Lane Votapka, Ph.D.

Assistant Professor of Chemistry

Dr. Lane Votapka teaches physical chemistry and general chemistry at PLNU. He earned his B.S. in Biology at Point Loma Nazarene University, then obtained a Masters in Chemistry, followed by a PhD in Chemistry with a specialty in Computation at UC San Diego. After brief postdoctoral fellowship at Stony Brook University, Dr. Votapka came to Point Loma Nazarene University in the Fall of 2017. Dr. Votapka's major research areas involve developing new algorithms and software for computational methods as applied to molecular biophysics. These methods use biomolecular simulations for the analysis of bioprocesses and protein folding. Additionally, his research involves prediction of drug efficacy at the molecular level.

Education

  • Ph.D. - University of California, San Diego, Chemistry with a Specialization in Computation, 2015
  • M.S. - University of California, San Diego, Chemistry & Biochemistry, 2013
  • B.S. - Point Loma Nazarene University, High Honors, Biology, 2009

Courses Taught

  • General Chemistry I – CHE 152
  • General Chemistry I Lab – CHE 152L
  • General Chemistry II Lab - CHE 153L
  • Physical Chemistry I - CHE 325
  • Physical Chemistry I Lab - CHE 325L
  • Physical Chemistry II - CHE 326
  • Physical Chemistry II Lab - CHE 327

Experience in Field

  • Point Loma Nazarene University (San Diego, CA), Assistant Professor, 2017 - present. Department Chair: Dr. Sara Yu Choung. Description: Teaching of assigned undergraduate chemistry classes and labs. Participating in assigned faculty committees. Developing and overseeing a student research program.
  • Stony Brook University (Stony Brook, NY), Postdoctoral Researcher. Mentor: Dr. Ken Dill, 2016-2017 

  • University of California, San Diego (San Diego, CA). Graduate Research and Teaching Assistant, Advisor: Dr. Rommie Amaro, 2011-2015 
  • University of California, Irvine (Irvine, CA). Lab Assistant, Supervisor: Dr. Rommie Amaro, 2010-2011 Lab Assistant. 
  • The Scripps Translational Science Institute (San Diego, CA). Research Intern, Supervisor: Dr. Nik Schork, 2009-2010 
  • Point Loma Nazarene University (San Diego, CA). Undergraduate Researcher, Advisor: Dr. Mike Mooring, 2009.

Awards and Honors

  • UCSD Department of Chemistry and Biochemistry Outstanding Dissertation Award 2016.
  • Bruno Zimm Award for excellence in research 2015.
  • NSF Graduate Research Fellowship. Three year annual stipend, travel allowance 2013-2015.
  • XSEDE Cyberinfrastructure Startup Allocation. 50,000 SUs on Stampede supercomputer at Texas Advanced Computing Center 2014
  • NBCR Summer Institute 2012. Poster presentation: 2nd place. “DelEnsembleElec & FTProd: Open Source Tools for Computational Biophysics” 2012
  • National Track and Field Athletic All-American (2-time)
  • National Academic All-American (2-time)

Dissertations, Presentations, and Publications

  • Dissertation: "Numerical and Computational Solutions for Biochemical Kinetics, Druggability, and Simulation." Ph.D., 2015 (UC San Diego)
  • Votapka LW, Jagger BR, Heyneman AL, Amaro RE, "SEEKR: Simulation Enabled Estimation of Kinetic Rates, a Computational Tool to Estimate Molecular Kinetics and its Application to Trypsin-Benzamidine Binding" J. Phys. Chem. B, Klaus Schulten festschrift (2017)

  • Votapka LW, Lee CT, Amaro RE, "Two Relations to Estimate Membrane Permeability Using Milestoning" Journal of Physical Chemistry B, J. Andrew McCammon festschrift, (2016)

  • Votapka LW, "Numerical and Computational Solutions for Biochemical Kinetics, Druggability, and Simulation" Doctoral Dissertation, (2016)

  • Votapka LW and Amaro RE, "Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning” PLOS Computational Biology, (2015)
  • Boras BW, Hirakis SP Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD "Bridging Scales Through Multiscale Modeling: A Case Study on Protein Kinase A". Frontiers in Physiology, (2015)
  • Durrant JD, Votapka LW, Sørensen J, Amaro RE "POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics". Journal of Chemical Theory and Computation, (2014)
  • Van Wart AT, Durrant JD, Votapka LW, Amaro RE “Weighted Implementation of Suboptimal Paths (WISP): An optimized algorithm and tool for dynamical network analysis”. Journal of Chemical Theory and Computation, (2014)
  • Votapka LW, Amaro RE “Multistructural Hot Spot Characterization with FTProd”. BMC Bioinformatics, doi: 10.1093/bioinformatics/bts689. (2012)
  • Votapka LW, Demir Ö, Swift RV, Walker RC, Amaro RE “Variable ligand-and receptor-binding hot spots in key strains of influenza neuraminidase”. Journal of Molecular and Genetic Medicine (2012)
  • Votapka LW; Czapla L; Zhenirovskyy M; Amaro RE “DelEnsembleElec: Computing ensemble-averaged electrostatics using DelPhi”. Communications in Computational Physics. (2012)
  • Amaro RE; Swift RV; Votapka LW; Li WW; Walker RC; Bush R “Mechanism of 150-Cavity Formation in Influenza Neuraminidase”. Nature Communications. 2: 388 doi 10.1038/ncomss1390 (2011)

See More Presentations and Publications

  • 2018 -  "Numerical and Computational Solutions for Biochemical Kinetics, Druggability, and Simulation" Research synopsis given to PLNU physics majors
  • 2015 - "Numerical and Computational Solutions for Biochemical Kinetics, Druggability, and Simulation" Doctoral dissertation defense
  • 2015 - "Multiscale Estimation of Binding Kinetics using Molecular Dynamics, Brownian Dynamics, and Milestoning" Invited Speaker to Laufer Center at Stony Brook University
  • 2015 - "Solvent Fragment Mapping with FTProd and FTMAP" National Biomedical Computation Resource Summer Workshop
  • 2015 - "Multiscale Estimation of Binding Kinetics using Molecular Dynamics, Brownian Dynamics, and Milestoning" Snowmass Free Energy Calculation Workshop
  • 2014 - "Multiscale Estimation of Binding Kinetics using Molecular Dynamics, Brownian Dynamics, and Markov State Models" Brainstorming Workshop on Biological Molecules, Cells, and Beyond
  • 2014 - "SEEKR: Multiscale Estimation of Binding Kinetics using Molecular Dynamics, Brownian Dynamics, and Markov State Models" Seminar in Mathematics in Biochemistry/Biophysics
  • 2013 - "SEEKR: Multiscale Estimation of Binding Kinetics using MD, BD, and MSMs" Seminar. BDBDB3 Conference
  • 2012 - “FTProd” Seminar. National Biomedical Computation Resource Summer Institute
  • 2012 - “DelEnsembleElec & FTProd: Open Source Tools for Computational Biophysics” Poster Presentation. American Chemical Society National Meeting
  • 2009 - “The Influence of Gates on Space Use by Plains Bison.” Poster Presentation. West Coast Biological Sciences Undergraduate Research Conference.