Welcome to the Sun Lab


Postdoctoral Scholars

We invite applications for two postdoctoral scholars:

One postdoctoral scholar is to investigate the decomposition mechanisms of energetic molecules and the hypergolic processes of ionic liquids. The work is supported by the Department of Defense and involves close collaboration with experiments supervised by Dr. Ralf Kaiser (www.uhmreactiondynamics.org). Successful applicants should have a strong background in one or more of the following: quantum chemistry, nonadiabatic dynamics, and molecular dynamics.

The other postdoctoral scholar is to investigate the passive permeation of peptide through lipid bilayers in the presence of permeation enhancers. The work is supported by Eli Lilly and Company (https://www.lilly.com/partners/research-award-program). Successful applicants should have a strong background in one or more of the following: molecular dynamics, enhanced sampling, and statistical mechanics.

Graduate Students and Undergraduate Researchers

If you are interested in conducting graduate/undergraduate research in our group, please contact Prof. Rui Sun (ruisun@hawaii.edu) with a letter of interest.


2023 Jan, National award to advance peptide drug development

2022 Aug, Menthol in e-cigs could hurt lungs, UH research finds

2022 May, Board of Regents honors faculty for excellence in research

2022 Apr, Celebrating UH Mānoa’s outstanding faculty, staff and students

2022 Feb, Faster chemical reaction simulations to aid environment, health, more

2022 Jan, How to fix your scientific coding errors

2021 Aug, Environmentally friendly space fuel research gets $550K boost

2021 Jun, $600K grant supports national defense through energetic material development

2020 Dec, Researchers reliant on high-performance computing get big boost

2020 Aug, Deep-space discovery debunks decades-old belief

2020 Feb, Students dive into high-performance computing

2019 Oct, UH team finds glitch that could affect more than 100 scientific studies

2019 Oct, NMR prediction glitch found and fixed

2019 Oct, Bad computer code jeopardizes results of 100 academic studies

2019 Oct, A code glitch may have caused errors in more than 100 published studies

We Model Chemistry and Biophysics

Computational modeling and simulations can provide important information on the mechanisms, dynamics, and kinetics of chemical and biophysical processes by following the motion of the system at a microscopic level. The research in our group focuses on developing novel computational methodologies and applying them to tackle outstanding chemical and biophysical challenges to human well-being.

An example: ab initio methods compute energies and molecular orbitals

Ab initio (Latin for "from first principles") quantum chemistry methods attempt to describe chemical systems by solving the Schrodinger equation. This quantum mechanical foundation has enabled computational chemists to calculate and predict properties such as energies and molecular orbitals. Below is an example of molecular orbitals of an Iridium organometallic complex.

Current Projects

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Simulations of Biological Membranes

Cellular membranes consist of mixed collections of lipids, steroids, and membrane proteins. The compositional heterogeneity, along with the morphology the of cellular membranes has been shown to be essential for the regulation of cellular activity through membrane-protein interactions.

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Machine Learning

Simulations with Active Learning

Direct dynamics (DD) simulations of chemical reactions reveal their complicated dynamics at atomistic level, elucidates discoveries from experiments that are nonintuitive. In DD, the interactions between atoms are calculated on-the-fly with ab initio methods and their positions are propagated iteratively.

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Drug Discovery

Permeation of Small Molecule Drugs

We are developing innovative molecular dynamics simulation protocols of assessing intestinal permeability of small molecule drug. This protocol employs the state of art enhanced sampling method to compute a multidimensional free energy surface of the permeation, and a novel statistical model to measure the diffusivity of the drug on this surface.

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Reaction Dynamics

Dynamics of Gas-Phase Reactions

Direct dynamics simulations of chemical reactions in gas phase have shown great success in revealing their complicated dynamics at atomistic level, elucidating discoveries from experiments that are nonintuitive, and predicting behaviors of chemical reactions whose conditions are difficult to realize.

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Rui Sun, PhD

Principal Investigator

Rui Sun received his B.S. degree in Chemistry in 2009 from Shandong University in China. He received his Ph.D. in Chemistry from Texas Tech University in 2014, working with Dr. William L. Hase on studying gas phase reactions mechanism and solvent effect in condensed phase reaction with ab initio molecular dynamics simulation.

Mrinmoy Mandal


Mrinmoy completed his PhD in Chemistry from Banaras Hindu University, India, where he worked on the bimolecular collision reactions and photodissocia dynamics. Before joining the Dr. Sun's group, he worked as a post-doc fellow at SCNU, China from May 2019 to December 2021. Currently, he is working on QM/MM dynamics.

Komal Yadav


Komal completed her Masters degree in Chemistry from Central University of Punjab, India in 2017 and received her PhD in Chemistry in 2022 from NISER Bhubaneswar, India. During her PhD, she worked on studying the stabilization of planar tetracoordinated centers and the mechanisms and dynamics of chemical reactions using different electronic structure methods and ab initio classical dynamics simulation technique.

Kazuumi Fujioka

Graduate student

My name is Kazuumi Fujioka. I am working towards a PhD in Chemistry. I like programming and chemistry, I suppose. Physics is also interesting. Right now I'm interested in machine learning applications for computational chemistry. My current project incorporates machine learning into molecular dynamics for efficiency gains.

Yuheng Luo

Graduate student

I am currently working toward a Ph.D. in Chemistry. My interests include quantum chemistry calculations and ab initio molecular dynamics simulations. My current projects: DFT NMR calculations for natural products, TD-DFT CD calculations for natural products, AIMD sumations for HBr+ + CO2, AIMD simuations for H2S + CH and AIMD simuations for C4H3 + CH.

Christopher Kang

Gradusate student

I am pursuing a masters degreee in chemistry. I currently work on Large-scale molecular dynaamics simulations for biological membranes (vesicles in particular), Interactions between lung surfactant and small organic compounds found in electronic cigarette vapor, and a neuronal protein named alpha synuclein.

Allen Vincent

Graduate student

I received a Bachelor of Science degree in Chemistry from St. Xavier's College, Mumbai, India (2011-2014) and a Master of Science degree in General Chemistry from Vellore Institute of Technology, Vellore, India (2014-2016). I am interested in Gas phase/Condensed phase Molecular Dynamics and Electronic structure theory calculations. My hobbies include reading, hiking, photography and amateur astronomy.

Mabel Bernaldez

Graduate student

I have a BS in Biochemistry from Chaminade University of Honolulu (2016-2020), and I am currently pursuing a PhD in Chemistry. I am open to learning more about the different applications in computational chemistry. Hobbies include anything creative and gacha games.

Rafael de la Zerda

Graduate Student

I'm a PhD student in chemistry with a master's in data science and a BS in marine science and chemistry, both from the University of Miami. I'm primarily interested in computational biophysics as applied to pharmaceutical drug design. My focus is on molecular dynamics simulations of cell membrane permeation. My hobbies include programming, snorkeling, and piano - mostly jazz.

Sohee Choi

Graduate Student

I received my Bachelor's degree in chemistry from the University of Illinois at Urbana-Champaign (UIUC) and my Master's degree in Bioinorganic chemistry from the University of San Francisco. My research interests include bioinorganic chemistry, medicinal chemistry, and computational chemistry. I am excited to expand my knowledge/skills in computational chemistry and apply them to my future research. In my free time, I enjoy exploring the outdoors and going on hikes with my dog.

Brandon Loi

Undergraduate Student

I graduated with a BS in Biochemistry at UH Manoa this past semester and am aiming to get into medical school in the future. I am currently working on a project which will help lower computation costs while still obtaining accurate data by predicting molecular dynamics with machine learning.

Ju-ling Chen

Undergraduate Student

I am originally from Japan and came to Hawaii to pursue B.S. in Biochemistry from University of Hawaii at Manoa. I have always enjoyed studying chemistry and biology, as well as human physiology! I am currently modeling the paracellular permeation of small molecules through tight junctions. After graduation, I plan to attend medical school in hopes of becoming a physician.


  • Airi Morita, UHM Undergraduate Student (BS Biochemistry)
  • Eric Lam, UHM Undergraduate Student (BS Computer Science, Chemistry)
  • Mizuki Ebihara, UHM Undergraduate Student (BS Biochemistry)
  • Pamela Toh, UHM Undergraduate Student (BS Biochemistry, Psychology)
  • Jackson Hornung, UHM Undergraduate Student (BS Chemistry)
  • Casie Kubota, UHM Undergraduate Student (BS Biochemistry)
  • Keiko Shimoji-Lentz, UHM Undergraduate Student (BA Biochemistry)


    Google Scholar
    $ denotes equal contribution to the publication; * denotes correspond author(s)

    In Revision

  1. Ab Initio Molecular Dynamics Benchmarking Study of Machine-Learned Potential Energy Surfaces for the HBr+ + HCl Reaction
  2. K Fujioka, E Lam, B Loi, R Sun,* Submitted

  3. Electron-Induced Decomposition of Solid 1,1-Diamino-2,2-Dinitroethylene (FOX-7) at Cryogenic Temperatures
  4. A Turner, J Marks, Y Luo, J Lechner, T Klapotke,* R Sun,* K Ralf,* Submitted

  5. Catalytic Asymmetric Metal Enolate Nazarov Cyclization - Vicinal Quaternary All-Carbon Atom Stereocenters
  6. C Dickinson, K Fujioka, R Sun, G Yap, M Tius,* Submitted

  7. The Dynamics of a Highly Curved Membrane Revealed by All-atom Molecular Dynamics Simulation of a Full-scale Vesicle
  8. C Kang,$ K Fujioka,$ R Sun,* Submitted


  9. Anti-inflammatory Quinoline Alkaloids from the Roots of Waltheria indica
  10. F Liu, S Mallick, T O'Donnell, E Park, S Kovacs, K Nakamura, A Dave, Y Luo, R Sun, M Wall, S Wongwiwatthananukit, D Silva, P Williams, J Pezzuto, L Chang,* Journal Natural Product, 86, 276 (2023)

  11. Unraveling the Initial Steps of the Ignition Chemistry of the Hypergolic Ionic Liquid 1-ethyl-3-methylimidazolium Cyanoborohydride ([EMIM][CBH]) with Nitric Acid (HNO3) Exploiting Chirped Pulse Triggered Droplet Merging
  12. S Biswas, I Antonov, K Fujioka, G. Rizzo, S. Chambreau, S Schneider, R Sun,* R Kaiser,* Physical Chemistry Chemical Physics, 25, 6602 (2023)

  13. Ion Molecule Reactions in the HBr+ + HCl (DCl) System : A Combined Experimental and Theoretical Study
  14. D Plamper,$ K Fujioka,$ S Schmidt,$ R Sun,* KM Weitzel,* Physical Chemistry Chemical Physics, 25, 2629 (2023)

  15. Unsupervised Reaction Pathways Search for the Oxidation of Hypergolic Ionic Liquids - 1-Ethyl-3-Methylimidazolium Cyanoborohydride (EMIM+/CBH-) as a Case Study
  16. K Fujioka, R Kaiser, R Sun,* Journal of Physical Chemistry A, 127, 913 (2023)


  17. The Potential Energy Profile of the Decomposition of 1,1-Diamino-2,2-dinitroethylene (FOX-7) in Gas Phase
  18. Y Luo, C Kang, R Kaiser, R Sun,* Physical Chemistry Chemical Physics, 24, 26836 (2022)

  19. Directed Gas Phase Preparation of Ethynylallene (CH2CCHCCH; X1A’) via the Crossed Molecular Beam Reaction of the Methylidyne Radical (CH; X2Π) with Vinylacetylene (H2CCHCCH; X1A’)
  20. C He, Z Yang, S Doddipatla, A Thomas, R Kaiser,* G Galimova, A Mebel,* K Fujioka, R Sun,* Physical Chemistry Chemical Physics, 24, 26499 (2022)

  21. Gas-Phase Formation of Silicon Monoxide via Non-Adiabatic Reaction Dynamics and its Role as a Building Block of Interstellar Silicates
  22. H Chao,$ Y Luo,$ S Doddipatla, Z Yang, T Millar, R Sun,* R Kaiser,* Physical Chemistry Chemical Physics, 24, 19761 (2022)

  23. Exploring the Photochemistry of Solid 1,1-Diamino-2,2-dinitroethylene (FOX-7) Spanning Simple Bond Ruptures, Nitro-to-Nitrite Isomerization, and Non-Adiabatic Dynamics
  24. A Turner,$ Y Luo,$ J Marks, R Sun,* J Lechner, T Klapotke,* R Kaiser,* Journal of Physical Chemistry A, 126, 4747 (2022)

  25. Menthol in Electronic Cigarettes Causes Biophysical Inhibition of Pulmonary Surfactant
  26. L Xu, Y Yang, J Simien, C Kang, E Haglund, R Sun, Y Zuo,* American Journal of Physiology, 323, 165, (2022)

  27. Coumarinolignans with Reactive Oxygen Species (ROS) and NF-kB Inhibitory Activities from the Roots of Waltheria indica
  28. F Liu, S Mallick, T O'Donnell, R Rouzimaimaiti, Y Luo, Rui Sun, M Wall, S Wongwiwatthananukit, A Date, D Silva, P Williams, L Chang,* Molecules, 27, 3270 (2022)

  29. Spirovetivane- and Eudesmane-type Sesquiterpenoids Isolated from the Culture Media of Two Cyanobacterial Strains
  30. T Donnell, Y Luo, W Yoshida, S Suzuki, R Sun, P Williams,* Journal of Natural Products, 2, 415 (2022)

  31. Interpolating Moving Ridge Regression (IMRR): A Machine Learning Algorithm to Predict Energy Gradients for ab initio Molecular Dynamics
  32. K Fujioka, R Sun,* Chemical Physics, 557, 111482, (2022)

  33. The Potential Energy Surface of the HCl + HBr+ Bimolecular Collision
  34. K Fujioka, KM Weitzel, R Sun,* Journal of Physical Chemistry A, 126, 1465, (2022)

  35. Biophysical Properties of Tear Film Lipid Layer II. Polymorphism of FAHFA
  36. X Xu, C Kang, R Sun, Y Zuo,* Biophysical Journal, 121, 451 (2022)

  37. A Chemical Dynamics Study of the Reaction of the Methylidyne Radical (CH) with Dimethylacetylene (CH3CCCH3)
  38. C He,$ K Fujioka,$ A Nikolayev,$ L Zhao, S Doddipatla, V Azyazov, A Mebel,* R Sun,* R Kaiser,* Physical Chemistry Chemical Physics, 24, 578 (2022)


  39. Assessing the Intestinal Permeability of Small Molecule Drugs via Diffusion Motion on a Multi-dimensional Free Energy Surface
  40. A Shoji, C Kang, K Fujioka, J Rose, R Sun,* Journal of Chemical Theory and Computation, 18, 503 (2021)

  41. A Chemical Dynamics Study of the HCl + HCl+ Reaction
  42. Y Luo, T Kreuscher, C Kang, W Hase, KM Weitzel,* R Sun,* International Journal of Mass Spectrometry, 462, 116515 (2021)

  43. Molecular Dynamics Study of the Interaction between the N-terminal of α-Synuclein and a Lipid Bilayer Mimicking Synaptic Vesicles
  44. C Kang, R Sun,* The Journal of Physical Chemistry B, 125, 1036 (2021)


  45. A Chemical Dynamics Study on the Gas-phase Formation of Triplet and Singlet C5H2 Carbenes
  46. C He,$ G Galimova,$ Y Luo,$ L Zhao, A Eckhardt, R Sun,* A Mebel,* R Kaiser,* Proceedings of the National Academy of Sciences, 117, 30142 (2020)

  47. A Chemical Theoretical Study of the Dynamics of the HBr+ + CO2 → HOCO+ + Br Reaction
  48. Y Luo, K Fujioka, A Shoji, WL Hase, KM Weitzel, Rui Sun,* The Journal of Physical Chemistry A, 124, 9119 (2020)

  49. A Chemical Dynamics Study on the Gas Phase Formation of Thioformaldehyde (H2CS) and its Elusive Thiohydroxy-Carbene Isomer (HCSH)
  50. S Doddipatla, C He, R Kaiser,* Y Luo, R Sun,* G Galimova, A Mebel,* T Millar,* Proceedings of the National Academy of Sciences, 117, 22712 (2020)

  51. 6-Deoxy- and 11-Hydroxy-Tolypodiols: Meroterpenoids from the Cyanobacterium HT-58-2
  52. J Gurr, T O'Donnell, Y Luo, W Yoshida, M Hall, A Mayer, R Sun, P Williams,* Journal of Natural Products, 83, 1691 (2020)


  53. Correlation between the Velocity Scattering Angle and Product Relative Translational Energy for SN2 Reactions. Comparison of Experiments and Direct Dynamics Simulations.
  54. J Xie, J Zhang, R Sun, R Wester, W Hase,* International Journal of Mass Spectrometry, 438, 115 (2019)

  55. Characterization of Leptazolines A-D, Polar Oxazolines from the Cyanobacterium Leptolyngbya sp., Reveals a Glitch with the "Willoughby-Hoye" Scripts for Calculating NMR Chemical Shifts
  56. J Neupane, R Neupane, Y Luo, W Yoshida, R Sun, P Williams,* Organic Letters, 21, 8449 (2019)

  57. Membrane Permeation of the Amphipathic Toxin Mycolactone: Insights from Atomistic versus Coarse-Grained MARTINI simulations
  58. F Aydin, R Sun, JMJ Swanson,* Biophysical Journal 117, 87 (2019)
    (PDF) (Supporting Material)

  59. Theoretical Study of the Potential Energy Profile of the HBr+ + CO2 → HOCO+ + Br Reaction.
  60. A Shoji, D Schanzenbach, R Merrill, J Zhang, L Yang, R Sun,* The Journal of Physical Chemistry A, 123, 9791 (2019)


  61. Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants
  62. R Sun, Y Han, JMJ Swanson, JS Tan, JP Rose, GA Voth,* The Journal of Chemical Physics 149, 072310 (2018)


  63. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics
  64. R Sun, O Sode, JF Dama, GA Voth,* Journal of Chemical Theory and Computation 13, 2332 (2017)

  65. Indirect Dynamics in SN2@N: Insight into the Influence of Central Atoms
  66. X Liu, C Zhao, L Yang,* J Zhang,* R Sun, Physical Chemistry Chemical Physics 19, 22691 (2017)


  67. Transition-tempered Metadynamics is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes
  68. R Sun, JF Dama, JS Tan, JP Rose, GA Voth. Journal of Chemical Theory and Computation 12, 5157 (2016)

  69. Theoretical Studies on F- + NH2Cl Reaction: Nucleophilic Substitution at Neutral Nitrogen
  70. X Liu, J Zhang, L Yang, R Sun. The Journal of Physical Chemistry A 120, 3740 (2016)


  71. Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust on-the-fly Bias Domain Restriction
  72. JF Dama, GM Hocky, R Sun, GA Voth. Journal of Chemical Theory and Computation 11, 5638 (2015)

  73. Potential Energy Surfaces for the HBr+ + CO2 → HOCO+ + Br reaction in the HBr+ 2Π3/2 and 2Π1/2 spin-orbit states
  74. R Sun, G Granucci, AK Paul, M Siebert, HJ Liang, G Cheong, WL Hase, M Persico. The Journal of Chemical Physics 142, 104302 (2015)

  75. The F- + CH3I → FCH3 + I- Entrance Channel Potential Energy Surface: Comparison of Electronic Structure Methods
  76. R Sun, J Xie, J Zhang, WL Hase. International Journal of Mass Spectrometry 377, 222 (2015)

  77. Direct Dynamics Simulation of Dissociation of the [CH3--I--OH]- Ion-Molecule Complex
  78. J Xie, M McClellan, R Sun, SC Kohale, N Govind, WL Hase. The Journal of Physical Chemistry A 119, 817 (2015)

  79. Comparison of Direct Dynamics Simulations with Different Electronic Structure Methods. F-+ CH3I with MP2 and DFT/B97-1
  80. R Sun, CJ Davda, J Zhang, WL Hase. Physical Chemistry Chemical Physics 17, 2589 (2015)


  81. A Unified Model for Simulating Liquid and Gas Phase, Intermolecular Energy Transfer: N2 + C6F6 Collisions
  82. AK Paul, SC Kohale, S Pratihar, R Sun, SW North, WL Hase. The Journal of Chemical Physics 140, 194103 (2014)

  83. Direct Dynamics Simulation of the Activation and Dissociation of 1,5-dinitrobiuret (HDNB)
  84. R Sun, MR Siebert, L Xu, SD Chambreau, GL Vaghjiani, H Lischka, J Liu, WL Hase. The Journal of Physical Chemistry A 118, 2228 (2014)

  85. The VENUS/NWChem Software Package. Tight Coupling Between Chemical Dynamics Simulations and Electronic Structure Theory
  86. U Lourderaj, R Sun, SC Kohale, GL Barnes, WA de Jong, TL Windus, WL Hase. Computer Physics Communications 185, 1074 (2014)


  87. Models for Intrinsic Non-RRKM Dynamics. Decomposition of the SN2 Intermediate [Cl--CH3Br]-
  88. M Paranjothy, R Sun, AK Paul, WL Hase. Zeitschrift fur Physikalische Chemie 227, 1361 (2013)

  89. Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl Methylphosphonate (DMMP)/TiO2 (110) Intermolecular Interaction
  90. L Yang, D Tunega, L Xu, N Govind, R Sun, R Taylor, H Lischka, WA DeJong, WL Hase. The Journal of Physical Chemistry C 117, 17613 (2013)

  91. Direct Chemical Dynamics Simulations: Coupling of Classical and Quasiclassical Trajectories with Electronic Structure Theory
  92. M Paranjothy, R Sun, Y Zhuang, WL Hase. Wiley Interdisciplinary Reviews: Computational Molecular Science 3, 296 (2013)

  93. Direct Dynamics Simulations of the Product Channels and Atomistic Mechanisms for the OH- + CH2I Reaction. Comparison with Experiment
  94. J Xie, R Sun, MR Siebert, R Otto, R Wester, WL Hase. The Journal of Physical Chemistry A 117, 7162 (2013)

  95. Simulation Studies of the Cl- + CH3I SN2 Nucleophilic Substitution Reaction: Comparison with Ion Imaging Experiments
  96. J Zhang, U Lourderaj, R Sun, J Mikosch, R Wester, WL Hase. The Journal of Chemical Physics 138, 114309.(2013)

  97. Indirect Dynamics in a Highly Exoergic Substitution Reaction
  98. J Mikosch, J Zhang, S Trippel, C Eichhorn, R Otto, R Sun, WA De Jong, WL Hase, R Wester. Journal of the American Chemical Society 135, 4250 (2013)


  99. Direct Dynamics Simulation of Dioxetane Formation and Decomposition via the Singlet .O-O-CH2-CH2. Biradical: Non-RRKM Dynamics
  100. R Sun, K Park, WA De Jong, H Lischka, TL Windus, WL Hase. The Journal of Chemical Physics 137, 044305 (2012)

  101. Direct Dynamics Determination of the Reaction Pathways for Decomposition of the Cross-linked Epoxy Resin Constituent CH3NHCHCHCH3
  102. L Yang, R Sun, WL Hase. Computational and Theoretical Chemistry 990, 62 (2012)

  103. Gas-phase Chemical Dynamics Simulations on the Bifurcating Pathway of the Pimaradienyl Cation Rearrangement: role of Enzymatic Steering in Abietic Acid Biosynthesis
  104. MR Siebert, P Manikandan, R Sun, DJ Tantillo, WL Hase. Journal of Chemical Theory and Computation 8, 1212 (2012)


  105. Use of Direct Dynamics Simulations to Determine Unimolecular Reaction Paths and Arrhenius Parameters for Large Molecules
  106. L Yang, R Sun, WL Hase. Journal of Chemical Theory and Computation 7, 3478 (2011)