With the advancement of nanotoxicology and nanomedicine, it has been realized that nanoparticles (NPs) interact readily with biomolecular species and other chemical and organic matter to result in biocorona formation. The field of the environmental health and safety of nanotechnology, or NanoEHS, is currently lacking significant molecular-resolution data, and we set out to characterize biocorona formation through electron microscopy imaging and circular dichroism spectroscopy that inspired a novel approach for molecular dynamics (MD) simulations of protein-NP interactions. In our present study, we developed a novel GPU-optimized coarse-grained MD simulation methodology for the study of biocorona formation, a first in the field. Specifically, we performed MD simulations of a spherical, negatively charged citrate-covered silver nanoparticle (AgNP) interacting with 15 apolipoproteins. At low ion concentrations, we observed the formation of an AgNP-apolipoprotein biocorona. Consistent with the circular dichroism (CD) spectra, we observed a decrease in α-helices coupled with an increase in β-sheets in apolipoprotein upon biocorona formation.
Wind power generation is growing fast as one of the most promising renewable energy sources that can serve as an alternative to fossil fuel-generated electricity. When the wind turbine generator (WTG) extracts power from the wind, the wake evolves and leads to a considerable reduction in the efficiency of the actual power generation. Furthermore, the wake effect can lead to the increase of turbulence induced fatigue loads that reduce the life time of WTGs. In this work, a pulsed coherent Doppler lidar (PCDL) has been developed and deployed to visualize wind turbine wakes and to characterize the geometry and dynamics of wakes. As compared with the commercial off-the-shelf coherent lidars, the PCDL in this work has higher updating rate of 4 Hz and variable physical spatial resolution from 15 to 60 m, which improves its capability to observation the instantaneous turbulent wind field. The wind speed estimation method from the arc scan technique was evaluated in comparison with wind mast measurements. Field experiments were performed to study the turbulent wind field in the vicinity of operating WTGs in the onshore and offshore wind parks from 2013 to 2015. Techniques based on a single and a dual Doppler lidar were employed for elucidating main features of turbine wakes, including wind velocity deficit, wake dimension, velocity profile, 2D wind vector with resolution of 10 m, turbulence dissipation rate and turbulence intensity under different conditions of surface roughness. The paper shows that the PCDL is a practical tool for wind energy research and will provide a significant basis for wind farm site selection, design and optimization.
While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes.
The folding of bacterial tRNAs with disparate sequences has been observed to proceed in distinct folding mechanisms despite their structural similarity. To explore the folding landscapes of tRNA, we performed ion concentration-dependent coarse-grained TIS model MD simulations of several E. coli tRNAs to compare their thermodynamic melting profiles to the classical absorbance spectra of Crothers and co-workers. To independently validate our findings, we also performed atomistic empirical force field MD simulations of tRNAs, and we compared the base-to-base distances from coarse-grained and atomistic MD simulations to empirical base-stacking free energies. We then projected the free energies to the secondary structural elements of tRNA, and we observe distinct, parallel folding mechanisms whose differences can be inferred on the basis of their sequence-dependent base-stacking stabilities. In some cases, a premature, nonproductive folding intermediate corresponding to the Ψ hairpin loop must backtrack to the unfolded state before proceeding to the folded state. This observation suggests a possible explanation for the fast and slow phases observed in tRNA folding kinetics.
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