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Biological and Medicinal Chemistry

Working Paper

Exploring CRISPR-Cas9 HNH-Domain Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

Richard Van, Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul Agarwal, Bernard Brooks, Rakhi Rajan, Yihan Shao

Version 1 posted 04 October 2024

146

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Theoretical and Computational Chemistry

Working Paper

The Training of Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models

Xiaoliang Pan, Ryan Snyder, Jia-Ning Wang, Chance Lander, Carly Wickizer, Richard Van, Andrew Chesney, Yuanfei Xue, Yuezhi Mao, Ye Mei, Jingzhi Pu, Yihan Shao

Version 1 posted 25 August 2023

569

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Theoretical and Computational Chemistry

Working Paper

On the Entanglement of Chromophore and Solvent Orbitals

Xinwei Ji, Zheng Pei, Kim Ngan Huynh, Junjie Yang, Xiaoliang Pan, Binju Wang, Yuezhi Mao, Yihan Shao

Version 1 posted 08 October 2024

186

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Theoretical and Computational Chemistry

Working Paper

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

Xiaoliang Pan, Richard Van, Jingzhi Pu, Kwangho Nam, Yuezhi Mao, Yihan Shao

Version 1 posted 25 August 2023

382

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Theoretical and Computational Chemistry

Working Paper

Visualization of Electron Density Changes Along Chemical Reaction Pathways

Chance Lander, Vardhan Satalkar, Junjie Yang, Xiaoliang Pan, Zheng Pei, Aayushi Chatterji, Chungen Liu, Kenneth Nicholas, Robert Cichewicz, Zhibo Yang, Yihan Shao

Version 1 posted 10 May 2022

407

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Physical Chemistry

Working Paper

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

Wenxin Hu, Pengfei Li, Jia-Ning Wang, Yuanfei Xue, Yan Mo, Jun Zheng, Xiaoliang Pan, Yihan Shao, Ye Mei

Version 1 posted 29 July 2020

294

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Theoretical and Computational Chemistry

Working Paper

Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

Xiaoliang Pan, junjie yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang, Jingzhi Pu, Ye Mei, Kwangho Nam, Yihan Shao

Version 1 posted 09 June 2021

674

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Theoretical and Computational Chemistry

Working Paper

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching

Xiaoliang Pan, Pengfei Li, Junming Ho, Jingzhi Pu, Ye Mei, Yihan Shao

Version 1 posted 16 July 2019

580

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Theoretical and Computational Chemistry

Working Paper

Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semi-empirical QM/MM Hamiltonian

Xiaoliang Pan, Richard Van, Evgeny Epifanovsky, Jian Liu, Jingzhi Pu, Kwangho Nam, Yihan Shao

Version 1 posted 04 April 2022

395

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Theoretical and Computational Chemistry

Working Paper

Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential

Yuanfei Xue, Jia-Ning Wang, Wenxin Hu, Jun Zheng, Yongle Li, Xiaoliang Pan, Yan Mo, Yihan Shao, Lu Wang, Ye Mei

Version 1 posted 02 August 2021

314

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Refine Search

11 results in Xiaoliang Pan in Authors: Xiaoliang Pan

Exploring CRISPR-Cas9 HNH-Domain Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

The Training of Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models

On the Entanglement of Chromophore and Solvent Orbitals

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

Visualization of Electron Density Changes Along Chemical Reaction Pathways

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching

Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semi-empirical QM/MM Hamiltonian

Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential

11 results in Authors: Xiaoliang Pan