FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3136228320> ?p ?o ?g. }

• W3136228320 endingPage "7009" @default.
• W3136228320 startingPage "6993" @default.
• W3136228320 abstract "We develop a new deep potential─range correction (DPRc) machine learning potential for combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical reactions in the condensed phase. The new range correction enables short-ranged QM/MM interactions to be tuned for higher accuracy, and the correction smoothly vanishes within a specified cutoff. We further develop an active learning procedure for robust neural network training. We test the DPRc model and training procedure against a series of six nonenzymatic phosphoryl transfer reactions in solution that are important in mechanistic studies of RNA-cleaving enzymes. Specifically, we apply DPRc corrections to a base QM model and test its ability to reproduce free-energy profiles generated from a target QM model. We perform these comparisons using the MNDO/d and DFTB2 semiempirical models because they differ in the way they treat orbital orthogonalization and electrostatics and produce free-energy profiles which differ significantly from each other, thereby providing us a rigorous stress test for the DPRc model and training procedure. The comparisons show that accurate reproduction of the free-energy profiles requires correction of the QM/MM interactions out to 6 Å. We further find that the model’s initial training benefits from generating data from temperature replica exchange simulations and including high-temperature configurations into the fitting procedure, so the resulting models are trained to properly avoid high-energy regions. A single DPRc model was trained to reproduce four different reactions and yielded good agreement with the free-energy profiles made from the target QM/MM simulations. The DPRc model was further demonstrated to be transferable to 2D free-energy surfaces and 1D free-energy profiles that were not explicitly considered in the training. Examination of the computational performance of the DPRc model showed that it was fairly slow when run on CPUs but was sped up almost 100-fold when using NVIDIA V100 GPUs, resulting in almost negligible overhead. The new DPRc model and training procedure provide a potentially powerful new tool for the creation of next-generation QM/MM potentials for a wide spectrum of free-energy applications ranging from drug discovery to enzyme design." @default.
• W3136228320 created "2021-03-29" @default.
• W3136228320 creator A5007304685 @default.
• W3136228320 creator A5008102135 @default.
• W3136228320 creator A5042165620 @default.
• W3136228320 creator A5076436548 @default.
• W3136228320 date "2021-10-13" @default.
• W3136228320 modified "2023-10-06" @default.
• W3136228320 title "Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution" @default.
• W3136228320 cites W1968994875 @default.
• W3136228320 cites W1978183953 @default.
• W3136228320 cites W1983493485 @default.
• W3136228320 cites W1989277973 @default.
• W3136228320 cites W1994740416 @default.
• W3136228320 cites W1994941561 @default.
• W3136228320 cites W1997231673 @default.
• W3136228320 cites W2017517197 @default.
• W3136228320 cites W2024726841 @default.
• W3136228320 cites W2025444507 @default.
• W3136228320 cites W2035266068 @default.
• W3136228320 cites W2037535298 @default.
• W3136228320 cites W2039167967 @default.
• W3136228320 cites W2052415011 @default.
• W3136228320 cites W2055210514 @default.
• W3136228320 cites W2063020900 @default.
• W3136228320 cites W2063721236 @default.
• W3136228320 cites W2065096041 @default.
• W3136228320 cites W2072683434 @default.
• W3136228320 cites W2076888175 @default.
• W3136228320 cites W2089989221 @default.
• W3136228320 cites W2095465216 @default.
• W3136228320 cites W2099805477 @default.
• W3136228320 cites W2117518744 @default.
• W3136228320 cites W2121676556 @default.
• W3136228320 cites W2132262459 @default.
• W3136228320 cites W2134450923 @default.
• W3136228320 cites W2147993766 @default.
• W3136228320 cites W2160498409 @default.
• W3136228320 cites W2166014002 @default.
• W3136228320 cites W2169678694 @default.
• W3136228320 cites W2324265905 @default.
• W3136228320 cites W2327851360 @default.
• W3136228320 cites W2398216955 @default.
• W3136228320 cites W2404280981 @default.
• W3136228320 cites W2410722695 @default.
• W3136228320 cites W2507479832 @default.
• W3136228320 cites W2541404351 @default.
• W3136228320 cites W2741173907 @default.
• W3136228320 cites W2741378630 @default.
• W3136228320 cites W2742127985 @default.
• W3136228320 cites W2749311864 @default.
• W3136228320 cites W2761947594 @default.
• W3136228320 cites W2766856748 @default.
• W3136228320 cites W2775708988 @default.
• W3136228320 cites W2778051509 @default.
• W3136228320 cites W2788317900 @default.
• W3136228320 cites W2790176708 @default.
• W3136228320 cites W2791032147 @default.
• W3136228320 cites W2885841934 @default.
• W3136228320 cites W2891791233 @default.
• W3136228320 cites W2892113269 @default.
• W3136228320 cites W2897803911 @default.
• W3136228320 cites W2917792379 @default.
• W3136228320 cites W2923693308 @default.
• W3136228320 cites W2945380370 @default.
• W3136228320 cites W2946396630 @default.
• W3136228320 cites W2954088480 @default.
• W3136228320 cites W2964658530 @default.
• W3136228320 cites W2968558338 @default.
• W3136228320 cites W2972646529 @default.
• W3136228320 cites W2973214268 @default.
• W3136228320 cites W2985776732 @default.
• W3136228320 cites W2990862336 @default.
• W3136228320 cites W3001132921 @default.
• W3136228320 cites W3003966510 @default.
• W3136228320 cites W3004021778 @default.
• W3136228320 cites W3004981459 @default.
• W3136228320 cites W3006005697 @default.
• W3136228320 cites W3013002235 @default.
• W3136228320 cites W3045664177 @default.
• W3136228320 cites W3045724025 @default.
• W3136228320 cites W3046877548 @default.
• W3136228320 cites W3087004338 @default.
• W3136228320 cites W3092006924 @default.
• W3136228320 cites W3094385606 @default.
• W3136228320 cites W3098509317 @default.
• W3136228320 cites W3100344218 @default.
• W3136228320 cites W3103689700 @default.
• W3136228320 cites W3106153623 @default.
• W3136228320 cites W3110925220 @default.
• W3136228320 cites W3119263526 @default.
• W3136228320 cites W3123300545 @default.
• W3136228320 cites W3129775554 @default.
• W3136228320 cites W3131995991 @default.
• W3136228320 cites W3148477737 @default.
• W3136228320 cites W3168813651 @default.
• W3136228320 cites W3184824705 @default.
• W3136228320 cites W4249946779 @default.

• next