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Dr. J. Nathan Scott

James Nathan Scott

Title: Assistant Professor
School: Sciences
Academic Department: Chemistry
Phone: 814-472-3995
E-mail: jscott@francis.edu
Office Location: Science Center 214


  • B.S., Louisiana Tech University ( Physics, summa cum laude)
  • Ph.D., University of Pennsylvania (Biochemistry and Biophysics)


Dr. Scott comes to Saint Francis from Montana State University in Bozeman, MT where he researched the photophysical properties of fluorescent proteins as a postdoctoral fellow. He conducted extensive undergraduate research in physics at Louisiana Tech University in areas as diverse as gravity wave physics, seismic analysis, solid state/materials physics, and high energy particle physics. Dr. Scott's graduate research at the University of Pennsylvania focused on experimental and theoretical investigations of the structure of water in biologically important contexts, as well as the nature of the hydrogen bond itself. As a graduate student he also worked as a teaching assistant in graduate level chemistry and biochemistry classes.

Dr. Scott has published in a number of peer-reviewed chemistry journals, and he has presented at seminars and conferences in Pennsylvania, California, Montana, Alabama, Louisiana, Massachusetts, and Belgium. He is a member of the Biophysical Society, the American Chemical Society, and the American Physical Society.



Scott, J.N.; Callis, P.R. MD+QM Investigations of the Length Scale and Forcefield Dependence of the Time Dependent Fluorescent Stokes Shift of Wild Type Staphylococcal Nuclease and Charge Mutants. Biophysical Journal (2015), 108(2) 622a.

Muiño, P.L.; Scott, J.N.; Callis, P.R. Fine-Grained Spatial and Temporal Resolution of Water and Protein Contributions to Ultra-Fast and Slower Fluorescence Shifts from MD + QM Simulations. Biophysical Journal 2014, 106(2) 205a.

Scott, J.N.; Callis, P.R. Insensitivity of Tryptophan Fluorescence to Local Charge Mutations. Journal of Physical Chemistry B 2013, 117 (33), 9598-605.

Scott, J.N.; Callis, P.R. MD+QM Calculations Explore the Origins of Differences Amongst the Red Fluorescent Proteins. Biophysical Journal (2013), 104(2) 684a.

Drobizhev, M.; Scott, J.N.; Callis, P.R.; Rebane, A. All-Optical Sensing of the Components of the Internal Local Electric Field in Proteins. IEEE Photonics Journal (2012), 4(5), 1996-2001.

 Drobizhev, M.; Hughes, T.E.; Stepanenko, Y.; Wnuk, P.; O'Donell, K.; Scott, J.N.; Callis, P.R.; Mikhaylov, A.; Dokken, L.; Rebane, A. Primary Role of the Chromophore Bond Length Alternation in Reversible Photoconversion of Red Fluorescence Proteins Nature Scientific Reports (2012), 2(688).

Drobizhev, M.; Hughes, T.E.; Rebane, A.; Davis, B.; Topol, I.; Scott, J.N.; Callis, P.R. Unified Description Of Optical Properties and Photostability Of Fluorescent Proteins By Means Of The Chromophore-Protein Electrostatic Interactions. Biophysical Journal (2012), 102(3) 403-4a.

Scott, J.N.; Callis, P.R. MD Simulations Reveal Ultrafast Dielectric Compensation By Water Of Large Stokes Shifts From Charged Groups In Staphylococcal Nuclease. Biophysical Journal (2012), 102(3) 734a.

 Scott, J. Nathan; Vanderkooi, Jane M. Evidence of a Structural Defect in Ice VII and the Side Chain Dependent Response of Small Model Peptides to Increased Pressure. Applied Spectroscopy (2011), 65(7), 756-64.

 Scott, J. Nathan; Vanderkooi, Jane M. A New Hydrogen Bond Angle/Distance Potential Energy Surface of the Quantum Water Dimer. WATER: A Multidisciplinary Online Journal (2010), Volume 2.

 Vorobyev, Dmitriy Yu.; Kuo, Chun-Hung; Kuroda, Daniel G.; Scott, J. Nathan; Vanderkooi, Jane M.; Hochstrasser, Robin M. Water Induced Relaxation of a Degenerate Vibration of

 Guanidinium Using 2D IR Echo Sectroscopy. Journal of Physical Chemistry B (2010), 114(8), 2944-53.

 Vorobyev, Dmitriy Yu.; Kuo, Chun-Hung; Chen, Jian-Xin; Kuroda, Daniel G.; Scott, J. Nathan; Vanderkooi, Jane M.; Hochstrasser, Robin M. Ultrafast Vibrational Spectroscopy of a Degenerate Mode of Guanidinium Chloride. Journal of Physical Chemistry B (2009), 113(46), 15382-91.

 Scott, J. Nathan; Nucci, Nathaniel V.; Vanderkooi, Jane M. Changes in Water Structure Induced by the Guanidinium Cation and Implications for Protein Denaturation. Journal of Physical Chemistry A (2008), 112(43), 10939-48.

 Nucci, Nathaniel V.; Scott, J. Nathan; Vanderkooi, Jane M. Coupling of Complex Aromatic Ring Vibrations to Solvent Through Hydrogen Bonds: Effect of Varied On-Ring and Off-Ring Hydrogen-Bonding Substitutions. Journal of Physical Chemistry B (2008), 112(13), 4022-4035.




  • SCI 101: Science for Active Citizenship
  • CHEM 101: Chemistry Principles I
  • CHEM 103: Human Chemistry I
  • CHEM 104: Human Chemistry II
  • CHEM 104L: Human Chemistry II Lab
  • CHEM 102L General Chemistry II Lab
  • CORE 113: The Future
  • CHEM 301: Physical Chemistry I
  • CHEM 301L/PHYS 301L: Physical Chemistry I Lab
  • CHEM 302L/PHYS 302L: Physical Chemistry II Lab
  • CHEM 251: Quantitative Chemical Analysis

Summer Workshops

  • 2013 Green Chemistry, Biodiesel Production and Testing
  • 2014 Investigations into Protein Chemistry
Research Interests

Dr. Scott's research interests are as varied as his background is diverse. He is currently investigating the optical properties of a class of proteins known as red fluorescent proteins. These proteins are ubiquitous in modern biochemistry, used world wide for a huge variety of purposes, but the physical and dynamic properties that differentiate them are very poorly understood. Dr. Scott employs modern dynamic simulation techniques and quantum chemical methods to elucidate the optical and physical properties of these proteins using the NSF-sponsored XSEDE system of computational resources, primarily the Gordon and Comet supercomputers at the San Diego Supercomputing Center.

Dr. Scott also maintains an interest in water structure, particularly water structure in unusual or extreme contexts, such as at extremely high pressures or temperatures. His interest in this area is motivated by the goal of understanding the physical limits to life as we know it with respect to intensive quantities such as pressure and temperature. Dr. Scott has used a Diamond Anvil Cell (DAC) to investigate condensed phase systems at pressures of over 70,000 atmospheres and biological systems across a wide range of temperatures and pressures using spectroscopic techniques. He is also interested in biomolecular structure and dynamics, and is currently using solution FTIR to study the side chain dependence of backbone dynamics in small model dipeptides while varying temperature, solvent viscosity, and confinement through the use of reverse micelles.

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