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Bioenergy & Defense

Susan Rempe, Ph.D.


Biographical Information - News - R&D 100 Award Videos - Symposium Speakers - Current Research Projects - Publications
Photo of Susan Rempe

Distinguished Member of the Technical Staff
Sandia National Laboratories
Department of Nanobiology
Center for Biological & Engineering Sciences

PO Box 5800
Albuquerque, NM 87185-1315
(505) 845-0253
slrempe@sandia.gov

Research Interests

Biomolecular structure-dynamics-function relationships

Membranes for selective transport

Ion channels

Enzyme-ligand binding & catalysis

Solvation & transport theory

Ab initio simulations


Biographical Information

Dr. Susan Rempe is a Distinguished Member of the Technical Staff at Sandia National Labs in Albuquerque, NM. She also holds Adjunct and Research Professor positions in Biology and Chemical and Biological Engineering at the University of New Mexico. She earned her Ph.D. in physical chemistry from the University of Washington working with Dr. Robert O. Watts on the theory of vibrational spectroscopy applied to force field development for molecular simulations. As a graduate student, she helped develop UW's first computational chemistry course, which won an educational prize from the Department of Energy. She earned B.A. degrees from Columbia University, in pre-medical sciences with concentrations in history and German literature, and U of Montana in chemistry. As an undergraduate, she studied the famous BZ oscillating chemical reaction in collaboration with Dr. Richard J. Field and funded by an undergraduate research grant from the NSF. During her postdoctoral fellowship at Los Alamos National Lab, she worked with Dr. Lawrence Pratt and Dr. Tony Redondo on a new theoretical framework for studying liquid state properties. Her current work focuses on theoretical studies and molecular simulations of solutions, polymers, and biomolecules. In addition to expanding our basic science understanding, insights from those studies inform synthesis of new materials for water purification, energy storage, and gas (CO2) separations.


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News

2016

CO2 Memzyme™ on the front page of the ABQ Journal: "Environmental game-changer"

News releases on CO2 Memzyme™: Sandia, Phys.org, ClimateNewsNetwork, Innovation Magazine

Dr. Rempe chairs the biennial Telluride Science Research Center Workshop on "Ions in Solution: Energy, Biology, and Environment" with Drs. Lawrence Pratt and Tom Beck

Dr. Rempe elected vice-chair of the Permeation and Transport sub-group of the Biophysical Society

Invited mini-review of hydrophobic interactions ACS Editor's Choice (J. Phys. Chem. B)

Invited articles to Bruce Garrett Festschrift published (J. Phys. Checm. B vol. 120)

U.S. patent issued "Biomimetic membranes"

U.S. patent issued "Enzymatically active high selectivity gas-permeable membranes"

New funding received from DTRA

Welcome to Prof. Lawrence Pratt on his sabbatical!

Congratulations to Dr. Juan Vanegas on his new position at U. of Vermont!


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R&D 100 Award & Other Videos

Nano-stabilized enzymatic membrane for CO2 capture

Biomimetic membranes for water purification

Statistical Analyses of Hydrophobic Interactions


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Symposium Speakers

Poul Petersen, Dept. of Chemistry and Chemical Biology, Cornell U., March 2017.

Tom Davis, “Electrodialysis - its capabilities and ways it can be improved,” Dept. of Civil Engineering, UT El Paso, November 2016.

Rob Coalson, “A Polymer Brush Model of the Nuclear Pore Complex (NPC),” Dept. of Chemistry, Pittsburgh University, November 2016.

John Weeks, “Solvation, structure, and scaling in models for simple and complex mixtures,” Dept. of Chemistry, UMD College Park, November 2016.

Jana Shen, "Mechanisms of pH-responsive biomaterials: from fatty acid, polysaccharide to enzyme and membrane transporter," Dept. of Pharma. Sciences, UMD School of Pharmacy, June 2016.

Oliver Beckstein, "Structure and function of sodium/proton antiporter membrane proteins," Arizona State U, April 2016.

Alex Wlodawer, "Structural studies of medically-interesting protease inhibitors and lectins," NIH, National Cancer Institute, March 2016.

Jessica Seeliger, "The making of a pathogen: the what, where and how of mycobacterial membrane biogenesis," Stony Brook U, December 2015.

Thomas Cheatham, "Molecular dynamics simulation of nucleic acids: Convergence, reproducibility, assessment/validation, and data dissemination enabled by XSEDE and Blue Waters," School of Pharm., University of Utah, May, 2014.

Doug Tobias, "Ions at the air-water and membrane-water interfaces," University of California, Irvine, May, 2014.

Luis Cuello, "A structurally driven kinetic cycle for potassium channels," December, Texas Tech U, Health Sciences Center, December 2013.

Steve Lockless, "Creating robust selectivity during K+ ion transport," Department of Biology, Texas A&M U, October 2013.

Mangesh Chaudhari, Tulane U, July 2013.

Juan Vanegas, Spain, July 2013.

Alan Soper, UK, September 2012.

Ed Moczydlowski, "Mutations in functional KcsA channels." Chair, Dept of Biology, Clarkson U, December 2009.

George Reiter, "Coherent proton motion in water confined in carbon nanotubes and on surfaces." Dept of Physics, U of Houston, August, 2009.

James van Etten, "Unusual lifestyle of giant algal viruses." Dept of Plant Pathology, U of Nebraska, May 2009.

Dian Jiao, "Ion modeling and ligand-protein simulation with polarizable force fields." Dept of Biomedical Engineering, UT Austin, May 2009.

Arjun Narayanan, "Study of local and global conformational changes induced by phosphorylation using all-atom computation." CA Institute for Quantitative Biosciences, UCSF, May 2009.

David Rogers, "Using Bayes' theorem for free energy calculations." Dept of Chemistry, U of Cincinnati, April 2009.

Hakan Gunaydin, "Accurate computation of enzymatic rate enhancement." Dept of Chem and Biochem, UCLA, February 2009.

Sergei Sukharev, "Mechanosensitive channels." Dept of Biology, U Maryland, January 2009.

Sony Joseph, "Toward ion channel based nanofluidic devices: Simulations of water and electrolyte transport in nanotubes and channels." Dept of Comp Micro/Nanotech, UIUC, January 2009.

Tianyi Yang, "Thermodynamic models of receptor-mediated cell-matrix adhesion." Dept of Physics, UT Austin, November 2008.

Dirk Gillespie, "Mechanisms of calcium ion channel permeation and selectivity." Dept of Molecular Biophys and Physiology, Rush U Medical Center, October 2008.

Lawrence Pratt, "From clusters to a molecular-field theory of liquids." Dept of Chem Eng, Tulane U, August 2008.

Jon Abramson, "Drug-protein interactions mediated by reversible exchange of electrons." Dept. of Physics, Portland State U, January 2008.

Chuan He, "Bacterial regulation of metal ions, virulence, and antibiotic resistance." Dept of Chemistry, The U of Chicago, December 2007.

Bob Eisenberg, "Ion channels: Proteins with a hole." Chair, Dept of Molecular Biophys and Physiology, Rush U Medical Center, November, 2007.

Dick Horn, "Plugging the pore: Hoodwinking ion channels with cationic blockers." Dept of Physiology, Thomas Jefferson Medical College, October 2007.

Dan Minor, "Structural studies of ion channel function and regulation." Dept of Biochem and Biophys, Dept of Cellular and Molecular Pharm, UCSF, September 2007.


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Current Research Projects

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Publications

Journal Articles

Articles available on Google Scholar.

2015 - Present

Chaudhari, MI; Pratt, LR; and SB Rempe. 2017. Utility of chemical computations in predicting solution free energies of metal ions. Molecular Simulation (invited special issue on Proceedings of the 4th International Conference on Molecular Simulation; submitted).

VanGordon, MR; Gyawali, G; Rick, SW; and SB Rempe. 2017. Atomistic study of intramolecular interactions in the closed-state channelrhodopsin chimera, C1C2. Biophys. J. (in print).

Stevens, MJ and SLB Rempe. 2016. Ion specific effects in carboxylate binding. J. Phys. Chem. B 120:12519-12530.

Chaudhari, MI; Pratt, LR; Soto, F; Balbuena, P; and SB Rempe. 2016. Scaling atomic partial charges of carbonate solvents for lithium ion solvation and diffusion. J. Chem. Theory Comput. 12:5709-5718.

La Bauve, S; Vernon, BC; Ye, D; Rogers, DM; Siegrist, CM; Carson, B; Zheng, A; Rempe, SB; Kielian, MC; Shreve, AP; Kent, MS. 2016. New method for measuring the anchoring energy of strongly-bound membrane-associated proteins. BBA: Biomembranes 1858:2753-2762.

Pratt, LR, Chaudhari, MI and SB Rempe. 2016. Statistical analyses of hydrophobic interactions: A mini-review. J. Phys. Chem. B 120:6455-6460 (invited).

You, X; Chaudhari, MI; Rempe, SB; and LR Pratt. 2016. Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations. J. Phys. Chem. B 120:1849-53 (invited Bruce Garrett Festschrift).

Chaudhari, MI; Rempe, SB; Asthagiri, D; Tan, L; and LR Pratt. 2016. Molecular theory and the effects of solute attractive forces on hydrophobic interactions. J. Phys. Chem. B 120:1864-70 (invited Bruce Garrett Festschrift).

You, X; Chaudhari, MI; Rempe, SB; and LR Pratt. 2015. Dielectric properties of ethylene carbonate and propylene carbonate using molecular dynamics simulations. ECS Trans. 69:107-111.

Anishkin, A; Vanegas, J.; Rogers, DM; Lorenzi, PL; Chan, WK; Purwaha, P; Weinstein, J; Sukharev, S; and SB Rempe. 2015. Catalytic role of the substrate defines specificity of therapeutic L-asparaginase. J. Mol. Bio. 427:2867-85.

Chaudhari, MI; Soniat, M; and SB Rempe. 2015. Octa-coordination and the aqueous Ba2+ ion. J. Phys. Chem. B 119:8746-53.

Soniat, M; Rogers, DM and SB Rempe. 2015. Dispersion- and exchange-corrected density functional theory for sodium ion hydration. J. Chem. Theory Comput. 11:2958-67.

Leung, K; Chaudhari, MI; Rempe, SB; Fenton, KR; Pratt, HD; Staiger, CL: and G. Nagasubramanian. 2015. Density functional theory and conductivity studies of boron-based anion receptors. J. Electrochem. Soc. 162:A1927-34.

Mason, PE; Ansell, S; Neilson, GW; and SB Rempe. 2015. Neutron scattering studies of the hydration structure of Li+(aq). J Phys Chem B. 119:2003-9.

Rogers, DM; Kent, M; and SB Rempe. 2015. Molecular basis of host-membrane association for the Dengue virus envelope protein. Biochim. Biophys. Acta-Biomembranes 1848:1041-52.


2010-2014

Chaudhari, MI; Sabo, D; LR Pratt and SB Rempe. 2014. Hydration of Kr(aq) in dilute and concentrated solutions. J. Phys. Chem. B 119:9098-9102 (invited Branka Ladanyi Festschrift).

Fu, Y; Li, B; Jiang, Y-B; Dunphy, DR; Tsai, A; Tam, S-Y; Li, B; Fan, H; Zhang, H; Rogers, DM; Rempe, SB, Atanassov, P; Cecchi, JL; and CJ Brinker. 2014. Atomic layer deposition of L-alanine polypeptide. J. Am. Chem. Soc. 136:15821-24.

Andersen, M; Rogers, DM; Mai, J; Schudel, B; Hatch, A; Rempe, SB; and A Mani. 2014. Spatiotemporal pH dynamics in concentration polarization near ion-selective membranes. Langmuir 30:7902-12.

Chan, WK; Lorenzi, PL; Anishkin, A; Purwaha, P; Rogers, DM; Sukharev, S; Rempe, SB; and JN Weinstein. 2014. The glutaminase activity of L-asparaginase is not required for anticancer activity against ASNS-negative cells. Blood 123:3596-3606.

Leung, K; Rempe, SB; Foster, ME; Ma, Y; Martinez del la Hoz, J; Sai, N and PB Balbuena. 2014. Modeling electrochemical decomposition of fluorethylene carbonate on silicon anode surfaces in lithium ion batteries. J. Electrochem. Soc. 161:A213-21.

Rossi, M; Tkatchenko, A; Rempe, SB; and S Varma. 2013. The role of methyl-induced polarization in ion binding. Proc. Natl. Acad. Sci. USA 110:12978-83.

Sabo, D.; Jiao, D.; Varma, S.; Pratt, LR and SB Rempe. 2013. Case study of Rb+(aq), quasi-chemical theory of ion hydration, and the no split occupancies rule. Ann. Rep. Prog. Chem., Sect C: Phys. Chem. 109:266 (commissioned by the Royal Society of Chemistry, UK).

Jiao, D; and SB Rempe. 2012. Combined DFT and continuum calculations of pKa in carbonic anhydrase. Biochem. 51:5979-89.

Rogers, DM; and SB Rempe. 2012. Reply to "Comment on 'Probing the thermodynamics of competitive ion binding using minimum energy structures.'" J. Phys. Chem. B 116:7994-995.

Rogers, DM; and SB Rempe. 2012. Irreversible thermodynamics. J. Phys.: Conf. Ser. 401:012014.

Varma, S; Rogers, DM; Pratt, LR; and SB Rempe. 2011. Design principles for K+ selectivity in membrane transport. J. Gen. Physiol. (Perspectives on Ion Selectivity) 137:479-88 (invited).

Alam, TM; Hart, D; and SLB Rempe. 2011. Computing the 7Li NMR chemical shielding of hydrated Li+ using cluster calculations and time-averaged configurations from ab initio molecular dynamics simulations. Phys. Chem. Chem. Phys. 13:13629 (back cover).

Jiao, D; and SB Rempe. 2011. CO2 solvation free energy using quasi-chemical theory. J. Chem. Phys. 134:224506-17.

Rogers, DM; and SB Rempe. 2011. Probing the thermodynamics of competitive ion binding using minimum energy structures. J. Phys. Chem. B 115:9116-9129.

Rogers, DM; Beck, TL; and SB Rempe. 2011. An information theory approach to nonlinear, non-equilibrium thermodynamics. J. Statistical Phys. 145:385-409 (invited).

Jiao, D; Leung, K; Rempe, SB; and TM Nenoff. 2011. First principles calculations of atomic nickel redox potentials and dimerization free energies: A study of metal nanoparticle growth. J. Chem. Theory Comput, 7:485-495.

Varma, S; and SB Rempe. 2010. Multi-body effects in ion binding and selectivity. Biophys. J. 99:3394.

Asthagiri, D; Dixit, PD; Merchant, S; Paulaitis, M; Pratt, LR; Rempe, SB; and S Varma. 2010. Ion selectivity from local configurations of ligands in solutions and ion channels. Chem. Phys. Lett. (Frontiers Article) 485:1-7 (invited, cover, dedicated feature on journal website).

Rempe, SB; and K Leung. 2010. Response to "Comment on 'Ab initio molecular dynamics calculation of ion hydration free energies' [JCP 133, 047103 (2010)]." J. Chem. Phys. 133:047104.

Davis, RW; Aaron, JS; Rempe, SL; and JA Timlin. 2010. Fluorescence fluctuation analysis of mixed chromophores from a line-scanning hyperspectral imaging system. Proc. SPIE 7570 (757002):1-11.

Lorenz, CD; Tsige, M; Rempe, SB; Chandross, M; Stevens, MJ; Grest, GS. 2010. Simulation study of the silicon oxide and water interface. J. Comput. Theor. Nanosci. 7(12):2586-2601 (invited).

Clawson, JS; Leung, K; Cygan, RT; Alam, TM; and SB Rempe. 2010. Ab initio study of hydrogen storage in water clathrates. J. Comput. Theor. Nanosci. 7(12):2602-2606 (invited).


2005 - 2009

Leung, K; and SB Rempe. 2009. Ion rejection by nanoporous membranes in pressure-driven molecular dynamics simulations. J. Comput. Theor. Nanosci. 6:1948-1955 (invited).

Leung, K; Rempe, SB; and A von Lilienfeld. 2009. Ab initio molecular dynamics calculation of ion hydration free energies. J. Chem. Phys. 130 (20):204507-18.

Rempe, SB; Mattsson, TR; Leung, K. 2008. On 'the complete basis set limit' and plane-wave methods in first-principles simulations of water. Phys. Chem. Chem. Phys. (Communication) 10:4685-87.

Varma, S; and SB Rempe. 2008. Structural transitions in coordination preferences of ions. J. Am. Chem. Soc. 130 (56):15405-15419.

Cygan, RT; Brinker, CJ; Nyman, M; Leung, K; and SB Rempe. 2008. A molecular basis for advanced materials in water treatment. Mater. Res. Soc. Bulletin 33:42-47 (invited).

Varma, S; Sabo, D; and SB Rempe. 2008. K+/Na+ selectivity in K-channels and valinomycin: Over-coordination versus cavity-size constraints. J. Molec. Biol. 376:13-22.

Sabo, D; Varma, S; Martin, MG; and SB Rempe. 2008. Studies of the thermodynamic properties of hydrogen in bulk water. J. Phys. Chem. B 112:867-876.

Whitfield, T; Varma, S; Harder, E; Lamoureux, G, Rempe, SB and B Roux. 2007. Theoretical study of aqueous solvation of K+ comparing ab initio, polarizable, and fixed-charge models. J. Chem. Theor. Comput. 3(6):2068-2082.

Varma, S; and SB . 2007. Tuning ion coordination architectures to enable selective partitioning. Biophys. J. 93:1093-1099.

Varma, S; and SB Rempe. 2006. Coordination numbers of alkali metal ions in aqueous solution. Biophys. Chem. 124:192-199 (invited).

Leung, K; and SB Rempe. 2006. Ab initio rigid water: Effect on water structure, ion hydration, and thermodynamics. Phys. Chem. Chem. Phys. 8:2153-2162.

Leung, K; Rempe, SB, et al. 2006. Density functional theory and DFT+U study of transition metal porphines adsorbed on Au (111) surfaces and effects of applied electric fields. J. Am. Chem. Soc. 128:3659-3668.

Sabo, D; Rempe, SB; Greathouse, JA; and MG Martin. 2006. Molecular structure of hydrogen gas in bulk water. Molecular Simulation 32:269-278 (invited).

Leung, K; Rempe, SB; and CD Lorenz. 2006. Salt permeation and exclusion in hydroxylated and functionalized silica pores. Phys. Rev. Lett. 96:095504.

Jakobsson, E; Aluru, N; Bayley, H; Brinker, J; Feller, S; Rempe, S, Roux, B, Saraniti, M; Scott, HL; and Zhu, X. 2006. The national center for the design of biomimetic nanoconductors. Nanomed.: Nanotech., Biol., Med. 2.4:289-290.

Leung, K; and SB Rempe. 2005. Ab initio molecular dynamics study of glycine intramolecular proton transfer in water. J. Chem. Phys. 122:184506-18.


Pre - 2004

Leung, K; and SB Rempe. 2004. Ab initio molecular dynamics study of formate ion hydration. J. Am. Chem. Soc.126:1285-1289.

Rempe, SB; Asthagiri, D and LR Pratt. 2004. Inner shell definition and absolute hydration free energy of K+(aq) on the basis of quasi-chemical theory and ab initio molecular dynamics. Phys. Chem. Chem. Phys. 6:1966-1969.

Asthagiri, D; Pratt, LR; Paulaitis, ME; and SB Rempe. 2004. Hydration structure and free energy of biomolecularly specific aqueous dications, including Zn2+ and first transition row metals. J. Am. Chem. Soc. 126:344-351.

Ashbaugh, HS; Asthagiri, D; Pratt, LR and SB Rempe. 2003. Hydration of krypton and consideration of clathrate models of hydrophobic effects from the perspective of quasi-chemical theory. Biophys. Chem. 105:323-338.

Tsige, M; Soddemann, T; Rempe, SB; et al. 2003. Interactions and structure of poly(dimethyl-siloxane) at silicon dioxide surfaces. J. Chem. Phys. 118:5132-42.

Rempe, SB and LR Pratt. 2001. The hydration number of Na+ in liquid water. Fl. Phase. Eq. 183:121-32.

Rempe, SB; Pratt, LR; Hummer, G; Kress, JD; Martin, RL and A Redondo. 2000. The hydration number of Li+ in liquid water. J. Am. Chem. Soc. (Letter) 122:966-967.

Rempe, SB and RO Watts. 1998. The exact quantum mechanical kinetic energy operator in internal coordinates for vibration of a hexatomic molecule. J. Chem. Phys. 108:10084-95.

Rempe, SB; and H Jonsson. 1998. A computational exercise illustrating molecular vibrations and normal modes. The Chemical Educator 3:04231-6.

Rempe, SB and RO Watts. 1997. The convergence properties of hindered rotor energy levels. Chem. Phys. Lett. 269:455-463.

Gyorgyi, L; Rempe, SL; and RJ Field. 1991. A novel model for the simulation of chaos in low-flow-rate CSTR experiments with the Belousov-Zhabotinsky reaction. J. Phys. Chem. 95:3159-3165.


Selected Book Chapters & Editorials

Rogers, DM; Jiao, D; Pratt, LR; and SB Rempe. 2012. Structural models and molecular thermodynamics of hydration of ions and small molecules, in Ann. Rep. Comp. Chem. Vol. 8 (ed. R. Wheeler, Chapt. 4, p 71- 127, Elsevier, New York) (invited).

Rempe, SB; and B Roux. 2006. Editorial for special issue on ions. Biophys. Chemistry 124:169-170.

Jarvinen, GB; et al. 2000. Robust membrane systems for actinide separations, in Plutonium Futures - The Science (AIP Conf Proc 532:71-72).

Pratt, LR and SB Rempe. 1999. Quasi-chemical theory and implicit solvent models for simulations, in Simulation and Theory of Electrostatic Interactions in Solution (AIP Conf Proc 492:172-201).

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