scholarly journals Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations

2016 ◽  
Vol 84 (9) ◽  
pp. 1203-1212 ◽  
Author(s):  
Kostas Papachristos ◽  
Stephen P. Muench ◽  
Emanuele Paci
Keyword(s):  
Atomistic Simulations ◽  
Peripheral Stalk

scholarly journals Characterization of the Peripheral Stalk of the Vacuolar ATPase

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Sarah Bilbo ◽  
Ryan Foreman ◽  
Margaret Owegi ◽  
Donald Pappas ◽  
Karlett Parra‐Belky
Keyword(s):  
Vacuolar Atpase ◽  
Peripheral Stalk

Theoretical Chemical Characterization of Energetic Materials

2005 ◽  
Vol 896 ◽  
Author(s):  
Betsy Mavity Rice ◽  
Edward F. C. Byrd
Keyword(s):  
Energetic Materials ◽  
Atomistic Simulation ◽  
State Of The Art ◽  
Energetic Material ◽  
Chemical Characterization ◽  
Theoretical Chemistry ◽  
Atomistic Simulations ◽  
Simulation Methods ◽  
Design Development

AbstractOur research is focused on developing computational capabilities for the prediction of properties of energetic materials associated with performance and sensitivity. Additionally, we want to identify and characterize the dynamic processes that influence conversion of an energetic material to products upon initiation. We are attempting to achieve these goals through the use of standard atomistic simulation methods. In this paper various theoretical chemistry methods and applications to energetic materials will be described. Current capabilities in predicting structures, thermodynamic properties, and dynamic behavior of these materials will be demonstrated. These are presented to exemplify how information generated from atomistic simulations can be used in the design, development, and testing of new energetic materials. In addition to illustrating current capabilities, we will discuss limitations of the methodologies and needs for advancing the state of the art in this area.

scholarly journals Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

2020 ◽  
Vol 22 (37) ◽  
pp. 21083-21093 ◽  
Author(s):  
Ilias Patmanidis ◽  
Alex H. de Vries ◽  
Tsjerk A. Wassenaar ◽  
Wenjun Wang ◽  
Giuseppe Portale ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Building Blocks ◽  
Atomistic Simulations ◽  
Self Assembled

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers.

Theoretical chemical characterization of energetic materials

2006 ◽  
Vol 21 (10) ◽  
pp. 2444-2452 ◽  
Author(s):  
Betsy M. Rice ◽  
Edward F.C. Byrd
Keyword(s):  
Energetic Materials ◽  
Atomistic Simulation ◽  
State Of The Art ◽  
Energetic Material ◽  
Chemical Characterization ◽  
Theoretical Chemistry ◽  
Atomistic Simulations ◽  
Simulation Methods ◽  
Design Development

Our research is focused on developing computational capabilities for the prediction of properties of energetic materials associated with performance and sensitivity. Additionally, we want to identify and characterize the dynamic processes that influence conversion of an energetic material to products upon initiation. We are attempting to achieve these goals through the use of standard atomistic simulation methods. In this paper, various theoretical chemistry methods and applications to energetic materials will be described. Current capabilities in predicting structures, thermodynamic properties, and dynamic behavior of these materials will be demonstrated. These are presented to exemplify how information generated from atomistic simulations can be used in the design, development, and testing of new energetic materials. In addition to illustrating current capabilities, we will discuss limitations of the methodologies and needs for advancing the state of the art in this area.

scholarly journals Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF3)4

2021 ◽  
Vol 12 ◽  
pp. 1151-1172
Author(s):  
Alexey Prosvetov ◽  
Alexey V Verkhovtsev ◽  
Gennady Sushko ◽  
Andrey V Solov’yov
Keyword(s):  
Molecular Dynamics ◽  
Electron Beam ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Molecular Systems ◽  
Nanostructure Formation ◽  
Spatially Resolved ◽  
Software Packages ◽  
Precursor Molecules

This paper presents a detailed computational protocol for the atomistic simulation of formation and growth of metal-containing nanostructures during focused electron beam-induced deposition (FEBID). The protocol is based upon irradiation-driven molecular dynamics (IDMD), a novel and general methodology for computer simulations of irradiation-driven transformations of complex molecular systems by means of the advanced software packages MBN Explorer and MBN Studio. Atomistic simulations performed following the formulated protocol provide valuable insights into the fundamental mechanisms of electron-induced precursor fragmentation and the related mechanism of nanostructure formation and growth using FEBID, which are essential for the further advancement of FEBID-based nanofabrication. The developed computational methodology is general and applicable to different precursor molecules, substrate types, and irradiation regimes. The methodology can also be adjusted to simulate the nanostructure formation by other nanofabrication techniques using electron beams, such as direct electron beam lithography. In the present study, the methodology is applied to the IDMD simulation of the FEBID of Pt(PF3)4, a widely studied precursor molecule, on a SiO2 surface. The simulations reveal the processes driving the initial phase of nanostructure formation during FEBID, including the nucleation of Pt atoms and the formation of small metal clusters on the surface, followed by their aggregation and the formation of dendritic platinum nanostructures. The analysis of the simulation results provides spatially resolved relative metal content, height, and growth rate of the deposits, which represents valuable reference data for the experimental characterization of the nanostructures grown by FEBID.

scholarly journals Structural Characterization of Supramolecular Hollow Nanotubes with Atomistic Simulations and SAXS

2020 ◽  
Author(s):  
Ilias Patmanidis ◽  
Alex H. de Vries ◽  
Tsjerk A. Wassenaar ◽  
Wenjun Wang ◽  
Giuseppe Portale ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Properties ◽  
Structural Characterization ◽  
Building Blocks ◽  
Structural Features ◽  
Cyanine Dye ◽  
Atomistic Simulations ◽  
Dynamics Simulations ◽  
Stable Structures

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers. Here, we study an amphiphilic cyanine dye (C8S3) that is known to self-assemble into doublewalled, hollow, nanotubes with interesting optical properties. The molecular packing of the dyes inside the nanotubes, however, remains elusive. To reveal the structural features of the C8S3 nanotubes, we performed atomistic Molecular Dynamics simulations of preformed bilayers and nanotubes. We find that different packing arrangements lead to stable structures, in which the tails of the C8S3 molecules are interdigitated. Our results are verified by SAXS experiments. Together our data provide a detailed structural characterization of the C8S3 nanotubes. Furthermore, our approach was able to resolve the ambiguity inherent from cryo-TEM measurements in calculating the wall thickness of similar systems. The insights obtained are expected to be generally useful for understanding and designing other supramolecular assemblies.<br>

scholarly journals Small scale tests of cement with focused ion beam and nanoindentation

2020 ◽  
Vol 310 ◽  
pp. 00053
Author(s):  
Jiří Němeček ◽  
Jan Maňák ◽  
Tomáš Krejčí ◽  
Jiří Němeček
Keyword(s):  
Cement Paste ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Atomistic Simulations ◽  
Small Scale ◽  
Fracture Characteristics ◽  
Multi Scale ◽  
Scale Modeling ◽  
Micrometer Scale

Nanoindentation is used for characterization of small scale material properties of hydrated cement. It is employed as a precise loading tool on samples fabricated with Focused Ion Beam milling (FIB). The effect of heat on the microstructure of cement during different FIB energy loads is studied. Milling currents as low as 0.1 nA can be considered as save and not damaging. Micrometer sized beams were bent to reveal strength and fracture characteristics. Small scale elastic properties, tensile strength and fracture energy of individual low scale microstructural constituents of cement paste like C-S-H rich phases and Portlandite were assessed. Very high tensile strengths at the micrometer scale were observed for cement paste hydration products (200-700 MPa) with fracture energies 4-20 J/m2 The results are consistent with atomistic simulations and multi-scale modeling from available literature.

A Review of In Situ Mechanical Characterization of Polymer Nanocomposites: Prospect and Challenges

2017 ◽  
Vol 69 (5) ◽  
Author(s):  
Samit Roy ◽  
John Ryan ◽  
Samantha Webster ◽  
Dhriti Nepal
Keyword(s):  
Polymer Nanocomposites ◽  
Review Paper ◽  
Mechanical Characterization ◽  
Nanocomposite Materials ◽  
Atomistic Simulations ◽  
In Situ Testing ◽  
Comprehensive Review ◽  
Material Systems

Mechanics at the nanoscale is radically different from mechanics at the macroscale. Atomistic simulations have revealed this important fact, and experiments are being performed to support it. Specifically, in situ testing is being performed by researchers using different approaches with different material systems to interrogate the material at the nanoscale and prove or disprove many of the proposed models. This paper attempts to provide a fairly comprehensive review of the in situ testing that is being performed at the nanoscale, together with a brief description of the models that in situ testing are being used to verify. This review paper intends to primarily provide a broad snapshot of in situ testing of different nanocarbon-based polymeric nanocomposite materials.

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