Characterization of Structural and Dynamical Behavior in Monolayers of Long-Chain Molecules Using Molecular-Dynamics Calculations

1988 ◽  
Vol 60 (21) ◽  
pp. 2152-2155 ◽  
Author(s):  
James P. Bareman ◽  
Gianni Cardini ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Dynamical Behavior ◽  
Chain Molecules ◽  
Molecular Dynamics Calculations ◽  
Long Chain

Characterization of a Langmuir-Blodgett monolayer using molecular dynamics calculations

1988 ◽  
Vol 145 (6) ◽  
pp. 493-498 ◽  
Author(s):  
Gianni Cardini ◽  
James P. Bareman ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Langmuir Blodgett ◽  
Molecular Dynamics Calculations

scholarly journals Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pablo Herrera-Nieto ◽  
Adrià Pérez ◽  
Gianni De Fabritiis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Intrinsically Disordered Proteins ◽  
Dynamical Behavior ◽  
Disordered Proteins ◽  
Partially Ordered ◽  
Intrinsically Disordered ◽  
State Models ◽  
Dynamics Simulations

Abstract The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for $$\sim $$ ∼ 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel $$\beta $$ β -sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.

Calculation of diffusion coefficient of long chain molecules using molecular dynamics

2015 ◽  
Vol 69 ◽  
pp. 371-377 ◽  
Author(s):  
Tanmoy Chakraborty ◽  
Abhiram Hens ◽  
Shashank Kulashrestha ◽  
Naresh Chandra Murmu ◽  
Priyabrata Banerjee
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Chain Molecules ◽  
Long Chain
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