A Legendre–Fenchel Transform for Molecular Stretching Energies

Single-molecular polymers can be used to analyze to what extent thermodynamics applies when the size of the system is drastically reduced. We have recently verified using molecular-dynamics simulations that isometric and isotensional stretching of a small polymer result in Helmholtz and Gibbs stretching energies, which are not related to a Legendre transform, as they are for sufficiently long polymers. This disparity has also been observed experimentally. Using molecular dynamics simulations of polyethylene-oxide, we document for the first time that the Helmholtz and Gibbs stretching energies can be related by a Legendre–Fenchel transform. This opens up a possibility to apply this transform to other systems which are small in Hill’s sense.

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Absorption of Mechanical Energy via Formation of Ice Nanotubes in Zeolite

Physical Chemistry Chemical Physics ◽

10.1039/d1cp01482j ◽

2021 ◽

Author(s):

Kenji Mochizuki

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Heterogeneous System ◽

Mechanical Energy ◽

Bulk Water ◽

Pure Silica ◽

Dynamics Simulations ◽

First Time

Abstract Molecular dynamics simulations are carried out for a heterogeneous system composed of bulk water and pure-silica zeolites of the AFI type. Our simulations show, for the first time, the...

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Molecular insight into the Mullins effect: irreversible disentanglement of polymer chains revealed by molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/c7cp01142c ◽

2017 ◽

Vol 19 (29) ◽

pp. 19468-19477 ◽

Cited By ~ 11

Author(s):

Chi Ma ◽

Tuo Ji ◽

Christopher G. Robertson ◽

R. Rajeshbabu ◽

Jiahua Zhu ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Model ◽

Polymer Chains ◽

Mullins Effect ◽

Key Characteristics ◽

Dynamics Simulations ◽

First Time ◽

Insight Into

For the first time, the key characteristics associated with the Mullins effect are captured by a molecular model.

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Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations

10.1101/558502 ◽

2019 ◽

Author(s):

Juan A. Bueren-Calabuig ◽

Marcus Bage ◽

Victoria H. Cowling ◽

Andrei V. Pisliakov

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Rna Polymerase Ii ◽

Active Site ◽

Allosteric Regulation ◽

Dynamic Network ◽

Binding Model ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations ◽

First Time

ABSTRACTThe RNA guanine-7 methyltransferase (RNMT) in complex with RNMT-Activating Miniprotein (RAM) catalyses the formation of a N7-methylated guanosine cap structure on the 5’ end of nascent RNA polymerase II transcripts. The mRNA cap protects the transcript from exonucleases and recruits cap-binding complexes that mediate RNA processing, export and translation. By using microsecond standard and accelerated molecular dynamics simulations, we provide for the first time a detailed molecular mechanism of allosteric regulation of RNMT by RAM. We show that RAM selects the RNMT active site conformations that are optimal for binding of substrates (AdoMet and the cap), thus enhancing their affinity. Furthermore, our results strongly suggest the likely scenario in which the cap binding promotes the subsequent AdoMet binding, consistent with the previously suggested cooperative binding model. By employing the dynamic network and community analyses, we revealed the underlying long-range allosteric networks and paths that are crucial for allosteric regulation by RAM. Our findings complement and explain previous experimental data on RNMT activity. Moreover, this study provides the most complete description of the cap and AdoMet binding poses and interactions within the enzyme’s active site. This information is critical for the drug discovery efforts that consider RNMT as a promising anti-cancer target.

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Interaction of stable aggregates drives the precipitation of calcium phosphate in supersaturated solutions

CrystEngComm ◽

10.1039/c9ce00658c ◽

2019 ◽

Vol 21 (42) ◽

pp. 6354-6364 ◽

Cited By ~ 5

Author(s):

R. Innocenti Malini ◽

C. L. Freeman ◽

J. H. Harding

Keyword(s):

Molecular Dynamics ◽

Calcium Phosphate ◽

Molecular Dynamics Simulations ◽

Amorphous Calcium Phosphate ◽

Calcium Phosphate Nanoparticles ◽

Dynamics Simulations ◽

First Time ◽

Supersaturated Solutions

Using molecular dynamics simulations, we show for the first time that calcium phosphate nanoparticles of eight formula units are thermodynamically stable and could be key in the nucleation of amorphous calcium phosphate.

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Molecular Dynamics simulations of thermal conductivity in composites consisting of aluminum oxide nanoparticles surrounded by polyethylene oxide

2015 IEEE 65th Electronic Components and Technology Conference (ECTC) ◽

10.1109/ectc.2015.7159863 ◽

2015 ◽

Cited By ~ 1

Author(s):

Barbara Poliks ◽

Cheng Chen ◽

Bruce E. White ◽

Bahgat Sammakia

Keyword(s):

Thermal Conductivity ◽

Molecular Dynamics ◽

Aluminum Oxide ◽

Molecular Dynamics Simulations ◽

Polyethylene Oxide ◽

Oxide Nanoparticles ◽

Aluminum Oxide Nanoparticles ◽

Dynamics Simulations

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MOLECULAR DYNAMICS SIMULATIONS OF LIQUID CRYSTAL ANCHORING AT AN AMORPHOUS POLYMER SURFACE

International Journal of Modern Physics C ◽

10.1142/s0129183199000310 ◽

1999 ◽

Vol 10 (02n03) ◽

pp. 415-429 ◽

Cited By ~ 8

Author(s):

T. P. DOERR ◽

P. L. TAYLOR

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Amorphous Polymer ◽

Polymer Surface ◽

The Other ◽

Substantial Fraction ◽

Dynamics Simulations ◽

First Time

Atomistic molecular dynamics simulations have been used, apparently for the first time, to investigate the anchoring behavior of a liquid crystal at the interface with an amorphous polymer. The simulations studied a system consisting of the nematogen 5CB at the surface of amorphous polyethylene, and used the simple Dreiding II force field. The simulations indicate a preference for nonplanar anchoring. Two distinct microscopic paths have been identified by which the liquid crystal changes orientation at the surface. In one case, only one or a few of the 5CB molecules are rotating at any particular time. In the other case, a substantial fraction of the molecules rotate simultaneously.

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