Molecular dynamic and monte carlo study on nanoenergetic binding sites of neuraminidase in different media

2012 ◽  
Vol 6 (8) ◽  
Author(s):  
M. Monajjemi
Keyword(s):  
Monte Carlo ◽  
Molecular Dynamic ◽  
Binding Sites ◽  
Monte Carlo Study

Analyzing Observed Composite Differences Across Groups

Methodology ◽  
2013 ◽  
Vol 9 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Holger Steinmetz
Keyword(s):  
Monte Carlo ◽  
Structural Equation Modeling ◽  
Measurement Invariance ◽  
Structural Equation ◽  
Monte Carlo Study ◽  
Equation Modeling ◽  
Factor Loadings ◽  
Latent Mean Differences ◽  
Partial Invariance ◽  
Mean Differences

Although the use of structural equation modeling has increased during the last decades, the typical procedure to investigate mean differences across groups is still to create an observed composite score from several indicators and to compare the composite’s mean across the groups. Whereas the structural equation modeling literature has emphasized that a comparison of latent means presupposes equal factor loadings and indicator intercepts for most of the indicators (i.e., partial invariance), it is still unknown if partial invariance is sufficient when relying on observed composites. This Monte-Carlo study investigated whether one or two unequal factor loadings and indicator intercepts in a composite can lead to wrong conclusions regarding latent mean differences. Results show that unequal indicator intercepts substantially affect the composite mean difference and the probability of a significant composite difference. In contrast, unequal factor loadings demonstrate only small effects. It is concluded that analyses of composite differences are only warranted in conditions of full measurement invariance, and the author recommends the analyses of latent mean differences with structural equation modeling instead.

Detecting Between-Groups Heteroscedasticity in MMR: A Monte Carlo Study

2011 ◽  
Author(s):  
Patrick J. Rosopa ◽  
Amber N. Schroeder ◽  
Jessica Doll
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Study

Monte Carlo study of 50 nm-long single and dual-gate MODFETs: suppression of short-channel effects

1993 ◽  
Vol 3 (9) ◽  
pp. 1719-1728
Author(s):  
P. Dollfus ◽  
P. Hesto ◽  
S. Galdin ◽  
C. Brisset
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Study ◽  
Short Channel Effects ◽  
Short Channel ◽  
Channel Effects ◽  
Dual Gate

MONTE CARLO STUDY OF EPITAXIAL OVERLAYER WITH SUBSTANTIAL LATTICE MISMATCH

1987 ◽  
Vol 48 (C5) ◽  
pp. C5-199-C5-202
Author(s):  
T. MIYASAKI ◽  
K. AIZAWA ◽  
H. AOKI ◽  
C. ITOH ◽  
M. OKAZAKI
Keyword(s):  
Monte Carlo ◽  
Lattice Mismatch ◽  
Monte Carlo Study

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

Sign in / Sign up

Export Citation Format

Share Document