on the rheological aspects, was evaluated. The increase in the storage modulus with the incorporation of superficially modified nanocrystals was demonstrated by rheological measurements and these materials exhibited better properties than those containing pristine cellulose nanocrystals. Moreover, we elucidate that the viscoelastic moduli of the elastomer nanocomposites are aligned with power-law model systems with characteristic relaxation time scales similar to commercial nanocomposites, also implying tunable mechanical properties. In this foreground, our findings have important implications in the development of fully bio-based nanocomposites in close competition with the commercial stock, thereby producing alternatives in favor of sustainable materials.
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| 4. |
- Strawn, Clayton, et al.
(author)
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The AGORA High-resolution Galaxy Simulations Comparison Project. VI. Similarities and Differences in the Circumgalactic Medium
- 2024
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In: Astrophysical Journal. - 0004-637X. ; 962:1
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Journal article (peer-reviewed)abstract
- We analyze the circumgalactic medium (CGM) for eight commonly-used cosmological codes in the AGORA collaboration. The codes are calibrated to use identical initial conditions, cosmology, heating and cooling, and star formation thresholds, but each evolves with its own unique code architecture and stellar feedback implementation. Here, we analyze the results of these simulations in terms of the structure, composition, and phase dynamics of the CGM. We show properties such as metal distribution, ionization levels, and kinematics are effective tracers of the effects of the different code feedback and implementation methods, and as such they can be highly divergent between simulations. This is merely a fiducial set of models, against which we will in the future compare multiple feedback recipes for each code. Nevertheless, we find that the large parameter space these simulations establish can help disentangle the different variables that affect observable quantities in the CGM, e.g., showing that abundances for ions with higher ionization energy are more strongly determined by the simulation’s metallicity, while abundances for ions with lower ionization energy are more strongly determined by the gas density and temperature.
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