Comparison of the Singer method and the constraints method for molecular dynamics with linear molecules on the vector computer CYBER 205

1987 ◽  
Vol 43 (2) ◽  
pp. 217-229 ◽  
Author(s):  
C. Hoheisel ◽  
R. Vogelsang ◽  
M. Schoen
Keyword(s):  
Molecular Dynamics ◽  
Vector Computer ◽  
Linear Molecules

Computer Simulation study of polar liquids: static and dynamic properties

1984 ◽  
Vol 394 (1806) ◽  
pp. 137-160 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Dynamic Properties ◽  
Memory Function ◽  
Complex Frequency ◽  
Point Dipole ◽  
Dipole Orientation ◽  
Ewald Summation ◽  
Polar Liquids ◽  
Reaction Field ◽  
Linear Molecules

The Berne-Pechukas-Kushick potential for linear molecules, together with a central electric point dipole, has been used as the model for polar liquids in a series of molecular dynamics computer simulations. Different simulations used Ewald summation, spherical cut off and spherical cut off with reaction field correction to sum the dipole-dipole interactions, and the relative merits of these methods are discussed. Results for thermodynamic properties and the distribution function h ∆ ( r ) are presented. Results for the autocorrelation functions for dipole orientation and angular velocity are also presented, and discussed in terms of memory functions, particularly with regard to the Steele perturbation theory. The complex, frequency-dependent dielectric constant has been calculated from the memory function of the autocorrelation function of the periodic cube dipole moment, and results are presented in the form of Cole-Cole plots. The ‘dielectric friction’ approach to polar liquids is examined against the evidence of the molecular dynamics data. Attention is drawn to the behaviour of the cross correlations between dipole orientations and their importance to the problem of dielectric relaxation is emphasized.

scholarly journals Molecular Dynamics Study of the Factors Influencing the β-Cyclodextrin Inclusion Complex Formation of the Isomers of Linear Molecules

2017 ◽  
Vol 2017 ◽  
pp. 1-9
Author(s):  
E. Alvira
Keyword(s):  
Molecular Dynamics ◽  
Complex Formation ◽  
Inclusion Complex ◽  
Size Composition ◽  
Dynamics Simulation ◽  
Inclusion Complex Formation ◽  
Cyclodextrin Inclusion ◽  
Preferential Binding ◽  
Linear Molecules ◽  
Cyclodextrin Inclusion Complex

The influence of the size, composition, and atomic distribution of linear guests on β-cyclodextrin inclusion complex formation is clarified by means of a molecular dynamics simulation at constant temperature. The intermolecular energy is modelled by a Lennard-Jones potential, where the molecular composition is represented by various parameters and by a continuum description of the guest and cavity walls. It is concluded that the parameters related to the atomic size require minimum values for the confinement of linear molecules inside the cavity. The isomer with optimal affinity for β-cyclodextrin as predicted by the free energy presents an asymmetrical molecular structure, and the position probability density shows that the isomer tends to insert the portion with largest atoms into the cavity, although the preferential binding site of the guest is not always located in regions of the host with maximum discriminatory power.

Two- and N-step correlated models for the analysis of molecular dynamics trajectories of linear molecules in silicalite

2000 ◽  
Vol 113 (17) ◽  
pp. 7588-7592 ◽  
Author(s):  
Pierfranco Demontis ◽  
Giuseppe B. Suffritti ◽  
Antonio Tilocca
Keyword(s):  
Molecular Dynamics ◽  
Linear Molecules

Flow of linear molecules through a 4:1:4 contraction–expansion using non-equilibrium molecular dynamics: Extensional rheology and pressure drop

2009 ◽  
Vol 161 (1-3) ◽  
pp. 48-59 ◽  
Author(s):  
J. Castillo-Tejas ◽  
A. Rojas-Morales ◽  
F. López-Medina ◽  
Juan F.J. Alvarado ◽  
G. Luna-Bárcenas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pressure Drop ◽  
Extensional Rheology ◽  
Linear Molecules ◽  
Non Equilibrium Molecular Dynamics ◽  
Non Equilibrium

Electron microscopic assays of restriction endonuclease cutting, exonuclease digestion, and hybridization

1984 ◽  
Vol 42 ◽  
pp. 686-687
Author(s):  
Mark Hannibal ◽  
Jacob Varkey ◽  
Michael Beer
Keyword(s):  
Electron Microscope ◽  
Low Temperature ◽  
Restriction Endonuclease ◽  
Double Helix ◽  
Test Material ◽  
Electron Microscopic ◽  
Exonuclease Iii ◽  
Dna Molecule ◽  
Linear Molecules ◽  
Exonuclease Digestion

Workman and Langmore have recently proposed a procedure for isolating particular chromatin fragments. The method requires restriction endonuclease cutting of the chromatin and a probe, their digestion with two exonucleases which leave complimentary single strand termini and low temperature hybridization of these. We here report simple electron microscopic monitoring of the four reactions involved.Our test material was ϕX-174 RF DNA which is cut once by restriction endonuclease Xho I. The conversion of circles to linear molecules was followed in Kleinschmidt spreads. Plate I shows a circular and a linear DNA molecule. The rate of cutting is shown in Figure 1.After completion of the endonuclease cutting, one portion of the DNA was treated with exonuclease III, an enzyme known to digest the 3' terminals of double helical DNA. Aliquots when examined in the electron microscope reveal a decreasing length of double helix and increasing bushes at the ends.

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