IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol

2013 ◽  
Vol 34 (20) ◽  
pp. 1707-1718 ◽  
Author(s):  
Ranieri V. de Carvalho ◽  
Daniel Lopez-Ferrer ◽  
Katia S. Guimarães ◽  
Roberto D. Lins
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Cross Section ◽  
Collision Cross Section ◽  
Dynamics Simulation ◽  
Cross Section Area ◽  
Section Area ◽  
Simulation Protocol

scholarly journals Anomalous Thermal Response of Graphene Kirigami Induced by Tailored Shape to Uniaxial Tensile Strain: A Molecular Dynamics Study

Nanomaterials ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 126 ◽  
Author(s):  
Hui Li ◽  
Gao Cheng ◽  
Yongjian Liu ◽  
Dan Zhong
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Heat Flux ◽  
Cross Section ◽  
Structural Deformation ◽  
Uniaxial Tensile ◽  
Mechanical And Thermal Properties ◽  
Atomic Lattice ◽  
Cross Section Area ◽  
Section Area

The mechanical and thermal properties of graphene kirigami are strongly dependent on the tailoring structures. Here, thermal conductivity of three typical graphene kirigami structures, including square kirigami graphene, reentrant hexagonal honeycomb structure, and quadrilateral star structure under uniaxial strain are explored using molecular dynamics simulations. We find that the structural deformation of graphene kirigami is sensitive to its tailoring geometry. It influences thermal conductivity of graphene by changing heat flux scattering, heat path, and cross-section area. It is found that the factor of cross-section area can lead to four times difference of thermal conductivity in the large deformation system. Our results are elucidated based on analysis of micro-heat flux, geometry deformation, and atomic lattice deformation. These insights enable us to design of more efficient thermal management devices with elaborated graphene kirigami materials.

Effect of oxide layer and size on the vibration frequency of silicon nanobeams

2021 ◽  
pp. 2150308
Author(s):  
Yanliang Li ◽  
Jing Wang
Keyword(s):  
Molecular Dynamics ◽  
Oxide Layer ◽  
Cross Section ◽  
Vibration Frequency ◽  
Molecular Dynamics Method ◽  
Vibration Frequencies ◽  
Cross Section Area ◽  
Section Area ◽  
Dynamics Method

We studied the vibration frequencies of small double-clamped silicon nanobeams using a molecular dynamics method. The effects of cross-section area, size, and oxide layer were investigated through simulation. The results show that the vibration frequency decreases with increasing length, whereas it increases slightly with increasing cross-section area of the nanobeam. The existence and thickness of an oxide layer lead to increasing of the vibration frequency of silicon nanobeams.

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