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Open accessJournal ArticleDOI: 10.2147/IJN.S298699

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

04 Mar 2021-International Journal of Nanomedicine (Dove Press)-Vol. 16, pp 1837-1847
Abstract: 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.

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Topics: Nanotube (57%)
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10 results found


Open access
Steven J. Plimpton1Institutions (1)
01 May 1993-
Abstract: 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.

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Topics: Intel Paragon (64%), Intel iPSC (62%), Parallel algorithm (58%)

24,496 Citations



Journal ArticleDOI: 10.1016/J.ENGFRACMECH.2021.107782
Abstract: 2D materials present promising features, but their intrinsic defects, especially at high temperatures, should be considered for usage under harsh conditions. Molecular dynamics simulations were utilized in this work to explore the mechanics of monocrystalline and polycrystalline (PC) silicon–germanium nanosheets (MSiGeNS and PSiGeNS, respectively) as a function of temperature. The mechanical properties of MSiGeNSs decreased by increase of temperature in both armchair and zigzag directions. Likewise, Young's modulus, E and failure stress, σf of decreased by increasing grain-size and randomness, while failure strain, ∊f remained almost unaffected. Ultimately, the study of the mechanical properties of MSiGeNS subjected to different sizes of cracks and notches as a function of temperature showed that increasing crack length, notch radius, and temperature reduced all the properties of defective MSiGeNS. Samples possessing circular notches showed poorer properties compared to those with a crack defect. Moreover, the stress intensity factor of cracked MSiGeNS dropped sharply by temperature rise.

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6 Citations


Journal ArticleDOI: 10.1016/J.JMGM.2021.107977
Abstract: Boron carbide nanosheets (BC3NSs) are semiconductors possessing non-zero bandgap. Nevertheless, there is no estimation of their thermal conductivity for practical circumstances, mainly because of difficulties in simulation of random polycrystalline structures. In the real physics world, BC3NS with perfect monocrystalline is rare, for the nature produces structures with disordered grain regions. Therefore, it is of crucial importance to capture a more realistic picture of thermal conductivity of these nanosheets. Polycrystalline BC3NS (PCBC3NSs are herein simulated by Molecular Dynamics simulation to take their thermal conductivity fingerprint applying ΔT of 40 K. A series of PCBC3NSs were evaluated for thermal conductivity varying the number of grains (3, 5, and 10). The effect of grain rotation was also modeled in terms of Kapitza thermal resistance per grain, varying the rotation angle ( θ /2 = 14.5, 16, 19, and 25°). Overall, a non-linear temperature variation was observed for PCBC3NS, particularly by increasing grain number, possibly because of more phonon scattering (shorter phonon relaxation time) arising from more structural defects. By contrast, the heat current passing across the slab decreased. The thermal conductivity of nanosheet dwindled from 149 W m−1 K−1 for monocrystalline BC3NS to the values of 129.67, 121.32, 115.04, and 102.78 W m−1 K−1 for PCBC3NSs having 2, 3, 5, and 10 grains, respectively. The increase of the grains rotation angle (randomness) from 14.5° to 16°, 19° and 25° led to a rise in Kapitza thermal resistance from 2⨯10−10 m2 K·W−1 to the values of 2.3⨯ 10−10, 2.9⨯10−10, and 4.7⨯ 10−10 m2 K·W−1, respectively. Thus, natural 2D structure would facilitate phonon scattering rate at the grain boundaries, which limits heat transfer across polycrystalline nanosheets.

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Topics: Grain boundary (62%), Thermal conductivity (60%), Thermal resistance (58%) ... show more

3 Citations


Open accessJournal ArticleDOI: 10.2147/IJN.S313855
Abstract: Introduction Antimicrobial peptides are potential therapeutics as anti-bacteria, anti-viruses, anti-fungi, or anticancers. However, they suffer from a short half-life and drug resistance which limit their long-term clinical usage. Methods Herein, we captured the encapsulation of antimicrobial peptide HA-FD-13 into boron nitride nanotube (BNNT) (20,20) and its release due to subsequent insertion of BNNT (14,14) with molecular dynamics simulation. Results The peptide-BNNT (20,20) van der Waals (vdW) interaction energy decreased to -270 kcal·mol-1 at the end of the simulation (15 ns). However, during the period of 0.2-1.8 ns, when half of the peptide was inside the nanotube, the encapsulation was paused due to an energy barrier in the vicinity of BNNT and subsequently the external intervention, such that the self-adjustment of the peptide allowed full insertion. The free energy of the encapsulation process was -200.12 kcal·mol-1, suggesting that the insertion procedure occurred spontaneously. Discussion Once the BNNT (14,14) entered into the BNNT (20,20), the peptide was completely released after 83.8 ps. This revealed that the vdW interaction between the BNNT (14,14) and BNNT (20,20) was stronger than between BNNT (20,20) and the peptide; therefore, the BNNT (14,14) could act as a piston pushing the peptide outside the BNNT (20,20). Moreover, the sudden drop in the vdW energy between nanotubes to the value of the -1300 Kcal·mol-1 confirmed the self-insertion of the BNNT (14,14) into the BNNT (20,20) and correspondingly the release of the peptide.

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1 Citations


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70 results found


Journal ArticleDOI: 10.1016/0263-7855(96)00018-5
Abstract: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.

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Topics: Rendering (computer graphics) (52%), Molecular graphics (52%), Visualization (51%) ... show more

36,939 Citations


Open accessJournal ArticleDOI: 10.1006/JCPH.1995.1039
Steven J. Plimpton1Institutions (1)
Abstract: 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.

... read more

Topics: Intel Paragon (64%), Intel iPSC (62%), Parallel algorithm (58%) ... show more

26,738 Citations


Open access
Steven J. Plimpton1Institutions (1)
01 May 1993-
Abstract: 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.

... read more

Topics: Intel Paragon (64%), Intel iPSC (62%), Parallel algorithm (58%)

24,496 Citations


Journal ArticleDOI: 10.1002/SMLL.200700595
18 Jan 2008-Small
Abstract: Human exposure to nanoparticles is inevitable as nanoparticles become more widely used and, as a result, nanotoxicology research is now gaining attention. However, while the number of nanoparticle types and applications continues to increase, studies to characterize their effects after exposure and to address their potential toxicity are few in comparison. In the medical field in particular, nanoparticles are being utilized in diagnostic and therapeutic tools to better understand, detect, and treat human diseases. Exposure to nanoparticles for medical purposes involves intentional contact or administration; therefore, understanding the properties of nanoparticles and their effect on the body is crucial before clinical use can occur. This Review presents a summary of the in vitro cytotoxicity data currently available on three classes of nanoparticles. With each of these nanoparticles, different data has been published about their cytotoxicity due to varying experimental conditions as well as differing nanoparticle physiochemical properties. For nanoparticles to move into the clinical arena, it is important that nanotoxicology research uncovers and understands how these multiple factors influence the toxicity of nanoparticles so that their undesirable properties can be avoided.

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Topics: Nanotoxicology (52%)

2,342 Citations


Open accessJournal ArticleDOI: 10.1158/1078-0432.CCR-07-1441
Kwangjae Cho1, Xu Wang1, Shuming Nie2, Zhuo Georgia Chen1  +1 moreInstitutions (2)
Abstract: Cancer nanotherapeutics are rapidly progressing and are being implemented to solve several limitations of conventional drug delivery systems such as nonspecific biodistribution and targeting, lack of water solubility, poor oral bioavailability, and low therapeutic indices. To improve the biodistribution of cancer drugs, nanoparticles have been designed for optimal size and surface characteristics to increase their circulation time in the bloodstream. They are also able to carry their loaded active drugs to cancer cells by selectively using the unique pathophysiology of tumors, such as their enhanced permeability and retention effect and the tumor microenvironment. In addition to this passive targeting mechanism, active targeting strategies using ligands or antibodies directed against selected tumor targets amplify the specificity of these therapeutic nanoparticles. Drug resistance, another obstacle that impedes the efficacy of both molecularly targeted and conventional chemotherapeutic agents, might also be overcome, or at least reduced, using nanoparticles. Nanoparticles have the ability to accumulate in cells without being recognized by P-glycoprotein, one of the main mediators of multidrug resistance, resulting in the increased intracellular concentration of drugs. Multifunctional and multiplex nanoparticles are now being actively investigated and are on the horizon as the next generation of nanoparticles, facilitating personalized and tailored cancer treatment.

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2,328 Citations


Performance
Metrics
No. of citations received by the Paper in previous years
YearCitations
20219
19931