Large Scale Membrane Movement Induced by a Cation Switch

10.26434/chemrxiv.13603325.v1 ◽

2021 ◽

Author(s):

Laura. H. John ◽

Gail. M. Preston ◽

Mark S. P. Sansom ◽

Luke Clifton

Keyword(s):

Large Scale ◽

Quartz Crystal ◽

Cell Signalling ◽

Md Simulations ◽

Neutron Reflectivity ◽

Analysis Tool ◽

Self Assembled Monolayer ◽

Standard Analysis ◽

Surface Distance ◽

Sample System

A biomembrane sample system where millimolar changes of cations induce reversible large scale (≥ 200 Å) changes in the membrane-to-surface distance is described. The system composes of a free-floating bilayer (FFB), formed adjacent to a self-assembled monolayer (SAM). To examine the membrane movements, differently charged FFBs in the presence and absence of Ca2+ and Na+, respectively, were examined using neutron reflectivity (NR) and quartz crystal microbalance (QCM) measurements, alongside molecular dynamics (MD) simulations. In NR the variation of Ca2+ and Na+ concentration enabled precision manipulation of the FFB-to-surface distance. Simulations suggest that Ca2+ ions bridge between SAM and bilayer whereas the more diffuse binding of Na+, especially to bilayers, is unable to fully overcome the repulsion between anionic FFB and anionic SAM. Reproduced NR results with QCM demonstrate the potential of this easily producible sample system to become a standard analysis tool for e.g. investigating membrane binding effects, endocytosis and cell signalling.

Download Full-text

Large Scale Membrane Movement Induced by a Cation Switch

10.26434/chemrxiv.13603325 ◽

2021 ◽

Author(s):

Laura. H. John ◽

Gail. M. Preston ◽

Mark S. P. Sansom ◽

Luke Clifton

Keyword(s):

Large Scale ◽

Quartz Crystal ◽

Cell Signalling ◽

Md Simulations ◽

Neutron Reflectivity ◽

Analysis Tool ◽

Self Assembled Monolayer ◽

Standard Analysis ◽

Surface Distance ◽

Sample System

A biomembrane sample system where millimolar changes of cations induce reversible large scale (≥ 200 Å) changes in the membrane-to-surface distance is described. The system composes of a free-floating bilayer (FFB), formed adjacent to a self-assembled monolayer (SAM). To examine the membrane movements, differently charged FFBs in the presence and absence of Ca2+ and Na+, respectively, were examined using neutron reflectivity (NR) and quartz crystal microbalance (QCM) measurements, alongside molecular dynamics (MD) simulations. In NR the variation of Ca2+ and Na+ concentration enabled precision manipulation of the FFB-to-surface distance. Simulations suggest that Ca2+ ions bridge between SAM and bilayer whereas the more diffuse binding of Na+, especially to bilayers, is unable to fully overcome the repulsion between anionic FFB and anionic SAM. Reproduced NR results with QCM demonstrate the potential of this easily producible sample system to become a standard analysis tool for e.g. investigating membrane binding effects, endocytosis and cell signalling.

Download Full-text

MODE-TASK: Large-scale protein motion tools

10.1101/217505 ◽

2017 ◽

Author(s):

Caroline Ross ◽

Bilal Nizami ◽

Michael Glenister ◽

Olivier Sheik Amamuddy ◽

Ali Rana Atilgan ◽

...

Keyword(s):

Large Scale ◽

Protein Complexes ◽

Normal Mode Analysis ◽

Md Simulations ◽

Supplementary Information ◽

Mode Analysis ◽

Analysis Tool ◽

Link Type ◽

Supplementary Material ◽

Anisotropic Network

AbstractSummaryMODE-TASK, a novel software suite, comprises Principle Component Analysis, Multidimensional Scaling, and t-Distributed Stochastic Neighbor Embedding techniques using molecular dynamics trajectories. MODE-TASK also includes a Normal Mode Analysis tool based on Anisotropic Network Model so as to provide a variety of ways to analyse and compare large-scale motions of protein complexes for which long MD simulations are prohibitive.Availability and ImplementationMODE-TASK has been open-sourced, and is available for download from https://github.com/RUBi-ZA/MODE-TASK, implemented in Python and C++.Supplementary informationDocumentation available at http://mode-task.readthedocs.io.

Download Full-text

Self-Assembled Fluid Phase Floating Membranes with Tuneable Water Interlayers

10.26434/chemrxiv.8307419 ◽

2019 ◽

Author(s):

Luke Clifton ◽

Nicoló Paracini ◽

Arwel V. Hughes ◽

Jeremy H. Lakey ◽

Nina-Juliane Seinke ◽

...

Keyword(s):

Fluid Phase ◽

Interlayer Thickness ◽

Supported Bilayers ◽

Self Assembled Monolayer ◽

High Coverage ◽

Nano Technology ◽

Surface Distance ◽

Potential Applications ◽

Self Assembled ◽

Coated Surfaces

We present a reliable method for the fabrication of fluid phase unsaturated bilayers which are readily self-assembled on charged self-assembled monolayer (SAM) surfaces producing high coverage floating supported bilayers where the membrane to surface distance could be controlled with nanometer precision. Vesicle fusion was used to deposit the bilayers onto anionic SAM coated surfaces. Upon assembly the bilayer to SAM solution interlayer thickness was 7-10 Å with evidence suggesting that this layer was present due to SAM hydration repulsion of the bilayer from the surface. This distance could be increased using low concentrations of salts which caused the interlayer thickness to enlarge to ~33 Å. Reducing the salt concentration resulted in a return to a shorter bilayer to surface distance. These accessible and controllable membrane models are well suited to a range of potential applications in biophysical studies, bio-sensors and Nano-technology.

Download Full-text

PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

npj Computational Materials ◽

10.1038/s41524-021-00506-8 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Mohammadreza Yaghoobi ◽

Krzysztof S. Stopka ◽

Aaditya Lakshmanan ◽

Veera Sundararaghavan ◽

John E. Allison ◽

...

Keyword(s):

Open Source ◽

Open Source Software ◽

Large Scale ◽

Metals And Alloys ◽

Analysis Tool ◽

Computational Framework ◽

Crystal Plasticity Finite Element ◽

Polycrystalline Metals ◽

Simulation Based ◽

Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

Download Full-text

Characterization of Pharmaceutical Tablets Using UV Hyperspectral Imaging as a Rapid Line to Line Analysis Tool

Sensors ◽

10.3390/s21134436 ◽

2021 ◽

Vol 21 (13) ◽

pp. 4436

Author(s):

Mohammad Al Ktash ◽

Mona Stefanakis ◽

Barbara Boldrini ◽

Edwin Ostertag ◽

Marc Brecht

Keyword(s):

Hyperspectral Imaging ◽

Large Scale ◽

Solid Phase ◽

Ultra Violet ◽

Principal Component ◽

Ccd Camera ◽

Conveyor Belt ◽

Hyperspectral Data ◽

Analysis Tool ◽

Sample Set

A laboratory prototype for hyperspectral imaging in ultra-violet (UV) region from 225 to 400 nm was developed and used to rapidly characterize active pharmaceutical ingredients (API) in tablets. The APIs are ibuprofen (IBU), acetylsalicylic acid (ASA) and paracetamol (PAR). Two sample sets were used for a comparison purpose. Sample set one comprises tablets of 100% API and sample set two consists of commercially available painkiller tablets. Reference measurements were performed on the pure APIs in liquid solutions (transmission) and in solid phase (reflection) using a commercial UV spectrometer. The spectroscopic part of the prototype is based on a pushbroom imager that contains a spectrograph and charge-coupled device (CCD) camera. The tablets were scanned on a conveyor belt that is positioned inside a tunnel made of polytetrafluoroethylene (PTFE) in order to increase the homogeneity of illumination at the sample position. Principal component analysis (PCA) was used to differentiate the hyperspectral data of the drug samples. The first two PCs are sufficient to completely separate all samples. The rugged design of the prototype opens new possibilities for further development of this technique towards real large-scale application.

Download Full-text

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

MRS Proceedings ◽

10.1557/opl.2014.715 ◽

2014 ◽

Vol 1700 ◽

pp. 61-66

Author(s):

Guttormur Arnar Ingvason ◽

Virginie Rollin

Keyword(s):

Molecular Dynamics ◽

Polymer Matrix ◽

Large Scale ◽

Md Simulations ◽

Dynamics Simulation ◽

Atomistic Simulations ◽

Polymer Molecules ◽

Molecular Potential ◽

Pull Out ◽

Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

Download Full-text

Packing Structure of OTS on Silicon Surfaces: A Computational Approach

World Tribology Congress III, Volume 2 ◽

10.1115/wtc2005-63497 ◽

2005 ◽

Author(s):

J. Barriga ◽

B. Coto ◽

B. Ferna´ndez

Keyword(s):

Molecular Orientation ◽

Md Simulations ◽

Silicon Surfaces ◽

Computational Simulations ◽

Self Assembled Monolayer ◽

Substitution Pattern ◽

Optimal Packing ◽

Packing Structure ◽

Energetic Balance ◽

Main Factors

Optimal packing structure of Octadecyltrichlorosilane (OTS) self-assembled monolayer (SAM) adsorbed on a SiO2 surface with a Si (100) substrate was studied performing molecular dynamics (MD) computational simulations. Molecular substitution, substitution pattern and molecular orientation of the OTS molecules on the SiO2 (100) are the main factors studied in order to determine the optimal packing structure taking into account energetic balance. We have used the optimal packing structure to study other properties usually used to characterize SAMs as molecular and system tilt angles, film thickness and gauche defects. These properties and monolayer stability were studied performing MD simulations in a temperature range from 100 K to 600 K and we found that results obtained agree with those from experimental measurements. We found that OTS films are stable up to 500 K. The optimal structure obtained could be used in further MD simulations studies in order to determine tribological properties of OTS-SiO2 systems.

Download Full-text

Simulation of Thermal Stability and Friction: A Lubricant Confined Between Monolayers of Wear Inhibitors on Iron Oxide

MRS Proceedings ◽

10.1557/proc-543-79 ◽

1998 ◽

Vol 543 ◽

Cited By ~ 2

Author(s):

T. Çağin ◽

Y. Zhou ◽

E. S. Yamaguchi ◽

R. Frazier ◽

A. Ho ◽

...

Keyword(s):

Molecular Dynamics ◽

Thermal Stability ◽

Quantum Chemical ◽

Md Simulations ◽

Atomic Level ◽

The Self ◽

Self Assembled Monolayer ◽

Thermal Stabilities ◽

Frictional Forces ◽

Thermal Stability Of

AbstractTo understand antiwear phenomena in motor engines at the atomic level and provide evidence inselecting future ashless wear inhibitors, we studied the thermal stability of the self-assembled monolayer(SAM) model for dithiophosphate (DTP) and dithiocarbamate (DTC) molecules on the iron oxidesurface using molecular dynamics. The interactions for DTP, DTC and Fe2O3 are evaluated based on aforce field derived from fitting to ab initio quantum chemical calculations of dimethyl DTP (and DTC)and Fe(OH)2(H2O)2-DTP (DTC) clusters. MD simulations at constant-NPT are conducted to assesrelative thermal stabilities of the DTP and DTC with different pendant groups (n-propyl, i-propyl, npentyl.and i-pentyl). To investigate frictional process, we employ a steady state MD method, in whichone of the Fe2O3 slabs maintained at a constant linear velocity. We obtain the time averaged normaland frictional forces from the interatomic forces. Then, we calculated the friction coefficient at theinterface between SAMs of DTP and the confined lubricant, hexadecane, to assess the shear stability ofDTPs with different pendant groups.

Download Full-text

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008439 ◽

2020 ◽

Vol 16 (12) ◽

pp. e1008439

Author(s):

Jennifer Lu ◽

Steven L. Salzberg

Keyword(s):

Large Scale ◽

Analysis Tool ◽

Index Test ◽

Bacterial Genomes ◽

Phylogenetic Groups ◽

Bacterial Phyla ◽

Link Type ◽

Gc Skew ◽

A Genome ◽

Web App

GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI’s Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.

Download Full-text