scholarly journals Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 46
Author(s):  
Juan Francisco Carrascoza Mayén ◽  
Jakub Rydzewski ◽  
Natalia Szostak ◽  
Jacek Blazewicz ◽  
Wieslaw Nowak
Keyword(s):  
Ab Initio ◽  
Elevated Temperatures ◽  
Distribution Functions ◽  
Complex Molecules ◽  
Ab Initio Simulations ◽  
Dynamics Simulations ◽  
New Compounds ◽  
Formation Efficiency ◽  
The Impact

The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.

scholarly journals Delineating the Polarized and Unpolarized Parton Structure of the Nucleon

2015 ◽  
Vol 37 ◽  
pp. 1560053
Author(s):  
Pedro Jimenez-Delgado
Keyword(s):  
Parton Distribution ◽  
Distribution Functions ◽  
Distribution Analysis ◽  
Coupling Constant ◽  
Parton Distribution Functions ◽  
Careful Treatment ◽  
Future Data ◽  
The Impact

Reports on our latest extractions of parton distribution functions of the nucleon are given. First an overview of the recent JR14 upgrade of our unpolarized PDFs, including NNLO determinations of the strong coupling constant and a discussion of the role of the input scale in parton distribution analysis. In the second part of the talk recent results on the determination of spin-dependent PDFs from the JAM collaboration are reported, including a careful treatment of hadronic and nuclear corrections, as well as reports on the impact of present and future data in our understanding of the spin of the nucleon.

scholarly journals Experimental heatwaves negatively impact sperm quality in the zebra finch

2018 ◽  
Vol 285 (1871) ◽  
pp. 20172547 ◽  
Author(s):  
Laura L. Hurley ◽  
Callum S. McDiarmid ◽  
Christopher R. Friesen ◽  
Simon C. Griffith ◽  
Melissah Rowe
Keyword(s):  
Male Fertility ◽  
Elevated Temperatures ◽  
Sperm Quality ◽  
Recovery Period ◽  
Heat Exposure ◽  
Effect Of Temperature ◽  
Normal Morphology ◽  
Warming World ◽  
The Impact

For sexually reproducing species, functionally competent sperm are critical to reproduction. While high atmospheric temperatures are known to influence the timing of breeding, incubation and reproductive success in birds, the effect of temperature on sperm quality remains largely unexplored. Here, we experimentally investigated the impact of ecologically relevant extreme temperatures on cloacal temperature and sperm morphology and motility in zebra finches Taeniopygia guttata . We periodically sampled males exposed to 30°C or 40°C temperatures daily for 14 consecutive days. Following a 12-day (23°C) recovery period, birds were again exposed to heat, but under the alternate treatment (e.g. birds initially exposed to 40°C were exposed to 30°C). Elevated temperatures led to an increase in cloacal temperature and a reduction in the proportion of sperm with normal morphology; these effects were most notable under 40°C conditions, and were influenced by the duration of heat exposure and prior exposure to high temperature. Our findings highlight the potential role of temperature in determining male fertility in birds, and perhaps also in constraining the timing of avian breeding. Given the increased frequency of heatwaves in a warming world, our results suggest the need for further work on climatic influences on sperm quality and male fertility.

Dielectric relaxation of water: assessing the impact of localized modes, translational diffusion, and collective dynamics

2021 ◽  
Vol 23 (37) ◽  
pp. 20875-20882
Author(s):  
Christoph Hölzl ◽  
Harald Forbert ◽  
Dominik Marx
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Dielectric Relaxation ◽  
Molecular Dynamics Simulations ◽  
Relaxation Spectrum ◽  
Translational Diffusion ◽  
Localized Modes ◽  
Collective Dynamics ◽  
Dynamics Simulations ◽  
The Impact

The dielectric relaxation spectrum of water can be quantitatively reproduced by ab initio molecular dynamics simulations. Its decomposition into auto- and crosscorrelation terms suggests that fits of experimental spectra may require revision.

The role of metals in amyloid aggregation—Experiments and ab initio simulations

2008 ◽  
Vol 108 (11) ◽  
pp. 1992-2015 ◽  
Author(s):  
V. Minicozzi ◽  
S. Morante ◽  
G. C. Rossi ◽  
F. Stellato ◽  
N. Christian ◽  
...  
Keyword(s):  
Ab Initio ◽  
Amyloid Aggregation ◽  
Ab Initio Simulations

Reliability modeling of multi-version software system incorporating the impact of infected patching

2020 ◽  
Vol 37 (6/7) ◽  
pp. 1071-1085 ◽  
Author(s):  
Adarsh Anand ◽  
Jasmine Kaur ◽  
Shinji Inoue
Keyword(s):  
Design Methodology ◽  
Distribution Functions ◽  
Software System ◽  
Reliability Growth ◽  
Optimal Resource Allocation ◽  
Reliability Modeling ◽  
Content Type ◽  
Optimal Resource ◽  
The Impact

PurposeThe purpose of the present work is to mathematically model the reliability growth of a multi-version software system that is affected by infected patches.Design/methodology/approachThe work presents a mathematical model that studies the reliability change due to the insertion of an infected patch in multi-version software. Various distribution functions have been considered to highlight the varied aspects of the model. Furthermore, weighted criteria approach has been discussed to facilitate the choice of the model.FindingsThe model presented here is able to quantify the effect of an infected patch on multi-version software. The model captures the hike in bug content due to an infected patch.Originality/valueMulti-version systems have been studied widely, but the role of an infected patch has not been yet explored. The effect of an infected patch has been quantified by modeling the extra bugs generated in the system. This bug count would prove helpful in further studies for optimal resource allocation and testing effort allocation.

Electronic Structure and Dynamics of Defect in a-Si:H by Ab-Initio Molecular Dynamics

1993 ◽  
Vol 297 ◽  
Author(s):  
N. Orita ◽  
T. Sasaki ◽  
H. Katayama–Yoshida
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Ab Initio ◽  
Hydrogenated Amorphous Silicon ◽  
Ab Initio Molecular Dynamics ◽  
Dangling Bond ◽  
Structure And Dynamics ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous

Electronic structure and dynamics of defects in hydrogenated amorphous silicon (a-Si:H) are investigated based upon ab–initio molecular–dynamics simulations. It is shown that (i) the hydrogen–passivated dangling bond (Si-H), (ii) the positively-ionized three–centered bond (Si– H+–Si), (iii) the negatively–ionized three–coordinated dangling bond (D−) and (iv) the five- coordinated floating bond (F5) are the intrinsic defects in a–Si:H. Based upon the calculated result, we discuss the role of hydrogen and the origin of the photo–induced defect in a-Si:H.

Proton transport mechanism of imidazole, triazole and phosphoric acid mixtures from ab initio molecular dynamics simulations

2015 ◽  
Vol 17 (45) ◽  
pp. 30551-30559 ◽  
Author(s):  
Swagata Pahari ◽  
Sudip Roy
Keyword(s):  
Molecular Dynamics ◽  
Phosphoric Acid ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Proton Transport ◽  
Transport Mechanism ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

We have performed first principles molecular dynamics simulations to elucidate the mechanism and role of 1,2,3-triazole in proton transport while it is mixed with phosphoric acid (PA) and a phosphoric acid imidazole mixture.

scholarly journals Local Distortions in a Prototypical Zeolite Framework Containing Double Four-Ring Cages: The Role of Framework Composition and Organic Guests

2020 ◽  
Author(s):  
Michael Fischer ◽  
Linus Freymann
Keyword(s):  
Density Functional ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Judicious Choice ◽  
Dynamics Simulations ◽  
The Impact ◽  
Local Distortions ◽  
Framework Composition

<p>Cube-like double four-ring (<i>d4r</i>) cages are among the most frequent building units of zeolites and zeotypes. In materials synthesised in fluoride-containing media, the fluoride anions are preferentially incorporated in these cages. In order to study the impact of framework composition and organic structure-directing agents (OSDAs) on the possible occurrence of local distortions of fluoride-containing <i>d4r</i> cages, density functional theory (DFT) calculations and DFT-based molecular dynamics simulations were performed for AST-type zeotypes, considering four different compositions (SiO<sub>2</sub>, GeO<sub>2</sub>, AlPO<sub>4</sub>, GaPO<sub>4</sub>) and two different OSDA cations (tetramethylammonium [TMA] and quinuclidinium [QNU]). All systems except SiO<sub>2</sub>-AST show significant deformations, with a pyritohedron-like distortion of the <i>d4r</i> cages occurring in GeO<sub>2</sub>- and GaPO<sub>4</sub>-AST, and a displacement of the fluoride anions towards one of the corners of the cage in AlPO<sub>4</sub>- and GaPO<sub>4</sub>-AST. While the distortions occur at random in TMA-containing zeotypes, they exhibit a preferential orientation in systems that incorporate QNU cations. </p><p>In addition to providing detailed understanding of the local structure of a complex host-guest system on the picosecond timescale, this work indicates the possibility to stabilise ordered distortions through a judicious choice of the OSDA, which might enable a tuning of the material’s properties.</p>

The role of Zn 2+ dopants in the acid-basic catalysis on MgO(001) surface: Ab initio simulations of the dissociative chemisorption of R-O-R′ and R-S-R′ (R,R′=H, CH 3 , C 2 H 5 )

2017 ◽  
Vol 661 ◽  
pp. 60-68 ◽  
Author(s):  
Carla G. Fonseca ◽  
Sérgio R. Tavares ◽  
Carla V. Soares ◽  
Bruno G. daFonseca ◽  
Fábio J.F.S. Henrique ◽  
...  
Keyword(s):  
Ab Initio ◽  
Dissociative Chemisorption ◽  
Basic Catalysis ◽  
Ab Initio Simulations ◽  
Role Of Zn
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