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Niel M. Henriksen home.chpc.utah.edu/nmhenriksen Contact Information Department of Medicinal Chemistry 30 South 2000 East, Rm 307 Salt Lake City, UT 84112 801.232.6272 nhenriksen@ucsd.edu
Biographical Information Birth Date: February 7, 1984 Citizenship: U.S. Citizen Birth Place: Eugene, Oregon Family: Married with one child
Education PhD student, Medicinal Chemistry Department, University of Utah, 2007-present B.S. Biochemistry, Walla Walla University, 2003-2007
Awards and Scholarships American Foundation for Pharmaceutical Education Pre-Doctoral Fellowship, 2012 Peter Salamon Award for Young Scientists, Telluride Science Research Center, 2011 Eccles College of Pharmacy Fellowship, University of Utah, 2008 Graduated Magna Cum Laude, 3.90 GPA, Walla Walla University, 2007 Chemistry Departmental Merit Scholarship, Walla Walla University, 2005 and 2006 Distinguished Deans List, Walla Walla University, 2003-2007 Entrance Awards in Chemistry and Physics, Walla Walla University, 2003 SAT/ACT and GPA Achievement Scholarship, Walla Walla University, 2003 Advanced Placement Scholar with Distinction, Walla Walla University, 2003
Peer Reviewed Publications Henriksen NM, Davis DR, and Cheatham TE 3rd. “Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations.” (in preparation). Henriksen NM, Roe DR, and Cheatham TE 3rd. “Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.” The Journal of Physical Chemistry B. Just Accepted Manuscript. Henriksen NM, Davis DR, Cheatham TE 3rd. “Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.” Journal of Biomolecular NMR. 2012, 53:321-339 Lin Z, Flores M, Forteza I, Henriksen NM, Concepcion GP, Rosenberg G, Haygood MG, Olivera BM, Light AR, Cheatham TE 3rd, and Schmidt EW. “Totopotensamides, Polyketide-Cyclic Peptide Hybrids from a Mollusk-Associated Bacterium Streptomyces sp.” Journal of Natural Products. 2012, 75:644-649 Wei X, Henriksen NM, Skalicky JJ, Harper MK, Cheatham TE 3rd, Ireland CM, and Van Wagoner RM. “Araiosamines A-D: Tris-bromoindole Cyclic Guanidine Alkaloids from the Marine Sponge Clathria (Thalysias) araiosa.” The Journal of Organic Chemistry. 2011, 76:5515-5523.
Conference Presentations and Research Highlights Projects in Scientific Computing (Publication), Pittsburg Supercomputing Center, 2012 “Force Field of the Sugar Pucker” ACS National Meeting, San Diego, 2012 “Simultaneous fitting of RNA torsion parameters to a large QM/MM dataset” Alma Mater Presentation, Walla Walla University, 2011 “Isaac Newton’s Structural Biology: Exploring the Limits of Molecular Dynamics Simulations” Telluride Science Research Center: RNA Dynamics, 2011 (Invited) “Molecular Dynamics of RNA … or Working With A Broken Tool” Teragrid 2011 Conference, Salt Lake City, Utah, 2011 “RNA Structure Refinement and Force Field Evaluation Using Molecular Dynamics Simulations” AIChE Annual Meeting, Salt Lake City, Utah, 2010 “MD Simulations On Two RNA Hairpins: Restrained Consensus and Unrestrained Failures.” HHMI Summer Undergraduate Research Symposium , Oregon State University, 2006 “The Identification and Characterization of the Cardioactive Principals in Hawthorn Extract.”
Leadership Positions Student Advisory Committee Member, College of Pharmacy, University of Utah, 2010 Teaching Assistant, Physiological Chemistry, College of Pharmacy, University of Utah, 2009 Student Co-Director of Recruiting, Biological Chemistry Program, University of Utah, 2009
Research Experience PhD Thesis Research with mentor Thomas E. Cheatham III, University of Utah. 2008-present Research on biomolecular structure and function using molecular dynamics simulations. Laboratory Rotations during the first year of PhD program, University of Utah. 2007-2008 Mentors: Eric Schmidt, David Jones, Jon Rainier, Michael Kay, and Thomas Cheatham (7 weeks each). Undergraduate Research Internship with mentor Phil Proteau, Oregon State University. 2006 (summer) Isolation and identification of cardioactive compounds in Hawthorn Extract. Funded by the HHMI.
Technical Skills and Experience Extensive use of biomolecular simulation methods in the AMBER software package. Experience in conventional MD, replica exchange, thermodynamic integration, umbrella sampling/PMF, accelerated MD, NMR refinement, implicit solvation, force field development, and simulation analysis. Quantum mechanical calculations.using Gaussian, NWChem, and GAMESS. Experience in geometry optimizations, vibrational analysis, and single point calculations using HF, DFT, and MP2 methods in conjunction with various solvent models. Frequent user of XSEDE computational resources and high performance computing clusters. Experience in proposal drafts, software installation, bundled execution, GPU nodes, and troubleshooting. Frequent user on University of Utah CHPC clusters as well as the following XSEDE systems: Queenbee, Ranger, Kraken, Lonestar, Gordon, Keeneland, Blacklight, and Stampede. Experience with data analysis scripting and HPC code modifications. Skilled in scripting, including MPI execution, using Perl and shell. Experience with modifications to the AMBER Fortran90 high performance computing code.
Mentorship and Community Student Mentor for the Juan Diego Catholic High School Summer Research Program, 2010 (summer) Guided a high school student through an eight week summer research project. Career Lecture Series Presentation, Channing Hall Elementary School, Kindergarten, 2008 “What do scientists do?” Designed a presentation and activity for kindergarteners.
Employment History Science Tutor, Teaching and Learning Center, Walla Walla University, 2005-2007 Duties: provide individualized instruction in general chemistry, organic chemistry, physics, and biology. Laboratory TA, General Chemistry and Organic Chemistry, Walla Walla University, 2004-2007 Duties: reagent preparation, instruction and supervision, grading laboratory exercises. Laboratory Assistant, Forrest Paint Company, Eugene, Oregon, 2004, 2005, (summers) Duties: Evaluation of experimental products, quality control, production tasks..
Faculty References Thomas Cheatham, Associate Professor, Department of Medicinal Chemistry 307 Skaggs Hall, 30 South 2000 East Salt Lake City, UT 84112-5820 801.587.9652 tec3@utah.edu
Darrell Davis, Professor and Chair, Department of Medicinal Chemistry 307 Skaggs Hall 30 South 2000 East Salt Lake City, UT 84112-5820 801.581.7006 darrell.davis@utah.edu
Kuberan Balagurunathan, Associate Professor, Department of Medicinal Chemistry 307 Skaggs Hall 30 South 2000 East Salt Lake City, UT 84112-5820 801.587.9474 kuby.balagurunathan@utah.edu
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“Tango.” Abstract representation of conformational clustering. |