scholarly journals Hydrodynamic interactions and extreme particle clustering in turbulence

2021 ◽  
Vol 933 ◽  
Author(s):  
Andrew D. Bragg ◽  
Adam L. Hammond ◽  
Rohit Dhariwal ◽  
Hui Meng

Expanding recent observations by Hammond & Meng (J. Fluid Mech., vol. 921, 2021, A16), we present a range of detailed experimental data of the radial distribution function (r.d.f.) of inertial particles in isotropic turbulence for different Stokes number, $St$ , showing that the r.d.f. grows explosively with decreasing separation r, exhibiting $r^{-6}$ scaling as the collision radius is approached, regardless of $St$ or particle radius $a$ . To understand such explosive clustering, we correct a number of errors in the theory by Yavuz et al. (Phys. Rev. Lett., vol. 120, 2018, 244504) based on hydrodynamic interactions between pairs of small, weakly inertial particles. A comparison between the corrected theory and the experiment shows that the theory by Yavuz et al. underpredicts the r.d.f. by orders of magnitude. To explain this discrepancy, we explore several alternative mechanisms for this discrepancy that were not included in the theory and show that none of them are likely the explanation. This suggests new, yet-to-be-identified physical mechanisms are at play, requiring further investigation and new theories.

Author(s):  
Jurica Novak ◽  
Maria A. Grishina ◽  
Vladimir A. Potemkin

: In this letter the newly introduced approach based on the radial distribution function (RDF) weighted by the number of va-lence shell electrons is applied for a series of HIV-1 protease enzyme and its complexes with inhibitors to evaluate the influ-ence of hydrogen atoms on the performance of the model. The multiple linear regression method was used for the selection of the relevant descriptors. Two groups of residues having dominant contribution to the RDF descriptor are identified as relevant for the inhibition. In the first group are residues like Arg8, Asp25, Thr26, Gly27 and Asp29, which establish direct interaction with the inhibitor, while the second group consists of the amino acids at the interface of the two homodimer sub-units or with the solvent. The crucial motif pointed out by our approach as the most important for inhibition of the enzyme’s activity and present in all inhibitors is hydroxyl group that establish hydrogen bond with Asp25 side chain. Additionally, the comparison to the model without hydrogen showed that both models are of similar quality, but the downside of the current model is the need for the determination of residues’ protonation states.


2008 ◽  
Vol 47-50 ◽  
pp. 375-378 ◽  
Author(s):  
Zheng Han Hong ◽  
Shun Fa Hwang ◽  
Te Hua Fang

The mixing situation of Co atoms implanting onto Cu(001) substrate is investigated with regard to incident energy and substrate temperature by molecular dynamics. The results indicate that higher substrate temperature and/or incident energy will result in higher intermixing between the incident atoms and the substrate atoms. Furthermore, the value of the first peak of the radial distribution function (RDF) becomes lower and wider for the Co-Cu system as the substrate temperature and/or incident energy are increased.


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