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1. Multi-resolution simulation of DNA transport through large synthetic nanostructures

   https://doi.org/10.1039/d1cp04589j  

   Choudhary, Adnan; Maffeo, Christopher; Aksimentiev, Aleksei (February 2022, Physical Chemistry Chemical Physics)

   Modeling and simulation has become an invaluable partner in development of nanopore sensing systems. The key advantage of the nanopore sensing method – the ability to rapidly detect individual biomolecules as a transient reduction of the ionic current flowing through the nanopore – is also its key deficiency, as the current signal itself rarely provides direct information about the chemical structure of the biomolecule. Complementing experimental calibration of the nanopore sensor readout, coarse-grained and all-atom molecular dynamics simulations have been used extensively to characterize the nanopore translocation process and to connect the microscopic events taking place inside the nanopore to the experimentally measured ionic current blockades. Traditional coarse-grained simulations, however, lack the precision needed to predict ionic current blockades with atomic resolution whereas traditional all-atom simulations are limited by the length and time scales amenable to the method. Here, we describe a multi-resolution framework for modeling electric field-driven passage of DNA molecules and nanostructures through to-scale models of synthetic nanopore systems. We illustrate the method by simulating translocation of double-stranded DNA through a solid-state nanopore and a micron-scale slit, capture and translocation of single-stranded DNA in a double nanopore system, and modeling ionic current readout from a DNA origami nanostructure passage through a nanocapillary. We expect our multi-resolution simulation framework to aid development of the nanopore field by providing accurate, to-scale modeling capability to research laboratories that do not have access to leadership supercomputer facilities. 

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2. Multi-physics simulations and experimental comparisons for the optical and electrical forces acting on a silica nanoparticle trapped by a double-nanohole plasmonic nanopore sensor

   Homayoun Asadzadeh, Scott Renkes (July 2023, Sensing and biosensing research)

   Bimodal optical-electrical data generated when a 20 nm diameter silica (SiO2) nanoparticle was trapped by a plasmonic nanopore sensor were simulated using Multiphysics COMSOL and compared with sensor measurements for closely matching experimental parameters. The nanosensor, employed self-induced back action (SIBA) to optically trap nanoparticles in the center of a double nanohole (DNH) structure on top a solid-state nanopores (ssNP). This SIBA actuated nanopore electrophoresis (SANE) sensor enables simultaneous capture of optical and electrical data generated by several underlying forces acting on the trapped SiO2 nanoparticle: plasmonic optical trapping, electroosmosis, electrophoresis, viscous drag, and heat conduction forces. The Multiphysics simulations enabled dissecting the relative contributions of those forces acting on the nanoparticle as a function of its location above and through the sensor’s ssNP. Comparisons between simulations and experiments demonstrated qualitative similarities in the optical and electrical time-series data generated as the nanoparticle entered and exited from the SANE sensor. These experimental parameter-matched simulations indicated that the competition between optical and electrical forces shifted the trapping equilibrium position close to the top opening of the ssNP, relative to the optical trapping force maximum that was located several nm above. The experimentally estimated minimum for the optical force needed to trap a SiO2 nanoparticle was consistent with corresponding simulation predictions of optical-electrical force balance. The comparison of Multiphysics simulations with experiments improves our understanding of the interplay between optical and electrical forces as a function of nanoparticle position across this plasmonic nanopore sensor. 

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3. Dynamics of ionic liquids in the presence of polymer-grafted nanoparticles

   https://doi.org/10.1039/c9nr04204k  

   Liu, Siqi; Liedel, Clemens; Tarakina, Nadezda V.; Osti, Naresh C.; Akcora, Pinar (October 2019, Nanoscale)

   null (Ed.)

   We incorporated polymer-grafted nanoparticles into ionic and zwitterionic liquids to explore the solvation and confinement effects on their heterogeneous dynamics using quasi-elastic neutron scattering (QENS). 1-Hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (HMIM-TFSI) mixed with deuterated poly(methyl methacrylate) (d-PMMA)-grafted nanoparticles is studied to unravel how dynamic coupling between PMMA and HMIM-TFSI influence the fast and slow diffusion characteristics of the HMIM + cations. The zwitterionic liquid, 1-butyl-3-methyl imidazole-2-ylidene borane (BMIM-BH 3 ) is critically selected and mixed with PMMA-grafted nanoparticles for comparison in this work as its ions do not self-dissociate and it does not couple with PMMA through ion-dipole interactions as HMIM-TFSI does. We find that long-range unrestricted diffusion of HMIM + cations is higher in well-dispersed particles than in aggregated particle systems, whereas the localized diffusion of HMIM + is measured to be higher in close-packed particles. Translational diffusion dynamics of BMIM-BH 3 is not influenced by any particle structures suggesting that zwitterions do not interact with PMMA. This difference between two ionic liquid types enables us to decouple polymer effects from the diffusion of ionic liquids, which is integral to understand the ionic transport mechanism in ionic liquids confined in polymer-grafted nanoparticle electrolytes. 

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4. Lattice thermal conductivity of embedded nanoparticle composites: the role of particle size distribution

   https://doi.org/10.1088/1361-6528/ad06d6  

   Maranets, Theodore; Cui, Haoran; Wang, Yan (November 2023, Nanotechnology)

   Abstract Nanoparticles embedded within a crystalline solid serve as impurity phonon scattering centers that reduce lattice thermal conductivity, a desirable result for thermoelectric applications. Most studies of thermal transport in nanoparticle-laden composite materials have assumed the nanoparticles to possess a single size. If there is a distribution of nanoparticle sizes, how is thermal conductivity affected? Moreover, is there a best nanoparticle size distribution to minimize thermal conductivity? In this work, we study the thermal conductivity of nanoparticle-laden composites through a molecular dynamics approach which naturally captures phonon scattering processes more rigorously than previously used analytical theories. From thermal transport simulations of a systematic variety of nanoparticle configurations, we empirically formulate how nanoparticle size distribution, particle number density, and volume fraction affect the lattice thermal conductivity. We find at volume fractions below 10%, the particle number density is by far the most impactful factor on thermal conductivity and at fractions above 10%, the effect of the size distribution and number density is minimal compared to the volume fraction. In fact, upon comparisons of configurations with the same particle number density and volume fractions, the lattice thermal conductivity of a single nanoparticle size can be lower than that of a size distribution which contradicts intuitions that a single size would attenuate phonon transport less than a spectrum of sizes. The random alloy, which can be considered as a single size configuration of maximum particle number density where the nanoparticle size is equal to the lattice constant, is the most performant in thermal conductivity reduction at volume fractions below 10%. We conclude that nanoparticle size distribution only plays a minor role in affecting lattice thermal conductivity with the particle number density and volume fraction being the more significant factors that should be considered in fabrication of nanoparticle-laden composites for potential improved thermoelectric performance. 

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5. Modeling nanoparticle charge distribution in the afterglow of non-thermal plasmas and comparison with measurements

   https://doi.org/https://doi.org/10.1088/1361-6463/abf70c  

   Suresh, Vikram; Li, Li; Redmond Go Felipe, Joshua; Gopalakrishnan, Ranganathan (June 2021, Journal of physics)

   null (Ed.)

   Particle charging in the afterglows of non-thermal plasmas typically take place in a non-neutral space charge environment. We model the same by incorporating particle-ion collision rate constant models, developed in prior work by analyzing particle-ion trajectories calculated using Langevin Dynamics simulations, into species transport equations for ions, electrons and charged particles in the afterglow. A scaling analysis of particle charging and additional Langevin Dynamics calculations of the particle-ion collision rate constant are presented to extend the range of applicability to ion electrostatic to thermal energy ratios of 300 and diffusive Knudsen number (that scales inversely with gas pressure) up to 2000. The developed collision rate constant models are first validated by comparing predictions of particle charge against measured values in a stationary, non-thermal DC plasma from past PK-4 campaigns published in Phys. Rev. Lett. 93(8): 085001 and Phys. Rev. E 72(1): 016406). The comparisons reveal excellent agreement within ±35% for particles of radius 0.6,1.0,1.3 μm in the gas pressure range of ~20-150 Pa. The experiments to probe particle charge distributions by Sharma et al. (J. Physics D: Appl. Phys. 53(24): 245204) are modeled using the validated particle-ion collision rate constant models and the calculated charge fractions are compared with measurements. The comparisons reveal that the ion/electron concentration and gas temperature in the afterglow critically influence the particle charge and the predictions are generally in qualitative agreement with the measurements. Along with critical assessment of the modeling assumptions, several recommendations are presented for future experimental design to probe charging in afterglows. 

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