Biosciences Graduate Program

Michael J. Schnieders, PhD

Portrait

Assistant Professor
Assistant Professor of Biochemistry
Assistant Professor of Biomedical Engineering

Contact Information

Primary Office: 4-516 Bowen Science Building
Iowa City, IA 52242
Primary Office Phone: 319-335-7891

Office: 5013 Seamans Center for the Engineering Arts and Sciences
Iowa City, IA 52242

Lab: 4-508 Bowen Science Building
Iowa City, IA 52242
Phone: 319-335-6723

Email: michael-schnieders@uiowa.edu
Web: Schnieders Laboratory
Web: Biomedical Engineering Department Profile
Web: Force Field X Software

Education

BS, Biomedical Engineering with High Distinction, The University of Iowa, Iowa City, IA
PhD, Biomedical Engineering, Washington University in St. Louis, St. Louis, MO

Post Doctoral, Chemistry, Stanford University, Stanford, CA
Post Doctoral, Biomedical Engineering, The University of Texas, Austin, TX

Education/Training Program Affiliations

Biosciences Graduate Program
Department of Biochemistry PhD

Research Summary

Our lab is focused on molecular biophysics theory and high performance computational algorithms that are needed to reduce the time and cost of engineering drugs and organic biomaterials. A complementary goal is to help open the door to personalized medicine by developing tools to map genetic information onto molecular phenotypes.

1. Next Generation Macromolecular X-ray Crystallography X-ray crystallography is a critical experimental method used by biochemists to determine the structure and function of the biomolecular foundations of medicine. We have recently demonstrated that the chemical information contained in a polarizable force field called AMOBEA significantly improves DNA and protein structures compared to X-ray refinements done with previous generation theory. We are now working to model experimental X-ray diffraction data as an ensemble using Bayesian inference.

2. Prediction of the Structure, Thermodynamics and Solubility of Drug Tablets Important unsolved problems for the engineering of organic biomaterials include prediction of their structure, thermodynamic stability and solubility from first principles. Solubility is the saturating concentration of a molecule within a liquid solvent, where the physical process consists of solvated molecules in equilibrium with their solid phase. We have developed the first consistent procedure for the prediction of the structure, thermodynamic stability, and solubility of organic crystals using molecular dynamics simulations. Currently the methodology is being extended to predict the properties for a range of organic crystals, including both pharmaceuticals and peptide models of neurological aggregation diseases.

3. Personalized Medicine: From Genome Sequencing to Molecular Phenotypes Since 2001, the cost to sequence a patient’s genome has fallen from $100 million to approximately $1,000. The rapid achievement of affordable genetic information is outpacing our ability to fully capitalize on opportunities to provide personalized healthcare. To help address this challenge, we are collaborating with The University of Iowa Center for Bioinformatics and Computational Biology to develop tools that tightly couple bioinformatics to the computational prediction of biomolecular structure, thermodynamics and kinetics.

4. Biomolecular Electrostatics and High-Performance Computing Application such as X-ray crystallography refinement, biomaterials thermodynamics and personalized medicine depend on an accurate, efficient description of molecular energetics. Our lab contributes a parallelized molecular biophysics computer code called Force Field X that includes novel biomolecular electrostatics algorithms such as particle-mesh Ewald with support for space group symmetry and the generalized Kirkwood implicit solvent model.

Center, Program and Institute Affiliations

Center for Biocatalysis and Bioprocessing
Center for Bioinformatics and Computational Biology
Iowa Initiative in Human Genetics
Stephen A. Wynn Institute for Vision Research

Selected Publications

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Park J, Nessler I, McClain B, Macikenas D, Baltrusaitis J, Schnieders M.  Absolute Organic Crystal Thermodynamics: Growth of the Asymmetric Unit into a Crystal via Alchemy.  Journal of Chemical Theory and Computation.  2014 May 20. 10(7):2781–2791.
[Link]

Lipparini F, Lagardère L, Stamm B, Cancès E, Schnieders M, Ren P, Maday Y, Piquemal J.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations.  Journal of Chemical Theory and Computation.  2014 February 28. 10(4):1638–1651.
[Link]

Shi Y, Schnieders M, Piquemal J, Ren P.  Polarizable Force Fields for Biomolecular Modeling.  Reviews in Computational Chemistry.  2014. 28.
[Link]

Schnieders M, Baltrusaitis J, Shi Y, Chattree G, Zheng L, Yang W, Ren P.  The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.  Journal of Chemical Theory and Computation.  2012 May. 8(5):1721-1736.
[Link]

Schnieders M, Kaoud T, Yan C, Dalby K, Ren P.  Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases.  Current Pharmaceutical Design.  2012. 18(9):1173-1185.
[Link]

Fenn T, Schnieders M.  Polarizable atomic multipole X-ray refinement: weighting schemes for macromolecular diffraction.  Acta Crystallographica Section D.  2011 November. 67(11):957-965.
[Link]

Schnieders M, Fenn T, Pande V.  Polarizable atomic multipole X-ray refinement: Particle mesh Ewald electrostatics for macromolecular crystals.  Journal of Chemical Theory and Computation.  2011 March 9. 7(4):1141-1156.
[Link]

Schnieders M, Fenn T, Pande V, Brunger A.  Polarizable atomic multipole X-ray refinement: application to peptide crystals.  Acta Crystallographica Section D.  2009 September. 65(9):952-965.
[Link]

Schnieders M, Ponder J.  Polarizable atomic multipole solutes in a generalized Kirkwood continuum.  Journal of Chemical Theory and Computation.  2007 October 18. 3(6):2083-2097.
[Link]

Schnieders M, Baker N, Ren P, Ponder J.  Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.  The Journal of Chemical Physics.  2007 March. 126(12):124114.
[Link]

Date Last Modified: 08/25/2014 - 16:25:05