scholarly journals On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

Author(s):  
Zenghui Yang

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

2020 ◽  
Author(s):  
Zenghui Yang

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.


2020 ◽  
Author(s):  
Zenghui Yang

Solids receive displacement damages (DD) when interacting with energetic particles, which may happen during the fabrication of semiconductor devices, in harsh environments and in certain analysis techniques. Simulations of the DD generation are usually carried out with classical molecular dynamics (MD), but classical MD does not account for all the effects in DD, as demonstrated by <i>ab initio</i> calculations of model systems in literature. A fully <i>ab initio</i> simulation of the DD generation is impractical due to the large number of atoms involved. In my previous paper [Phys. Chem. Chem. Phys. 22, 19307 (2020)], I developed an adaptive-center (AC) method for adaptive-partitioning (AP) quantum mechanics/molecular mechanics (QM/MM) simulations, allowing the active region centers and the QM/MM partition to be determined on-the-fly for energy-conserving AP-QM/MM methods. I demonstrated that the AC-AP-QM/MM is applicable to the simulation of the DD generation, so that the active regions can be treated with an <i>ab initio</i> method. The AC method was unable to identify the fast-moving recoil ions in the DD generation as active region centers, however, and the accuracy is negatively affected by the rapid change in QM/MM partition of the system. In this paper, I extend the AC method and develop a speed-dependent adaptive-center (SDAC) method for proper AP-QM/MM simulations of DD. The SDAC method is applicable to general problems with speed-dependent active regions, and is compatible with all existing energy-conserving partition-by-distance AP-QM/MM methods. The artifact due to the speed-dependent potential energy surface can be made small by choosing proper criteria. I demonstrate the SDAC method by simulations of the DD generation in bulk Silicon.<br>


2020 ◽  
Author(s):  
Zenghui Yang

Solids receive displacement damages (DD) when interacting with energetic particles, which may happen during the fabrication of semiconductor devices, in harsh environments and in certain analysis techniques. Simulations of the DD generation are usually carried out with classical molecular dynamics (MD), but classical MD does not account for all the effects in DD, as demonstrated by <i>ab initio</i> calculations of model systems in literature. A fully <i>ab initio</i> simulation of the DD generation is impractical due to the large number of atoms involved. In my previous paper [Phys. Chem. Chem. Phys. 22, 19307 (2020)], I developed an adaptive-center (AC) method for adaptive-partitioning (AP) quantum mechanics/molecular mechanics (QM/MM) simulations, allowing the active region centers and the QM/MM partition to be determined on-the-fly for energy-conserving AP-QM/MM methods. I demonstrated that the AC-AP-QM/MM is applicable to the simulation of the DD generation, so that the active regions can be treated with an <i>ab initio</i> method. The AC method was unable to identify the fast-moving recoil ions in the DD generation as active region centers, however, and the accuracy is negatively affected by the rapid change in QM/MM partition of the system. In this paper, I extend the AC method and develop a speed-dependent adaptive-center (SDAC) method for proper AP-QM/MM simulations of DD. The SDAC method is applicable to general problems with speed-dependent active regions, and is compatible with all existing energy-conserving partition-by-distance AP-QM/MM methods. The artifact due to the speed-dependent potential energy surface can be made small by choosing proper criteria. I demonstrate the SDAC method by simulations of the DD generation in bulk Silicon.<br>


2020 ◽  
Vol 22 (34) ◽  
pp. 19307-19317
Author(s):  
Zeng-hui Yang

The QM/MM partition is determined on-the-fly using any geometrical property as a criterion, while satisfying energy conservation.


Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.


Author(s):  
Katharina Kerschan-Schindl ◽  
Ursula Föger-Samwald ◽  
Andreas Gleiss ◽  
Stefan Kudlacek ◽  
Jacqueline Wallwitz ◽  
...  

Summary Background Circulating serum sclerostin levels are supposed to give a good estimation of the levels of this negative regulator of bone mass within bone. Most studies evaluating total serum sclerostin found different levels in males compared to females and in older compared to younger subjects. Besides an ELISA detecting total sclerostin an ELISA determining bioactive sclerostin has been developed. The aim of this study was to investigate serum levels of bioactive sclerostin in an Austrian population-based cohort. Methods We conducted a cross-sectional observational study in 235 healthy subjects. Using the bioactive ELISA assay (Biomedica) bioactive sclerostin levels were evaluated. Results Serum levels of bioactive sclerostin were higher in men than in women (24%). The levels correlated positively with age (r = 0.47). A positive correlation could also be detected with body mass index and bone mineral density. Conclusion Using the ELISA detecting bioactive sclerostin our results are consistent with data in the literature obtained by different sclerostin assays. The determination of sclerostin concentrations in peripheral blood thus appears to be a robust parameter of bone metabolism.


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