Education⌗

March 2018 Ph.D. in Physical Chemistry, University of North Texas Dissertation: Computational Simulations of Cancer and Disease-Related Enzymatic Systems using Molecular Dynamics and Combined Quantum Methods September 2013-August 2016 Ph.D. Candidate in Physical Chemistry, Wayne State University May 2011 B.S. in Chemistry with distinction, University of Michigan-Dearborn

Awards and Honors⌗

Promise in COMP Award, 258th ACS National Meeting, San Diego, CA (2019) Robert Wade Brown Award, University of North Texas (2018) Chemical Computing Group Excellence Award, 255th ACS National Meeting, New Orleans, LA (2018) American Society for Mass Spectrometry Sanibel Conference Travel Award, St. Petersburg, FL (2018) Award for Best Poster, 6th EU-US Conference on Repair of Endogenous DNA Damage, University of Udine (2017) College of Science Travel Grant, University of North Texas (2017) Ed and Julie Hodges Memorial Scholarship, University of North Texas (2017) ANTON Molecular Dynamics Simulations Computing Award, PSCA15038 (2015) Chemistry-Biology Interface (CBI) Fellowship, Chemistry Division (2015-16) Honor Citation for Teaching Services in Chemistry, Wayne State University (2013) Chancellor’s Scholarship, University of Michigan-Dearborn (2005-9) Honor’s Program, University of Michigan-Dearborn (2005-11)

Research & Professional Experience⌗

+:———————————————————————+ | Postdoctoral Scholar at Stanford Linear Accelerator Lab/Stanford | | University (Stanford, CA), May 2018-Present | +———————————————————————-+ | Adviser: Prof. Todd J. Martínez | | | | - Simulated the initial steps of the previously unknown mechanism | | for fatty acid photodecarboxylase. | | | | - Collaborated with time-resolved single photon spectroscopy | | experiments to explain the excited state mechanism of pyranine, | | a weak photoacid, in aprotic solvent and water. | | | | - Heading an interdisciplinary collaboration of crystallography, | | spectroscopy and theory groups to characterize effect of | | mutations on quantum yield for red fluorescent proteins. | | | | - Simulating the excited state mechanism of green fluorescent | | protein variant rsEGFP2 to determine the effect of crystal | | packing with ab initio multiple spawning. | | | | - Correlating ring strain in ICH ralstonia to allosteric networks | | and reaction mechanism from high-resolution crystal structures. | +———————————————————————-+ | | +———————————————————————-+ | Graduate Research Assistant at University of North Texas | | (Denton, TX), Sept. 2016-May 2018 | +———————————————————————-+ | Graduate Research Assistant at Wayne State University (Detroit, | | MI), Sept. 2013-August 2016 | +———————————————————————-+ | Adviser: Prof. G. Andrés Cisneros | +———————————————————————-+ | | +———————————————————————-+ | Analytical Chemist at RTI Laboratories (Livonia, MI), Sept. | | 2011-May 2013 | +———————————————————————-+ | | +———————————————————————-+ | Undergraduate Research at University of Michigan-Dearborn | | (Dearborn, MI), June 2009-Nov. 2010 | +———————————————————————-+ | Adviser: Prof. Daniel B. Lawson | +———————————————————————-+

Peer Reviewed Publications⌗

10. Joseph E. Thomaz*, [Alice R. Walker]{.ul}*, Stephen J. Van Wyck, Jan Meisner, Todd J. Martínez, and Michael D. Fayer. Proton transfer dynamics in the aprotic proton accepting solvent 1-methylimidazole. The Journal of Physical Chemistry B, 2020. https://doi.org/10.1021/acs.jpcb.0c05525 9.
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          Manuscripts in preparation:

$\bullet$ [Alice R. Walker]{.ul}, Erik Vasquez Montelongo, and G. Andrés Cisneros. “Computational investigation of the rate-limiting step of dsDNA dealkylase AlkBH2 with AMOEBA/QMMM.” $\bullet$ [Alice R. Walker]{.ul}, T.J. Lane, Henry van den Bedem and Todd J. Martínez. “Theoretical insights into the excitation mechanism of fatty acid photodecarboxylase.” $\bullet$ [Alice R. Walker]{.ul}, Chey Jones, Nanna List, and Todd J. Martínez. " Simulations of crystal structure packing effect on green fluorescent protein variant isomerization." $\bullet$ Elisa Pieri*, [Alice R. Walker]{.ul}*, Todd J. Martínez. “Computational study of relationship between quantum yield, structure and energy of red fluorescent protein variants.”

Teaching and Mentoring Experience⌗

+:———————————————————————+ | Quantum Molecular Design Summer School | | Instructor at Stanford | | University (Stanford, CA), August 2019 | +———————————————————————-+ | Designed a curriculum for an interdisciplinary group of graduate | | students and postdoctoral researchers to explore how to structure | | theory-experiment collaborations in the context of excited state | | QM/MM simulations of proteins. | | | | - Taught and created a curriculum in the context of a hands-on | | tutorial to explore the excited state dynamics of photoactive | | yellow protein in explicit solvent. | | | | - Organized and facilitated a set of relevant lectures from | | graduate students and postdocs. | | | | Protein Subgroup Leader, Martínez Group at Stanford University | | (Stanford, CA) June 2018-present | +———————————————————————-+ | Leader for protein related research in the Martinez group. Act as a | | research coordinator and prepare monthly targeted meetings for group | | members working on simulations of photoswitchable and fluorescent | | proteins, including discussion of relevant computational techniques | | and presentations of current work. | | | | BUILD Program Coordinator and Lecturer at Wayne State University | | (Detroit, MI), July 2015/July 2016 | +———————————————————————-+ | Co-created and co-implemented, with another graduate student, a | | two-week chemistry curriculum aimed at advancing and supporting | | incoming underrepresented minority undergraduate students majoring | | in scientific fields. | | | | - Lessons focused on active learning, integration of laboratory | | and interactive lecture, and completion of a group oral | | presentation on literature research. | | | | - BUILD is part of an interdisciplinary program at multiple local | | universities, and funded by the NIH. | +———————————————————————-+ | Graduate Teaching Assistant at Wayne State University (Detroit, | | MI), Sept. 2013-Aug. 2015 | +———————————————————————-+ | Assisted with teaching for Chemistry Skills and Reasoning, General | | Chemistry I Laboratory, General Chemistry II: Analytical Chemistry, | | and General Chemistry II: Analytical Chemistry Laboratory. | +———————————————————————-+ | Student Teacher at Southfield-Lathrup High School (Southfield, | | MI), Jan. 2011-April 2011 | +———————————————————————-+ | Created and implemented consistent lesson plans throughout the | | semester for four chemistry classes and one English class, as well | | as a variety of classroom materials and activities for students, | | including demonstrations and laboratories. | +———————————————————————-+

Highlighted Presentations⌗

15. “Awarded Long Talk for Outstanding Lightning Talk: Simulations of crystal structure packing effect on green fluorescent protein variant isomerization.” Alice R. Walker, Chey Jones, Nanna List, Todd J. Martínez. Talk. Virtual Conference on Theoretical Chemistry, July 2020. 14. “Mechanistic insights into photodecarboxylation of fatty acids from classical and QM/MM simulations.” Alice R. Walker, T.J. Lane, Henry van den Bedem, Todd J. Martínez. Talk. Division of Computers in Chemistry: Women Make COMP, 258th ACS National Meeting, San Diego, CA. August 26, 2019. 13. “Mechanistic insights into photodecarboxylation of fatty acids from classical and QM/MM simulations.” Alice R. Walker, T.J. Lane, Henry van den Bedem, Todd J. Martínez. Talk. Northern California Theoretical Chemistry Meeting, Berkeley, CA. May 19, 2019. 12. “Mechanistic insights into photodecarboxylation of fatty acids from classical and QM/MM simulations.” Alice R. Walker, T.J. Lane, Henry van den Bedem, Todd J. Martínez. Poster. D. E. Shaw Research Graduate and Postdoc Women’s Forum, New York, NY. May 9, 2019. 11. “Effects of a single point mutation and mismatched base on DNA polymerase III holoenzyme proofreading.” Alice R. Walker, Hailey Gahlon, David Rueda, G. Andrés Cisneros. Talk. Division of Computers in Chemistry: Insights into Structure, Function, Dynamics & Evolution of Enzymatic Mechanisms from Computational Simulation, 255th ACS National Meeting, New Orleans, LA. March 20, 2018. 10. “Unfolding of hen egg white lysozyme in high alcohol solutions: Insights from molecular dynamics and IMS-MS.” Alice R. Walker, Daniel W. Woodall, Ellen Inutan, Nikhil Baddam, G. Andrés Cisneros, Sarah Trimpin. Poster. Division of Computers in Chemistry Poster Session, 255th ACS National Meeting, New Orleans, LA. March 20, 2018. 9. “Hot Topic Talk: Unfolding of hen egg white lysozyme in high alcohol solutions: Insights from molecular dynamics and IMS-MS.” Alice R. Walker, Daniel W. Woodall, Ellen Inutan, Nikhil Baddam, G. Andrés Cisneros, Sarah Trimpin. Talk and Poster. 30th ASMS Sanibel Conference on Mass Spectrometry, St Petersburg, FL. January 27, 2018. 8. “ALKBH7 variant related to prostate cancer exhibits altered substrate binding.” Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert H. Podolsky, Gregory Dyson, Robert P. Hausinger, G. Andrés Cisneros. Poster. 6th EU-US Conference on Repair of Endogenous DNA Damage, University of Udine, Udine, Italy. September 26/27, 2017. 7. “ALKBH7 variant related to prostate cancer exhibits altered substrate binding.” Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert H. Podolsky, Gregory Dyson, Robert P. Hausinger, G. Andrés Cisneros. Poster. Division of Computers in Chemistry Poster Session, 253rd ACS National Meeting, San Francisco, CA. April 4, 2017. 6. “ALKBH7 variant related to prostate cancer exhibits altered substrate binding.” Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert H. Podolsky, Gregory Dyson, Robert P. Hausinger, G. Andrés Cisneros. Poster. Graduate Student Research Symposium, Texas Women’s University, Denton, TX. March 31, 2017. 5. “GPU-enabled binding free energy calculations of potential ligands for pancreatic cancer imaging.” Alice R. Walker, Robin Bonomi, Juri Gelovani, G. Andrés Cisneros. Poster. Division of Computers in Chemistry Poster Session, 251st ACS National Meeting, San Diego, CA. March 16, 2016. 4. “Computational studies on potential PET imaging ligands for Galectin-3 in pancreatic cancer tumors.” Alice R. Walker, Robin Bonomi, Juri Gelovani, G. Andrés Cisneros. Poster. Division of Computers in Chemistry Poster Session, 250th ACS National Meeting, Boston, MA. August 18, 2015. 3. “Computational Studies on Potential Ligands for Imaging Cancer Tumors and Examination of Dealkylation Mechanism of AlkBH2.” Alice R. Walker, G. Andrés Cisneros. Talk. Second year seminar at Wayne State University. February 25, 2015. 2. “Computational Studies of Inhibitors for Galectin-3.” Alice R. Walker, G. Andrés Cisneros. Poster. Wayne State University 16th Annual Chemistry Graduate Research Symposium, Detroit, MI. October 11 2014. 1. “Binding of Ethene to Carbon Nanotubes.” Alice R. Walker, Daniel B. Lawson. Talk. 20th Annual Argonne Undergraduate Research Symposium, Argonne, IL. November 13, 2009.

Service⌗

divSTEM Mentorship Group Leader (July 2020-present) Facilitating the mentorship wing of the Martínez lab diversity outreach initiative with regular meetings, literature review and actively participating in mentorship opportunities at Stanford. Physical Chemistry Faculty Hiring Committee, at University of North Texas (Spring 2018) UNT Chemistry Graduate Social Group, at University of North Texas (January 2016-April 2018) Phoenix Mentoring Project, Mentor (June 2007-June 2010) Women in Learning and Leadership, Member (2005-2011)

Professional Organizations & Development⌗

Association for Women in Science (November 2018-present) Software Summer School at Virginia Tech (June 2015) NVDIA CUDA qwiklabs (April 2015) American Chemical Society, Member (January 2015-present) AGEP Seminar Series (January 2015-September 2016) STEM Pedagogy Seminar Series (September 2014-September 2016) BEST Professional Development Program (September 2014-September 2016)

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