Higher-order symplectic integration in Born–Oppenheimer molecular dynamics

2009 ◽  
Vol 131 (24) ◽  
pp. 244106 ◽  
Author(s):  
Anders Odell ◽  
Anna Delin ◽  
Börje Johansson ◽  
Nicolas Bock ◽  
Matt Challacombe ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Higher Order ◽  
Symplectic Integration

scholarly journals Higher-Order Extended Lagrangian Born–Oppenheimer Molecular Dynamics for Classical Polarizable Models

2018 ◽  
Vol 14 (2) ◽  
pp. 499-511 ◽  
Author(s):  
Alex Albaugh ◽  
Teresa Head-Gordon ◽  
Anders M. N. Niklasson
Keyword(s):  
Molecular Dynamics ◽  
Higher Order

Molecular dynamics studies of shock wave propagation in argon by using higher order symplectic integrators

Shock Waves ◽  
2005 ◽  
pp. 1199-1204
Author(s):  
Y. Kohno ◽  
T. Yashima ◽  
O. Takahashi ◽  
K. Saito ◽  
T. Saito ◽  
...  
Keyword(s):  
Shock Wave ◽  
Molecular Dynamics ◽  
Wave Propagation ◽  
Higher Order ◽  
Shock Wave Propagation ◽  
Symplectic Integrators

scholarly journals An integrated molecular dynamics and experimental study of higher order human telomeric quadruplexes

Biopolymers ◽  
2010 ◽  
pp. NA-NA ◽  
Author(s):  
Luigi Petraccone ◽  
Nichola Garbett ◽  
Jonathan B. Chaires ◽  
John O. Trent
Keyword(s):  
Molecular Dynamics ◽  
Experimental Study ◽  
Higher Order

scholarly journals Probing into Methylene Blue Interaction with Polyglutamic Acid: Spectroscopic and Molecular Dynamics Simulation Studies

2019 ◽  
Vol 31 (9) ◽  
pp. 1949-1958
Author(s):  
Poonam Mishra Chatterjee ◽  
Deepika Pandey Tiwari ◽  
Silpi Datta ◽  
Suman Chakrabarty ◽  
Ritu Raval ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Methylene Blue ◽  
Molecular Dynamics Simulation ◽  
Hydrophobic Interactions ◽  
Interaction Mechanism ◽  
Higher Order ◽  
Dynamics Simulation ◽  
Polyglutamic Acid ◽  
Quenching Effect ◽  
Electrostatic And Hydrophobic Interactions

Polyglutamic acid (PGA) is an anionic biopolymer which is stained with methylene blue (MB) in agar or polyacrylamide gels for analysis. Polyglutamic acid identification involves a tedious extraction and analytical process. The molecular association of polyglutamic acid and methylene blue can be used for rapid spectroscopic detection of polyglutamic acid production during fermentation. This triggered the study on investigation of polymer-dye interaction mechanism. Concentration range of polyglutamic acid, 0.001 to 0.06 μM with a fixed methylene blue concentration of 25 μM exhibited significant differences in the spectra. Preferential higher order aggregate formation of methylene blue molecules was substantiated with molecular dynamics simulation results. Fluorescence spectroscopy demonstrated a quenching effect of polyglutamic acid on methylene blue fluorescence until a certain concentration range, beyond which the Stern-Volmer (SV) plot shows a negative deviation. Polyglutamic acid was observed to promote higher order of intramolecular stacking interactions of methylene blue, possibly due to interplay of electrostatic and hydrophobic interactions between polyglutamic acid, methylene blue alone and PGA-MB systems

Self-assembly of water molecules using graphene nanoresonators

RSC Advances ◽  
2016 ◽  
Vol 6 (112) ◽  
pp. 110466-110470 ◽  
Author(s):  
Cuixia Wang ◽  
Chao Zhang ◽  
Jin-Wu Jiang ◽  
Ning Wei ◽  
Harold S. Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Higher Order ◽  
The Self ◽  
Water Molecules ◽  
Classical Molecular Dynamics ◽  
Resonant Modes

Inspired by macroscale self-assembly using the higher order resonant modes of Chladni plates, we use classical molecular dynamics to investigate the self-assembly of water molecules using graphene nanoresonators.

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