Micromechanics and Microdynamics Via Atomistic Simulations

1988 ◽  
Vol 140 ◽  
Author(s):  
Uzi Landman ◽  
W. D. Luedtke ◽  
M. W. Ribarsky
Keyword(s):  
Microscopic Level ◽  
Atomistic Simulations ◽  
Dynamical Response ◽  
Natural Phenomena ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
External Perturbations ◽  
Atomic Force ◽  
Basic Understanding ◽  
Dynamics Simulations

AbstractBasic understanding of the structure and dynamics of materials and their response to external perturbations requires knowledge on the microscopic level, of the underlying energetics and atomic dynamics, whose consequences we observe and measure. Coupled with the above is the everlasting quest to observe and understand natural phenomena on refined microscopic scales, which provides the impetus for the development of experimental and theoretical techniques for the interrogation of materials with refined spatial and temporal resolution. In this paper we review the development of molecular dynamics simulations for studies of the energetics and dynamical response of materials to external mechanical perturbations. Applications to investigations of solid and liquid interfacial systems under stress and to studies of the consequences of tip-substrate interactions in atomic force microscopy are demonstrated.

Dynamics and metastable surface structure of double atomic layer of water molecules and ions at the interface between KBr(c) and water

2004 ◽  
Vol 76 (1) ◽  
pp. 115-122 ◽  
Author(s):  
K. Ichikawa ◽  
S. Sato ◽  
N. Shimomura
Keyword(s):  
Surface Structure ◽  
Vertical Motion ◽  
Atomic Layer ◽  
Water Molecules ◽  
Potassium Ions ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Bromide Ions

The metastable surface structure and dynamics of water molecules, cations, and anions at the interface between KBr(001) and water have been demonstrated from the images in situ observed in atomic resolution using atomic force microscopy. The vertical motion of potassium ions, which means their own transfer from the equilibrium sites to the upper height right on the underlying bromide ions, has been observed at the interface. They are used to be located in some steady state stabilized by their interaction with water molecules in the double atomic layer at the interface. The observed water molecules bridge two bromide ions by hydrogen bond; the water molecules are sandwiched by the potassium ions and vice versa.

scholarly journals Planar Boronic Graphene and Nitrogenized Graphene Heterostructure for Protein Stretch and Confinement

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1756
Author(s):  
Xuchang Su ◽  
Zhi He ◽  
Lijun Meng ◽  
Hong Liang ◽  
Ruhong Zhou
Keyword(s):  
Single Molecule ◽  
Intrinsically Disordered Proteins ◽  
Electron Tunneling ◽  
Amyloid Β ◽  
Protein Sequencing ◽  
Disordered Proteins ◽  
Force Microscopy ◽  
Intrinsically Disordered ◽  
Atomic Force ◽  
Dynamics Simulations

Single-molecule techniques such as electron tunneling and atomic force microscopy have attracted growing interests in protein sequencing. For these methods, it is critical to refine and stabilize the protein sample to a “suitable mode” before applying a high-fidelity measurement. Here, we show that a planar heterostructure comprising boronic graphene (BC3) and nitrogenized graphene (C3N) sandwiched stripe (BC3/C3N/BC3) is capable of the effective stretching and confinement of three types of intrinsically disordered proteins (IDPs), including amyloid-β (1–42), polyglutamine (Q42), and α-Synuclein (61–95). Our molecular dynamics simulations demonstrate that the protein molecules interact more strongly with the C3N stripe than the BC3 one, which leads to their capture, elongation, and confinement along the center C3N stripe of the heterostructure. The conformational fluctuations of IDPs are substantially reduced after being stretched. This design may serve as a platform for single-molecule protein analysis with reduced thermal noise.

scholarly journals Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

2021 ◽  
Author(s):  
Hiroki Koide ◽  
Noriyuki Kodera ◽  
Shveta Bisht ◽  
Shoji Takada ◽  
Tsuyoshi Terakawa
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dna Loop ◽  
Dynamics Simulations ◽  
Dsdna Binding ◽  
Hinge Domain

The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.

scholarly journals Towards an Understanding of Crystallization by Attachment

Crystals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 463
Author(s):  
Haihua Pan ◽  
Ruikang Tang
Keyword(s):  
Capillary Condensation ◽  
Force Measurements ◽  
Force Microscopy ◽  
Physical Conditions ◽  
Driving Mechanisms ◽  
Atomic Force ◽  
Wide Range ◽  
Dynamics Simulations ◽  
Hydration Layers

Crystallization via particle attachment was used in a unified model for both classical and non-classical crystallization pathways, which have been widely observed in biomimetic mineralization and geological fields. However, much remains unknown about the detailed processes and driving mechanisms for the attachment. Here, we take calcite crystal as a model mineral to investigate the detailed attachment process using in situ Atomic Force Microscopy (AFM) force measurements and molecular dynamics simulations. The results show that hydration layers hinder the attachment; however, in supersaturated solutions, ionic bridges are formed between crystal gaps as a result of capillary condensation, which might enhance the aggregation of calcite crystals. These findings provide a more detailed understanding of the crystal attachment, which is of vital importance for a better understanding of mineral formation under biological and geological environments with a wide range of chemical and physical conditions.

Molecular Dynamics Simulations and Theory of Interfaces of Oligomers

1992 ◽  
Vol 291 ◽  
Author(s):  
Jonathan G. Harris ◽  
Yantse Wang
Keyword(s):  
Surface Tension ◽  
Glassy State ◽  
Surface Force ◽  
Molecular Motions ◽  
Molecular Fluids ◽  
Force Microscopy ◽  
Atomic Force ◽  
Branched Alkanes ◽  
Dynamics Simulations ◽  
Solvation Forces

ABSTRACTThese proceedings summarize recent work in our group studying the structure of interfaces involving molecular fluids. Two types of systems are discussed. First, we summarize simulations of the structure and surface tension of liquid-vapor interfaces of the alkanes eicosane and decane. Then, we describe the results of simulations of the confined films studied in surface force apparatus and atomic force microscopy experiments. Our simulations show that in both films of normal and branched alkanes, the formation of a layered structure is observed. The branching inhibits this layering, especially in the narrowest pores. In addition an examination of the molecular motions indicates that a transition to a solid or glassy state is not a prerequisite for layering or oscillating solvation forces.

Probe-Tip Induced Damage in Compliant Substrates

2010 ◽  
Vol 132 (3) ◽  
Author(s):  
Michael Chandross ◽  
Christian D. Lorenz ◽  
Mark J. Stevens ◽  
Gary S. Grest
Keyword(s):  
Data Storage ◽  
Realistic Model ◽  
Experimental Measurements ◽  
Material Transfer ◽  
Force Microscopy ◽  
Compliant Substrates ◽  
Atomic Force ◽  
Low Load ◽  
Afm Tips ◽  
Dynamics Simulations

Nanofabrication using arrays of modified atomic force microscopy (AFM) tips can drastically reduce feature sizes and increase data storage densities. Additionally, AFM experiments are valuable tools for characterizing the tribological properties of surfaces. In order to maximize the potential of nanofabrication techniques, it is necessary to understand fully the interactions between AFM tips and substrates, particularly when the latter is compliant and more damage-prone. To address this issue, we have carried out extensive molecular dynamics simulations of the nanotribological properties of self-assembled alkylsilane monolayers (SAMs) on amorphous silica with a realistic model of an AFM tip. Our simulations demonstrate that for fully physisorbed SAMs, even low load contacts can damage the SAM and cause material transfer to the probe tip. This effect, which is commonly ignored, can have a strong effect on the interpretation of experimental measurements. Partial chemisorption of the SAM lowers, but does not remove the possibility of damage.

scholarly journals Structure and Dynamics of Membrane-embedded KcsA Potassium Channel Revealed by Atomic Force Microscopy

2015 ◽  
Vol 55 (1) ◽  
pp. 005-010 ◽  
Author(s):  
Ayumi SUMINO ◽  
Daisuke YAMAMOTO ◽  
Takashi SUMIKAMA ◽  
Masayuki IWAMOTO ◽  
Takehisa DEWA ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Potassium Channel ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Kcsa Potassium Channel

scholarly journals Characterization of Lipid Membrane Properties for Tunable Electroporation

2012 ◽  
Author(s):  
H. Jeremy Cho ◽  
Shalabh C. Maroo ◽  
Evelyn N. Wang
Keyword(s):  
Lipid Bilayers ◽  
Lipid Membrane ◽  
Contact Angle Measurement ◽  
Angle Measurement ◽  
Membrane Properties ◽  
Force Microscopy ◽  
Packing Structure ◽  
Atomic Force ◽  
Dynamics Simulations

Lipid bilayers form nanopores on the application of an electric field. This process of electroporation can be utilized in different applications ranging from targeted drug delivery in cells to nano-gating membrane for engineering applications. However, the ease of electroporation is dependent on the surface energy of the lipid layers and thus directly related to the packing structure of the lipid molecules. 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid monolayers were deposited on a mica substrate using the Langmuir-Blodgett (LB) technique at different packing densities and analyzed using atomic force microscopy (AFM). The wetting behavior of these monolayers was investigated by contact angle measurement and molecular dynamics simulations. It was found that an equilibrium packing density of liquid-condensed (LC) phase DPPC likely exists and that water molecules can penetrate the monolayer displacing the lipid molecules. The surface tension of the monolayer in air and water was obtained along with its breakthrough force.

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