Molecular features of hydration layers probed by atomic force microscopy

2018 ◽  
Vol 20 (48) ◽  
pp. 30492-30501 ◽  
Author(s):  
Zhengqing Zhang ◽  
Seol Ryu ◽  
Yoonho Ahn ◽  
Joonkyung Jang
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Dynamic ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Force Microscopy ◽  
Molecular Features ◽  
Atomic Force ◽  
Hydration Layers

The molecular features of the hydration layers probed by a nanoscale tip were uncovered by using molecular dynamic simulations.

Characterization of Hydrophobic Forces for in Liquid Self-Assembly of Micron-Sized Functional Building Blocks

2011 ◽  
Vol 1299 ◽  
Author(s):  
M. R. Gullo ◽  
L. Jacot-Descombes ◽  
L. Aeschimann ◽  
J. Brugger
Keyword(s):  
Atomic Force Microscopy ◽  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Numerical Study ◽  
Building Blocks ◽  
Dynamic Simulations ◽  
Hydrophobic Force ◽  
Force Microscopy ◽  
Molecular Arrangement ◽  
Atomic Force

ABSTRACTThis paper presents the experimental and numerical study of hydrophobic interaction forces at nanometer scale in the scope of engineering micron-sized building blocks for self-assembly in liquid. The hydrophobic force distance relation of carbon, Teflon and dodeca-thiols immersed in degassed and deionized water has been measured by atomic force microscopy. Carbon and dodeca-thiols showed comparable attractive and binding forces in the rage of pN/nm2. Teflon showed the weakest binding and no attractive force. Molecular dynamic simulations were performed to correlate the molecular arrangement of water molecules and the hydrophobic interactions measured by atomic force microscopy. The simulations showed a depletion zone of 2Å followed by a layered region of 8Å in the axis perpendicular to the hydrophobic surface.

scholarly journals Modes of action of the archaeal Mre11/Rad50 DNA-repair complex revealed by fast-scan atomic force microscopy

2020 ◽  
Vol 117 (26) ◽  
pp. 14936-14947 ◽  
Author(s):  
Ekaterina Zabolotnaya ◽  
Ioanna Mela ◽  
Mark J. Williamson ◽  
Sian M. Bray ◽  
Siu Kei Yau ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Dna Repair ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Dna Unwinding ◽  
Dna Breaks ◽  
Dynamic Simulations ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dna Substrates

Mre11 and Rad50 (M/R) proteins are part of an evolutionarily conserved macromolecular apparatus that maintains genomic integrity through repair pathways. Prior structural studies have revealed that this apparatus is extremely dynamic, displaying flexibility in the long coiled-coil regions of Rad50, a member of the structural maintenance of chromosome (SMC) superfamily of ATPases. However, many details of the mechanics of M/R chromosomal manipulation during DNA-repair events remain unclear. Here, we investigate the properties of the thermostable M/R complex from the archaeonSulfolobus acidocaldariususing atomic force microscopy (AFM) to understand how this macromolecular machinery orchestrates DNA repair. While previous studies have observed canonical interactions between the globular domains of M/R and DNA, we observe transient interactions between DNA substrates and the Rad50 coiled coils. Fast-scan AFM videos (at 1–2 frames per second) of M/R complexes reveal that these interactions result in manipulation and translocation of the DNA substrates. Our study also shows dramatic and unprecedented ATP-dependent DNA unwinding events by the M/R complex, which extend hundreds of base pairs in length. Supported by molecular dynamic simulations, we propose a model for M/R recognition at DNA breaks in which the Rad50 coiled coils aid movement along DNA substrates until a DNA end is encountered, after which the DNA unwinding activity potentiates the downstream homologous recombination (HR)-mediated DNA repair.

Molecular dynamic study for nanopatterning using atomic force microscopy

2005 ◽  
Vol 36 (1) ◽  
pp. 169-176 ◽  
Author(s):  
Young-Suk Kim ◽  
Chan-Il Kim ◽  
Jun-Young Park ◽  
Kyung-Hoan Na
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Dynamic ◽  
Dynamic Study ◽  
Force Microscopy ◽  
Atomic Force ◽  
Molecular Dynamic Study

scholarly journals STRUCTURAL CHARACTERISTICS OF 8-CROWN-6 MOLECULE IN METHANOL AND ACETONITRILE

2018 ◽  
Vol 59 (4) ◽  
pp. 22 ◽  
Author(s):  
Irina A. Kuz'mina ◽  
Tatiana R. Usacheva ◽  
Mariya A. Volkova ◽  
Natalia V. Belova ◽  
Valentin A. Sharnin
Keyword(s):  
Hydrogen Bonds ◽  
Force Field ◽  
Molecular Dynamic ◽  
Quantum Chemical ◽  
Structural Characteristics ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Stable Conformation ◽  
Atomic Force ◽  
Basic Set

Quantum-chemical calculations of stable conformation of the molecule of 18-crown-6 ether (18C6) were carried for its free state in methanol (MeOH) and acetonitrile (AN) using GAUSSIAN 03 program. The DFT version and cc-pVTZ basic set was used. The values of mean lifetimes of hydrogen bonds between the methanol molecules as well as between 18C6 and methanol in MeOH-MeOH и 18C6-{MeOH-MeOH} systems were calculated by molecular dynamic simulations in NVT- ensemble applying GROMACS 4.5.4 software for OPLS-AA full-atomic force field .

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