Jason Wagoner
Junior Laufer Fellow
Laufer Center for Physical and Quantiative Biology
Stony Brook University
Stony Brook, NY 11790
jason.wagoner at stonybrook.edu


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Research Interests

My scientific interests can be broadly defined as the study of chemical/biological problems using the perspective and tools drawn from chemical physics and statistical mechanics.  At the moment, this has been realized in the following ways: 

Statistical mechanics and simulation methods:  Theoretical methods provide an extremely useful complement to experimental studies, but the extension of such tools to greater length- and time-scales will depend on our ability to develop new simulation and sampling methods.  I'm particularly interested in the subset of new algorithms emerging from nonequilibrium statistical mechanics.  See publications for more information. 

Molecular assembly:  Molecular assembly occurs via the self-organization of molecules into complex, stable structures.  Broadly speaking, this is realized in protein aggregation, pharmaceutical crystallization, biomineralization, and many other molecular processes.  Theory has the ability to clarify the mechanistic details of such processes, but is currently limited by the demands of sampling such high-dimensional systems and the contraints of constant-particle simulations.  I hope to apply new multiscale simulation methods (see below) to the study of these problems.  This approach has the technical advantage of a reduced system and the scientific advantages provided by a fluctuating number of particles:  using grand canonical methods, the local densities of molecular components can be relaxed with respect to the evolving chemical environment. 

Multiscale modeling:  The focus of my Ph.D. work was on the development and application of a hybrid explicit/implicit solvent model.  This model demonstrates three significant benefits:

  • A finite domain.  With an implementation of new boundary methods, this model demonstrates the ability to significantly reduce the number of degrees of freedom explicitly simulated while reproducing solute thermodynamic and kinetic properties exactly (within statistical error).
  • Adjustable boundaries that shrink and expand with response to an evolving solute configuration.  The algorithms that update the system boundary are based on new applications of nonequilibrium statistical mechanics.  A movie of a simple application can be found here.
  • Grand Canonical control.  The particular nature of our boundary methods circumvent problems of insertion/deletion algorithms, which have thus far been prohibitively inefficient for simulations in dense media.  This provides potential application to problems of assembly, aggregation, and crystallization. A simple example of micelle formation can be found here.

The proof of concept for this model has been worked out on a relatively simple, coarse-grained, water model (based on the MARTINI forcefield).  Our current methods are demonstrating promise in extending to fixed charge water models and QM/MM simulations.  In the future, we hope to expand applicability to polarizable forcefields. 


My CV can be downloaded here.


Ph.D. Chemistry, Stanford University, 2012 (advisor Vijay Pande)

B.S. magna cum laude Biomedical Engineering and Chemistry (dual major) with a minor in Mathematics, Washington University in St. Louis, 2006

Research Experience

Junior Laufer Fellow, Stony Brook University, 2013-present

  • Research on (1) Predicting ligand binding affinities; (2) Membrane protein structure prediction; (3) Multiscale simulation methods; and (4) Protein aggregation.

Postdoctoral research with Vijay S. Pande, Stanford University, 2012-2013

  • Developed hybrid explicit-implicit solvent methods with a focus on extending transferability and applicability for a wide range of solvent models.  Applied this model to various problems in biomolecular simulation including ionic equilibria, role of solvent kinetics in protein folding, and biomolecular assembly.

Graduate research with Vijay S. Pande, Stanford University, 2006-2012

  • Developed and applied hybrid explicit-implicit solvent methods with a focus on (1) reproducing
    solute properties from full explicit solvent methods within statistical accuracy, and (2) developing new algorithms that dynamically alter the simulation domain with respect to an evolving solute configuration. 

Undergraduate research with Nathan A. Baker, Washington University in St. Louis, 2002-2006

  • Developed and tested new implicit solvent methods.

Teaching Experience

Teaching Assistant, Department of Chemistry, Stanford University, 2006-2010

  • Administrator, instructor for discussion sections, and guest lecturer for undergraduate and graduate chemistry courses.

Tutor for A+ Home Tutors, 2007-2008

Cornerstone Mentor, Washington University in St. Louis, 2005-2006

Honors and Awards

  • National Science Foundation Graduate Research Fellowship, 2008-2011
  • Department of Energy Computational Science Graduate Fellowship, 2008 (declined)
  • AHMB Biomedical Engineering Honor Society, 2006-present
  • Tau Beta Pi Engineering Honor Society, 2005-present
  • NIH Summer Undergraduate Research Fellowship, 2004
  • HHMI Summer Undergraduate Research Fellowship, 2003
  • Calvin M. Woodward Scholar, 2002-2006
  • Robert C. Byrd Scholarship, 2002-2006
  • James R. Hoffa Memorial Scholarship, 2002-2006
  • Missouri Bright Flight Scholar, 2002-2006
  • National Merit Scholar, 2002


My google citations page maintains an updated list of publications

  1. Wagoner JA and Baker NA, Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. J Comput Chem 25 (13), 1623-1629, 2004 PubMed

  2. Wagoner JA and Baker, NA, Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA 103 (22), 8331-8336, 2006 PubMed

  3. Swanson JMJ, Wagoner JA, Baker NA, and McCammon JA, Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions. J Chem Theory Comput 3, 170-184, 2007 J Chem Theory Comput

  4. Dong F, Wagoner JA, and Baker NA, Assessing the performance of implicit solvation models at a nucleic acid surface Phys Chem Chem Phys 10, 4889-4902, 2008 PubMed

  5. Wagoner JA and Pande VS, A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent. J Chem Phys 134 (21), 214103, 2011 PubMed

  6. Wagoner JA and Pande VS,  Reducing the effect of Metropolization on mixing times in molecular dynamics simulationsJ Chem Phys 137  (21), 214105, 2012 PubMed

  7. Wagoner JA and Pande VS, Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets. J Chem Phys 139  (23), 234114, 2013 PubMed

  8. Wagoner JA and Pande VS,  Molecular simulations of varying domain size: A nonequilibrium exploration of adaptive boundaries in hybrid solvent models.  to be submitted