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D-Index & Metrics

Chemistry

D-Index
56
Citations
18177
World Ranking
11435
National Ranking
3092

Research.com Recognitions

  • 2015 - Fellow of the Indian National Academy of Engineering (INAE)

Overview

Pengyu Ren is affiliated with The University of Texas at Austin in the United States and has a research focus primarily within the field of Biochemistry, Genetics, and Molecular Biology, with 90 publications in this area. Their work covers several subfields, including Molecular Biology, Atomic and Molecular Physics and Optics, Electrical and Electronic Engineering, Materials Chemistry, and Spectroscopy.

The scientist's research emphasizes topics such as Protein Structure and Dynamics, Spectroscopy and Quantum Chemical Studies, DNA and Nucleic Acid Chemistry, Advanced Chemical Physics Studies, RNA and protein synthesis mechanisms, Computational Drug Discovery Methods, and Mass Spectrometry Techniques and Applications.

Among their recent published papers are:

  • Hydrothermal Synthesis of Hierarchical SnO2 Nanostructures for Improved Formaldehyde Gas Sensing, 2022, Nanomaterials
  • Automation of AMOEBA polarizable force field for small molecules: Poltype 2, 2022, Journal of Computational Chemistry
  • Comparative Proteomic Analysis of Polarized Human THP-1 and Mouse RAW264.7 Macrophages, 2021, Frontiers in Immunology
  • Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems, 2021, Journal of Chemical Theory and Computation
  • High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling, 2021, Chemical Science

Pengyu Ren frequently collaborates with several co-authors, including Chengwen Liu, Jean-Philip Piquemal, Zhifeng Jing, Louis Lagardère, and Brandon Walker.

The scientist has published extensively in several venues, with multiple publications in:

  • Faculty Opinions - Post-Publication Peer Review of the Biomedical Literature
  • The Journal of Physical Chemistry B
  • Journal of Chemical Theory and Computation
  • Chemical Science
  • Biophysical Journal

Among the awards received, Pengyu Ren was recognized as a Fellow of the Indian National Academy of Engineering (INAE) in 2015.

Best Publications

  • The COMPASS force field: parameterization and validation for phosphazenes

    H. Sun;P. Ren;J.R. Fried

  • Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

    Pengyu Ren;Jay W. Ponder

  • Current Status of the AMOEBA Polarizable Force Field

    Jay W. Ponder;Chuanjie Wu;Pengyu Ren;Vijay S. Pande

  • Tinker 8: Software Tools for Molecular Design.

    Joshua A Rackers;Zhi Wang;Chao Lu;Marie L Laury

  • Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

    Yue Shi;Zhen Xia;Jiajing Zhang;Robert Best

  • Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

    Pengyu Y. Ren;Jay W. Ponder

  • Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field

    Alan Grossfield;Pengyu Ren;Jay W. Ponder

  • Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

    Pengyu Ren;Chuanjie Wu;Jay W. Ponder

  • Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.

    Zhifeng Jing;Chengwen Liu;Sara Y. Cheng;Rui Qi

  • Systematic improvement of a classical molecular model of water.

    Lee Ping Wang;Teresa Head-Gordon;Jay W. Ponder;Pengyu Ren

  • Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

    Dian Jiao;Christopher King;Alan Grossfield;Thomas A. Darden

  • Calculation of protein–ligand binding free energy by using a polarizable potential

    Dian Jiao;Pavel A. Golubkov;Thomas A. Darden;Pengyu Ren

  • AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

    Changsheng Zhang;Chao Lu;Zhifeng Jing;Chuanjie Wu

  • Classical electrostatics for biomolecular simulations.

    G. Andrés Cisneros;Mikko Karttunen;Pengyu Ren;Celeste Sagui

  • Temperature and Pressure Dependence of the AMOEBA Water Model

    Pengyu Ren;Jay W. Ponder

  • Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure.

    Jean Philip Piquemal;Lalith Perera;G. Andrés Cisneros;Pengyu Ren

  • Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

    Louis Lagardère;Luc-Henri Jolly;Filippo Lipparini;Félix Aviat

  • Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis.

    Changhao Wang;Peter H. Nguyen;Kevin Pham;Danielle Huynh

  • Virtual screening using molecular simulations

    Tianyi Yang;Johnny C. Wu;Chunli Yan;Yuanfeng Wang

  • Biomolecular electrostatics and solvation: a computational perspective.

    Pengyu Ren;Jaehun Chun;Dennis G. Thomas;Michael J. Schnieders

Frequent Co-Authors

Jean-Philip Piquemal
Jean-Philip Piquemal Sorbonne University
Yvon Maday
Yvon Maday Sorbonne University
Eric V. Anslyn
Eric V. Anslyn The University of Texas at Austin
Vijay S. Pande
Vijay S. Pande Stanford University
Ruhong Zhou
Ruhong Zhou Columbia University
Ray Luo
Ray Luo University of California, Irvine
John D. Chodera
John D. Chodera Memorial Sloan Kettering Cancer Center
Teresa Head-Gordon
Teresa Head-Gordon University of California, Berkeley
Nohad Gresh
Nohad Gresh Centre national de la recherche scientifique, CNRS
Robin R. Gutell
Robin R. Gutell The University of Texas at Austin

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