Multiscaling for Molecular Models: Investigating Interface Thermomechanics

2015 ◽  
pp. 81-92
Author(s):  
Vikas Tomar ◽  
Tao Qu ◽  
Devendra K. Dubey ◽  
Devendra Verma ◽  
Yang Zhang
Keyword(s):  
Molecular Models

Structural Determination of the Hydrofullerene C60D36 by Neutron Diffraction

1998 ◽  
Vol 54 (3) ◽  
pp. 345-350 ◽  
Author(s):  
L. E. Hall ◽  
D. R. McKenzie ◽  
R. L. Davis ◽  
M. I. Attalla ◽  
A. M. Vassallo
Keyword(s):  
Neutron Diffraction ◽  
Density Function ◽  
Diffraction Data ◽  
Fourier Transformation ◽  
Structural Determination ◽  
Molecular Models ◽  
Reduced Density ◽  
C Nmr

A mixture of C60D36 with 24.5 \pm 4.5% C60 by weight has been analysed by neutron diffraction techniques. The diffraction data was converted to a reduced density function G(r) by Fourier transformation. The C60 component of the G(r) was subtracted out. This enabled a comparison for five molecular models of C60D36, with symmetries T, Th , S 6 and two D 3 d isomers, with the experimental G(r). This specimen of C60D36 was found to be best described by a T symmetry isomer, in agreement with 13C NMR and IR data for C60H36 [Attalla et al. (1993). J. Phys. Chem. pp. 6329–6331].

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

scholarly journals Involvement of single-stranded tails in homologous recombination of DNA injected into Xenopus laevis oocyte nuclei.

1991 ◽  
Vol 11 (6) ◽  
pp. 3268-3277 ◽  
Author(s):  
E Maryon ◽  
D Carroll
Keyword(s):  
Homologous Recombination ◽  
Xenopus Laevis ◽  
Gel Electrophoresis ◽  
Xenopus Laevis Oocyte ◽  
Molecular Models ◽  
Mixed Substrates ◽  
Two Dimensional Gel Electrophoresis ◽  
Recombination Pathway ◽  
Made In

Homologous recombination of DNA molecules injected into Xenopus laevis oocyte nuclei is extremely efficient when those molecules are linear and have overlapping homologous ends. It was previously shown that a 5'----3' exonuclease activity in oocytes attacks injected linear DNAs and leaves them with single-stranded 3' tails. We tested the hypothesis that such tailed molecules are early intermediates on the pathway to recombination products. Substrates with 3' tails were made in vitro and injected into oocytes, where they recombined rapidly and efficiently. In experiments with mixed substrates, molecules with 3' tails entered recombination intermediates and products more rapidly than did molecules with flush ends. Molecules endowed in vitro with 5' tails also recombined efficiently in oocytes, but their rate was not faster than for flush-ended substrates. In most cases, the 5' tails served as templates for resynthesis of the 3' strands, regenerating duplex ends which then entered the normal recombination pathway. In oocytes from one animal, some of the 5' tails were removed, and this was exacerbated when resynthesis was partially blocked. Analysis by two-dimensional gel electrophoresis of recombination intermediates from 5'-tailed substrates confirmed that they had acquired 3' tails as a result of the action of the 5'----3' exonuclease. These results demonstrate that homologous recombination in oocytes proceeds via a pathway that involves single-stranded 3' tails. Molecular models incorporating this feature are discussed.

scholarly journals Toward a mechanistic understanding of electrocatalytic nanocarbon

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Erik J. Askins ◽  
Marija R. Zoric ◽  
Matthew Li ◽  
Zhengtang Luo ◽  
Khalil Amine ◽  
...  
Keyword(s):  
Spectroscopic Studies ◽  
Synthetic Methods ◽  
Computational Studies ◽  
Molecular Models ◽  
Chemical Production ◽  
True Nature ◽  
Catalytic Mechanisms ◽  
Mechanistic Understanding ◽  
Further Development

AbstractElectrocatalytic nanocarbon (EN) is a class of material receiving intense interest as a potential replacement for expensive, metal-based electrocatalysts for energy conversion and chemical production applications. The further development of EN will require an intricate knowledge of its catalytic behaviors, however, the true nature of their electrocatalytic activity remains elusive. This review highlights work that contributed valuable knowledge in the elucidation of EN catalytic mechanisms. Experimental evidence from spectroscopic studies and well-defined molecular models, along with the survey of computational studies, is summarized to document our current mechanistic understanding of EN-catalyzed oxygen, carbon dioxide and nitrogen electrochemistry. We hope this review will inspire future development of synthetic methods and in situ spectroscopic tools to make and study well-defined EN structures.

Molecular Models of Nucleic Acid Triple Helixes. II. PNA and 2‘-5‘ Backbone Complexes

1998 ◽  
Vol 120 (3) ◽  
pp. 492-499 ◽  
Author(s):  
A. R. Srinivasan ◽  
Wilma K. Olson
Keyword(s):  
Nucleic Acid ◽  
Molecular Models

Improved Evaluation of Liquid Densities Using van der Waals Molecular Models

2006 ◽  
Vol 110 (34) ◽  
pp. 17182-17187 ◽  
Author(s):  
Didier Mathieu ◽  
Jean-Paul Becker
Keyword(s):  
Van Der Waals ◽  
Molecular Models
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