papers | scholar | code | che@ur | book | class | talk

research	deep learning, molecular dynamics, molecular design, ar/vr
pi	@andrewwhite01 in chem eng
phd	@gandhi_heta, @GWellawatte, @ZiyueYang37, @SamCox822, @MehradAnsari, shane michtavy, wei zhu
postdoc	@_navneeth_
contact	andrew.white@rochester.edu
acknowledgements	nsf che #1764415, nsf cbet #1751471, nsf iis #2029095, nsf dmr #2103553, nih #R35GM137966

🧪.🐕 | ⚗️💤 | ⚡ | 🥳⚗️ | 🥳🧮

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papers

1. Ansari, M., Soriano-Paños, D., Ghoshal, G. & White, A. D. Inferring spatial source of disease outbreaks using maximum entropy. arXiv preprint arXiv:2110.03846 (2021).
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2. Zhu, W., White, A. & Luo, J. Federated learning of molecular properties in a heterogeneous setting. arXiv preprint arXiv:2109.07258 (2021).
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3. Hocky, G. M. & White, A. D. Natural language processing models that automate programming will transform chemistry research and teaching. arXiv preprint arXiv:2108.13360 (2021).
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4. Ansari, M., Gandhi, H. A., Foster, D. G. & White, A. D. Iterative symbolic regression for learning transport equations. arXiv preprint arXiv:2108.03293 (2021).
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5. Wellawatte, G. P., Seshadri, A. & White, A. D. Model agnostic generation of counterfactual explanations for molecules. (2021).
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6. Gandhi, H. A. & White, A. D. City-wide modeling of vehicle-to-grid economics to understand effects of battery performance. ACS Sustainable Chemistry & Engineering (2021).
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7. Yang, Z., Chakraborty, M. & White, A. D. Predicting chemical shifts with graph neural networks. Chemical Science (2021).
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8. Barrett, R., Ansari, M., Ghoshal, G. & White, A. D. Simulation-based inference with approximately correct parameters via maximum entropy. arXiv preprint arXiv:2104.09668 (2021).
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9. Barrett, R. & White, A. D. Investigating active learning and meta-learning for iterative peptide design. Journal of chemical information and modeling 61, 95–105 (2020).
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10. Gandhi, H. A., Jakymiw, S., Barrett, R., Mahaseth, H. & White, A. D. Real-time interactive simulation and visualization of organic molecules. (2020).
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11. Amirkulova, D. B., Chakraborty, M. & White, A. D. Experimentally consistent simulation of aβ21–30 peptides with a minimal NMR bias. The Journal of Physical Chemistry B 124, 8266–8277 (2020).
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12. Barrett, R., Chakraborty, M., Amirkulova, D., Gandhi, H., Wellawatte, G. & White, A. Hoomd-tf: Gpu-accelerated, online machine learning in the hoomd-blue molecular dynamics engine. Journal of Open Source Software 5, (2020).
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13. Tang, J., Zhang, Y., Luehmann, A. & White, A. Augmented reality improved learning of lower-level students by empowering their participation in collaborative activities. (2020).
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14. Li, Z., Wellawatte, G. P., Chakraborty, M., Gandhi, H. A., Xu, C. & White, A. D. Graph neural network based coarse-grained mapping prediction. Chemical science 11, 9524–9531 (2020).
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15. Chakraborty, M., Ziatdinov, M., Dyck, O., Jesse, S., White, A. & Kalinin, S. V. Reconstruction of the interatomic forces from dynamic scanning transmission electron microscopy data. Journal of Applied Physics 127, 224301 (2020).
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16. Chakraborty, M., Xu, J. & White, A. D. Is preservation of symmetry necessary for coarse-graining? Physical Chemistry Chemical Physics 22, 14998–15005 (2020).
17. Bonomi, M. Promoting transparency and reproducibility in enhanced molecular simulations. Nature methods 16, 670–673 (2019).
18. Amirkulova, D. B. & White, A. D. Recent advances in maximum entropy biasing techniques for molecular dynamics. Molecular Simulation 45, 1285–1294 (2019).
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19. Barrett, R., Gandhi, H. A., Naganathan, A., Daniels, D., Zhang, Y., Onwunaka, C., Luehmann, A. & White, A. D. Social and tactile mixed reality increases student engagement in undergraduate lab activities. Journal of Chemical Education 95, 1755–1762 (2018).
20. Barrett, R., Jiang, S. & White, A. D. Classifying antimicrobial and multifunctional peptides with bayesian network models. Peptide Science 110, e24079 (2018).
21. Chakraborty, M., Xu, C. & White, A. D. Encoding and selecting coarse-grain mapping operators with hierarchical graphs. The Journal of chemical physics 149, 134106 (2018).
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22. Amirkulova, D. B. & White, A. D. Combining enhanced sampling with experiment-directed simulation of the GYG peptide. Journal of Theoretical and Computational Chemistry 17, 1840007 (2018).
23. Mayes, H. B., Lee, S., White, A. D., Voth, G. A. & Swanson, J. M. Multiscale kinetic modeling reveals an ensemble of cl–/h+ exchange pathways in ClC-ec1 antiporter. Journal of the American Chemical Society 140, 1793–1804 (2018).
24. Freeman, G. M., Drennen, T. E. & White, A. D. Can parked cars and carbon taxes create a profit? The economics of vehicle-to-grid energy storage for peak reduction. Energy Policy 106, 183–190 (2017).
25. White, A. D., Knight, C., Hocky, G. M. & Voth, G. A. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data. The Journal of chemical physics 146, 041102 (2017).
26. Dannenhoffer-Lafage, T., White, A. D. & Voth, G. A. A direct method for incorporating experimental data into multiscale coarse-grained models. Journal of chemical theory and computation 12, 2144–2153 (2016).
27. White, A. D., Dama, J. F. & Voth, G. A. Designing free energy surfaces that match experimental data with metadynamics. Journal of chemical theory and computation 11, 2451–2460 (2015).
28. White, A. D. & Voth, G. A. Efficient and minimal method to bias molecular simulations with experimental data. Journal of chemical theory and computation 10, 3023–3030 (2014).
29. Mi, L., White, A. D., Shao, Q., Setlow, P., Li, Y. & Jiang, S. Chemical insights into dodecylamine spore lethal germination. Chemical Science 5, 3320–3324 (2014).
30. Nowinski, A. K., White, A. D., Keefe, A. J. & Jiang, S. Biologically inspired stealth peptide-capped gold nanoparticles. Langmuir 30, 1864–1870 (2014).
31. Shao, Q., White, A. D. & Jiang, S. Difference of carboxybetaine and oligo (ethylene glycol) moieties in altering hydrophobic interactions: A molecular simulation study. The Journal of Physical Chemistry B 118, 189–194 (2014).
32. White, A. D., Keefe, A. J., Ella-Menye, J.-R., Nowinski, A. K., Shao, Q., Pfaendtner, J. & Jiang, S. Free energy of solvated salt bridges: A simulation and experimental study. The Journal of Physical Chemistry B 117, 7254–7259 (2013).
33. Keefe, A. J., Caldwell, K. B., Nowinski, A. K., White, A. D., Thakkar, A. & Jiang, S. Screening nonspecific interactions of peptides without background interference. Biomaterials 34, 1871–1877 (2013).
34. White, A. D., Huang, W. & Jiang, S. Role of nonspecific interactions in molecular chaperones through model-based bioinformatics. Biophysical Journal 103, 2484–2491 (2012).
35. Brault, N. D., White, A. D., Taylor, A. D., Yu, Q. & Jiang, S. A directly functionalizable surface platform for protein arrays in undiluted human blood plasma. Analytical Chemistry 85, 1447–1453 (2013).
36. White, A. D., Keefe, A. J., Nowinski, A. K., Shao, Q., Caldwell, K. & Jiang, S. Standardizing and simplifying analysis of peptide library data. Journal of chemical information and modeling 53, 493–499 (2013).
37. Shao, Q., He, Y., White, A. D. & Jiang, S. Different effects of zwitterion and ethylene glycol on proteins. The Journal of chemical physics 136, 06B607 (2012).
38. White, A. D., Nowinski, A. K., Huang, W., Keefe, A. J., Sun, F. & Jiang, S. Decoding nonspecific interactions from nature. Chemical Science 3, 3488–3494 (2012).
39. White, A. & Jiang, S. Local and bulk hydration of zwitterionic glycine and its analogues through molecular simulations. The Journal of Physical Chemistry B 115, 660–667 (2011).
40. Nowinski, A. K., Sun, F., White, A. D., Keefe, A. J. & Jiang, S. Sequence, structure, and function of peptide self-assembled monolayers. Journal of the American Chemical Society 134, 6000–6005 (2012).
41. Shao, Q., He, Y., White, A. D. & Jiang, S. Difference in hydration between carboxybetaine and sulfobetaine. The Journal of Physical Chemistry B 114, 16625–16631 (2010).
42. Yang, W., Zhang, L., Wang, S., White, A. D. & Jiang, S. Functionalizable and ultra stable nanoparticles coated with zwitterionic poly (carboxybetaine) in undiluted blood serum. Biomaterials 30, 5617–5621 (2009).