Protein Conformation Motion Modeling Using Sep-CMA-ES

Author(s):  
Maxim Buzdalov ◽  
Sergey Knyazev ◽  
Yury Porozov
2020 ◽  
Vol 110 (2) ◽  
pp. 471-488 ◽  
Author(s):  
Samantha M. Palmer ◽  
Gail M. Atkinson

ABSTRACT Spectral decay of ground-motion amplitudes at high frequencies is primarily influenced by two parameters: site-related kappa (κ0) and regional Q (quality factor, inversely proportional to anelastic attenuation). We examine kappa and apparent Q-values (Qa) for M≥3.5 earthquakes recorded at seismograph stations on rock sites in eastern and western Canada. Our database contains 20 earthquakes recorded on nine stations in eastern Canada and 404 earthquakes recorded on eight stations in western Canada, resulting in 105 and 865 Fourier amplitude spectra, respectively. We apply two different methods: (1) a modified version of the classical S-wave acceleration method; and (2) a new stacking method that is consistent with the use of kappa in ground-motion modeling. The results are robust with respect to the method used and also with respect to the frequency band selected, which ranges from 9 to 38 Hz depending on the region, event, and method. Kappa values obtained from the classical method are consistent with those of the stacked method, but the stacked method provides a lower uncertainty. A general observation is that kappa is usually larger, and apparent Q is smaller, for the horizontal component in comparison to the vertical component. We determine an average regional κ0=7  ms (horizontal) and 0 ms (vertical) for rock sites in eastern Canada; we obtain κ0=19  ms (horizontal) and 14 ms (vertical) for rock sites in western Canada. We note that kappa measurements are quite sensitive to details of data selection criteria and methodology, and may be significantly influenced by site effects, resulting in large site-to-site variability.


Biomedicines ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 359
Author(s):  
Hsiang-Hao Chuang ◽  
Yen-Yi Zhen ◽  
Yu-Chen Tsai ◽  
Cheng-Hao Chuang ◽  
Ming-Shyan Huang ◽  
...  

Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) specifically binds and isomerizes the phosphorylated serine/threonine-proline (pSer/Thr-Pro) motif, which leads to changes in protein conformation and function. Pin1 is widely overexpressed in cancers and plays an important role in tumorigenesis. Mounting evidence has revealed that targeting Pin1 is a potential therapeutic approach for various cancers by inhibiting cell proliferation, reducing metastasis, and maintaining genome stability. In this review, we summarize the underlying mechanisms of Pin1-mediated upregulation of oncogenes and downregulation of tumor suppressors in cancer development. Furthermore, we also discuss the multiple roles of Pin1 in cancer hallmarks and examine Pin1 as a desirable pharmaceutical target for cancer therapy. We also summarize the recent progress of Pin1-targeted small-molecule compounds for anticancer activity.


2011 ◽  
Vol 90 (2) ◽  
pp. A77
Author(s):  
Isabelle Valarche ◽  
Amaya Berecibar ◽  
Mehdi Lahmar ◽  
Luc Batard ◽  
Aurelie Martin ◽  
...  

Author(s):  
Reza Alebrahim ◽  
Pawel Packo ◽  
Mirco Zaccariotto ◽  
Ugo Galvanetto

In this study, methods to mitigate anomalous wave propagation in 2-D Bond-Based Peridynamics (PD) are presented. Similarly to what happens in classical non-local models, an irregular wave transmission phenomenon occurs at high frequencies. This feature of the dynamic performance of PD, limits its potential applications. A minimization method based on the weighted residual point collocation is introduced to substantially extend the frequency range of wave motion modeling. The optimization problem, developed through inverse analysis, is set up by comparing exact and numerical dispersion curves and minimizing the error in the frequency-wavenumber domain. A significant improvement in the wave propagation simulation using Bond-Based PD is observed.


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