Molecular Dynamics Simulations and Theory of Interfaces of Oligomers

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.

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Determination of solid surface tension at the nano-scale using atomic force microscopy

Contact Angle, Wettability and Adhesion, Volume 4 ◽

10.1201/b12166-17 ◽

2006 ◽

pp. 249-276

Keyword(s):

Surface Tension ◽

Atomic Force Microscopy ◽

Solid Surface ◽

Force Microscopy ◽

Nano Scale ◽

Atomic Force ◽

Solid Surface Tension

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

Biomolecules ◽

10.3390/biom11121756 ◽

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.

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

10.1101/2021.02.25.432963 ◽

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.

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Anomalous Interfacial Structuring of a Non-Halogenated Ionic Liquid: Effect of Substrate and Temperature

Colloids and Interfaces ◽

10.3390/colloids2040060 ◽

2018 ◽

Vol 2 (4) ◽

pp. 60 ◽

Cited By ~ 5

Author(s):

Milad Radiom ◽

Patricia Pedraz ◽

Georgia Pilkington ◽

Patrick Rohlmann ◽

Sergei Glavatskih ◽

...

Keyword(s):

Ionic Liquid ◽

Surface Charge ◽

Force Measurement ◽

Surface Force ◽

Solid Surfaces ◽

Effect Of Temperature ◽

Decay Length ◽

Force Microscopy ◽

Large Size ◽

Atomic Force

We investigate the interfacial properties of the non-halogenated ionic liquid (IL), trihexyl(tetradecyl)phosphonium bis(mandelato)borate, [P6,6,6,14][BMB], in proximity to solid surfaces, by means of surface force measurement. The system consists of sharp atomic force microscopy (AFM) tips interacting with solid surfaces of mica, silica, and gold. We find that the force response has a monotonic form, from which a characteristic steric decay length can be extracted. The decay length is comparable with the size of the ions, suggesting that a layer is formed on the surface, but that it is diffuse. The long alkyl chains of the cation, the large size of the anion, as well as crowding of the cations at the surface of negatively charged mica, are all factors which are likely to oppose the interfacial stratification which has, hitherto, been considered a characteristic of ionic liquids. The variation in the decay length also reveals differences in the layer composition at different surfaces, which can be related to their surface charge. This, in turn, allows the conclusion that silica has a low surface charge in this aprotic ionic liquid. Furthermore, the effect of temperature has been investigated. Elevating the temperature to 40 °C causes negligible changes in the interaction. At 80 °C and 120 °C, we observe a layering artefact which precludes further analysis, and we present the underlying instrumental origin of this rather universal artefact.

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Towards an Understanding of Crystallization by Attachment

Crystals ◽

10.3390/cryst10060463 ◽

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.

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Surface defects characterization with frequency and force modulation atomic force microscopy using molecular dynamics simulations

Current Applied Physics ◽

10.1016/j.cap.2009.08.002 ◽

2010 ◽

Vol 10 (2) ◽

pp. 583-591 ◽

Cited By ~ 19

Author(s):

Hossein Nejat Pishkenari ◽

Ali Meghdari

Keyword(s):

Molecular Dynamics ◽

Atomic Force Microscopy ◽

Molecular Dynamics Simulations ◽

Surface Defects ◽

Force Microscopy ◽

Force Modulation ◽

Atomic Force ◽

Dynamics Simulations

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REAL-TIME VISUALIZATION OF MORPHOLOGICAL EVOLUTION OF N, N'-di(naphthalene-1-yl)-N, N'-diphthalbenzidine THIN FILMS: VARIABLE TEMPERATURE ATOMIC FORCE MICROSCOPY STUDY

International Journal of Nanoscience ◽

10.1142/s0219581x02000966 ◽

2002 ◽

Vol 01 (05n06) ◽

pp. 725-730 ◽

Cited By ~ 1

Author(s):

M. S. XU ◽

J. B. XU ◽

J. AN

Keyword(s):

Thin Film ◽

Atomic Force Microscopy ◽

Morphological Evolution ◽

Variable Temperature ◽

Glassy State ◽

Microscopy Study ◽

Light Emitting ◽

Force Microscopy ◽

Atomic Force ◽

Real Time Visualization

Variable temperature tapping mode atomic force microscopy is exploited to in situ visualize the morphological evolution of N, N'-di(naphthalene-1-yl)-N, N'-diphthalbenzidine (NPB) thin film. The apparent glass transition of the NPB thin film initially occurred at 60°C, proceeded until 95°C, and crystallization from the glassy state quickly appeared at 135°C. The NPB thin film gradually melted and disappeared when the temperature was above 175°C, revealing the underlying layer. These observations are technically helpful and significant to gauge the temperature dependent lifetime and luminance of organic light-emitting diodes.

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2P305 A method for calculating the solvation structure from force curves measured by atomic force microscopy and surface force apparatus(27. Bioimaging,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s245_5 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S245

Author(s):

Ken-ichi Amano

Keyword(s):

Atomic Force Microscopy ◽

Annual Meeting ◽

Surface Force ◽

Surface Force Apparatus ◽

Force Microscopy ◽

Atomic Force ◽

Solvation Structure ◽

Biophysical Society ◽

Force Curves

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Probe-Tip Induced Damage in Compliant Substrates

Journal of Manufacturing Science and Engineering ◽

10.1115/1.4001660 ◽

2010 ◽

Vol 132 (3) ◽

Cited By ~ 14

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.

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