Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Herein, the NH2-UiO-66 metal organic framework (MOF) has been green synthesized with the assistance of high gravity to provide a suitable and safe platform for drug loading. The NH2-UiO-66 MOF was characterized using a field-emission scanning electron microscope, transmission electron microscope (TEM), X-ray diffraction, and zeta potential analysis. Doxorubicin was then encapsulated physically on the porosity of the green MOF. Two different stimulus polymers, p(HEMA) and p(NIPAM), were used as the coating agents of the MOFs. Doxorubicin was loaded onto the polymer-coated MOFs as well, and a drug payload of more than 51% was obtained, which is a record by itself. In the next step, pCRISPR was successfully tagged on the surface of the modified MOFs, and the performance of the final nanosystems were evaluated by the GFP expression. In addition, successful loadings and internalizations of doxorubicin were investigated via confocal laser scanning microscopy. Cellular images from the HeLa cell line for the UiO-66@DOX@pCRISPR and GMA-UiO-66@DOX@pCRISPR do not show any promising and successful gene transfections, with a maximum EGFP of 1.6%; however, the results for the p(HEMA)-GMA-UiO-66@DOX@pCRISPR show up to 4.3% transfection efficiency. Also, the results for the p(NIPAM)-GMA-UiO-66@DOX@pCRISPR showed up to 6.4% transfection efficiency, which is the first and superior report of a MOF-based nanocarrier for the delivery of pCRISPR. Furthermore, the MTT assay does not shown any critical cytotoxicity, which is a promising result for further biomedical applications. At the end of the study, the morphologies of all of the nanomaterials were screened after drug and gene delivery procedures and showed partial degradation of the nanomaterial. However, the cubic structure of the MOFs has been shown in TEM, and this is further proof of the stability of these green MOFs for biomedical applications.

Polymer-Coated NH2-UiO-66 for the Codelivery of DOX/pCRISPR.

Multifunctional 3D Hierarchical Bioactive Green Carbon-Based Nanocomposites

Introduction Nanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance.
 Methods
 In this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation.
 Results
 The peptide was absorbed into the BNNT by van der Waals (vdW) interaction between cRW3 and the BNNT, in which the vdW interaction decreased during the simulation process and reached the value of −142.7 kcal·mol−1 at 4 ns.
 Discussion
 The increase in the potential mean force profile of the encapsulated peptide during the pulling process of cRW3 out of the nanotube showed that its insertion into the BNNT occurred spontaneously and that the inserted peptide had the desired stability. The energy barrier at the entrance of the BNNT caused a pause of 0.45 ns when half of the peptide was inside the BNNT during the encapsulation process. Therefore, during this period, the peptide experienced the weakest movement and the smallest conformational changes.

/pdf/boron-nitride-nanotube-as-an-antimicrobial-peptide-carrier-a-4q8tznk3se.pdf

Boron Nitride Nanotube as an Antimicrobial Peptide Carrier: A Theoretical Insight.

Fracture mechanics of polycrystalline beryllium oxide nanosheets: A theoretical basis

Nanotubes have been considered as promising candidates for protein delivery purposes due to distinct features such as their large enough volume of cavity to encapsulate the protein, providing the sustain and target release. Moreover, possessing the properties of suitable cell viabilities, and biocompatibility on the wide range of cell lines as a result of structural stability, chemical inertness, and noncovalent wrapping ability, boron nitride nanotubes (BNNTs) have caught further attention as protein nanocarriers. However, to assess the encapsulation process of the protein into the BNNT, it is vital to comprehend the protein-BNNT interaction. In the present work, the self-insertion process of the protein SmtA, metallothionein, into the BNNT has been verified by means of the molecular dynamics (MD) simulation under NPT ensemble. It was revealed that the protein was self-inserted into the BNNT through the protein-BNNT van der Waals (vdW) interaction, which descended and reached the average value of -189.63 kcal·mol-1 at 15 ns of the simulation time. The potential mean force (PMF) profile of the encapsulated protein with increasing trend, which was obtained via the pulling process unraveled that the encapsulation of the protein into the BNNT cavity proceeded spontaneously and the self-inserted protein had reasonable stability. Moreover, due to the strong hydrogen interactions between the nitrogen atoms of BNNT and hydrogen atoms of SmtA, there was no evidence of an energy barrier in the vicinity of the BNNT entrance, which resulted in the rapid adsorption of this protein into the BNNT.

https://pubs.acs.org/doi/pdf/10.1021/acsomega.0c05080

Insight into the Self-Insertion of a Protein Inside the Boron Nitride Nanotube.

MEL-type zeolite was selected as a typical porous material to theoretically capture the purification scenario of a model landfill leachate comprising PbCl2 and CuCl2 varying the pressure (2.4–48 MPa). Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) was applied to simulate the equilibrium state (0.5 ns) and dynamics of Pb2+, Cu2+ and Cl− and water molecules (4 ns). Overall, the flux through the MEL membrane was increased by the increase of pressure. Lennard-Jones potential was used to explain non-bonded interactions between the membrane and ions as well as water molecules, in terms of values of energy and snapshots were taken from the evolution of purification phenomenon. The molecular patterns of accumulation of ions in the vicinity of zeolitic membrane were also captured as functions of the energies of the interaction between the contaminants and porous membrane. Mean square displacement (MSD) variation was indicative of the effect of pressure on dynamics of heavy metal separation; higher energies obtained at higher pressures, as reflected in alteration of van der Waals (vdW) force between ions and water molecules. The membrane revealed rejection above 70% for Pb2+, and almost 100% against Cu2+ and Cl−, respectively. Density of water remained almost 1 g cm3, but depending on population of water molecules decreased after passage into the zeolite membrane.

Abbasali Nasiriasayesh

Papers

Boron Nitride Nanotube as an Antimicrobial Peptide Carrier: A Theoretical Insight.

Insight into the Self-Insertion of a Protein Inside the Boron Nitride Nanotube.

MEL zeolite nanosheet membranes for water purification: insights from molecular dynamics simulations