Nanocellulose/graphene oxide layered membranes: elucidating their behaviour during filtration of water and metal ions in real time

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5–4.5×. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. The in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

Download Full-text

Graphene/ Graphene Oxide Based Pyrimidine Hybrid Materials for Metal Ion Sensing and DFT Study

International Journal of Computational Physics Series ◽

10.29167/a1i1p228-235 ◽

2018 ◽

Vol 1 (1) ◽

pp. 228-235

Author(s):

Pramanand Kumar ◽

Chandramika Bora ◽

Pradip K. Sukul ◽

Subrata Das

Keyword(s):

Graphene Oxide ◽

Metal Ions ◽

Hybrid Materials ◽

Metal Ion ◽

Density Functional ◽

Analytical Techniques ◽

Functionalized Graphene ◽

Functionalized Graphene Oxide ◽

Ion Sensing ◽

Device Applications

Chemical and biological sensors are gaining wide popularity in day-to-day life and significantly help to increase the survivability by providing early warning for explosives, metal pollutant, and chemical warfare. GR analog based sensor devices have several advantages for chemical and biological sensing. The structural or chemical modifications of GR remarkably improve the properties of such device applications. Keeping this in mind, we have designed and synthesized pyrimidinedione-functionalized graphene oxide (FGO) and functionalized graphene (FG) sequentially. Synthesis of the hybrid materials was done using the simple hydrothermal method. The materials were characterized by various spectroscopic and analytical techniques. XRD study showed formation of well exfoliated GO sheets in the composite. FTIR data indicates the formation of GO-NO-Ur composites. Density functional theory (DFT) calculation was also investigated to understand the various non-covalent interactions of the NO-Ur and FGO. For the detection of metal ions, synthesized nanocomposite was analyzed to sense many metal ions (Ag+, Cd2+, Cu2+, Fe3+, Hg2+, Mo2+, Ni2+, and Zn2+) and we observed strong binding mood against Fe3+ ions having LOD and LOQ value of 0.0032 μM and 0.01 μM respectively.

Download Full-text

Metal ions affect the formation and stability of amyloid β aggregates at multiple length scales

Physical Chemistry Chemical Physics ◽

10.1039/c7cp05072k ◽

2018 ◽

Vol 20 (13) ◽

pp. 8951-8961 ◽

Cited By ~ 16

Author(s):

Myeongsang Lee ◽

Jae In Kim ◽

Sungsoo Na ◽

Kilho Eom

Keyword(s):

Molecular Dynamics ◽

Metal Ions ◽

Neurodegenerative Disease ◽

Molecular Dynamics Simulations ◽

Metal Ion ◽

Amyloid Β ◽

Length Scales ◽

Multiple Length Scales ◽

Dynamics Simulations

The effect of metal ion on the formation of amyloid β (Aβ) aggregates, which are a hallmark for neurodegenerative disease, was studied based on full atomistic molecular dynamics simulations.

Download Full-text

A study on the Adsorption of Graphene/Graphene Oxide–reinforced Polymer ‎Nanocomposites using Reactive Molecular Dynamics

Journal of Advanced Materials In Engineering ◽

10.29252/jame.37.3.25 ◽

2018 ◽

Vol 37 (3) ◽

pp. 25-47

Author(s):

G. Pishevarz ◽

H. Erfan Niya ◽

E. Zaminpayma ◽

◽

...

Keyword(s):

Molecular Dynamics ◽

Graphene Oxide ◽

Polymer Nanocomposites ◽

Reactive Molecular Dynamics ◽

Reinforced Polymer

Download Full-text

Oxidizing metal ions with graphene oxide: the in situ formation of magnetic nanoparticles on self-reduced graphene sheets for multifunctional applications

Chemical Communications ◽

10.1039/c1cc14789g ◽

2011 ◽

Vol 47 (42) ◽

pp. 11689 ◽

Cited By ~ 134

Author(s):

Yuhua Xue ◽

Hao Chen ◽

Dingshan Yu ◽

Shuangyin Wang ◽

Michal Yardeni ◽

...

Keyword(s):

Graphene Oxide ◽

Magnetic Nanoparticles ◽

Metal Ions ◽

Graphene Sheets ◽

Reduced Graphene ◽

In Situ Formation

Download Full-text

Recent Advances in AIEgens for Metal Ion Biosensing and Bioimaging

Molecules ◽

10.3390/molecules24244593 ◽

2019 ◽

Vol 24 (24) ◽

pp. 4593 ◽

Cited By ~ 7

Author(s):

Yongming Li ◽

Huifei Zhong ◽

Yanyan Huang ◽

Rui Zhao

Keyword(s):

Metal Ions ◽

Biological System ◽

Metal Ion ◽

Fluorescence Probes ◽

Aggregation Induced Emission ◽

The Past ◽

Recent Advances ◽

System Approaches ◽

Sensing Performance

Metal ions play important roles in biological system. Approaches capable of selective and sensitive detection of metal ions in living biosystems provide in situ information and have attracted remarkable research attentions. Among these, fluorescence probes with aggregation-induced emission (AIE) behavior offer unique properties. A variety of AIE fluorogens (AIEgens) have been developed in the past decades for tracing metal ions. This review highlights recent advances (since 2015) in AIE-based sensors for detecting metal ions in biological systems. Major concerns will be devoted to the design principles, sensing performance, and bioimaging applications.

Download Full-text