NASA Astrobiology Institute (NAI)

Publications

Hargreaves, W.W., S.J. Mulvihill and D.W. Deamer. 1977. Synthesis of phospholipids and membranes in prebiotic conditions. Nature 266:78-80

Hargreaves, W.R. and D.W. Deamer. 1978. Liposomes from ionic single chain amphiphiles. Biochem 17: 3759-3768.

Deamer, D.W. and J. Oro. 1980. Role of lipids in prebiotic structures. BioSystems 12:167-175.

A. Pohorille and R. L. Pratt, (1990) Cavities in molecular liquids and the theory of hydrophobic solubilities’‘, J. Am. Chem. Soc. 112, 5066-5074.

L. R. Pratt and A. Pohorille (1992) Theory of hydrophobicity: transient cavities in molecular liquids, Proc. Natl. Acad. Sci., 89, 2995-2999.

M. A. Wilson and A. Pohorille, (1994) Molecular dynamics of a water – lipid bilayer interface, J. Am. Chem. Soc. 116, 1490-1501.

A. Pohorille and M. A. Wilson, (1995) Molecular dynamics studies of simple membrane-water interfaces: structure and functions in the beginnings of cellular life, Orig. Life Evol. Biosphere 25, 21-46.

M. A. Wilson, A. Pohorille, P. Jenniskens and D. Blake, (1995) Probing the structure of prebiotic ice, Orig. Life and Evol. Biosphere 25, 21-46.

P. Jenniskens, D. F. Blake, M. A. Wilson and A. Pohorille, (1995) High density amorphous ice, the frost on interstellar grains, Astrophys. J. 455, 389-401.

G, Hummer, S. Garde, A. E. Garcia, A. Pohorille and L. R. Pratt, (1996) An information theory model of hydrophobic interactions, Proc. Natl. Acad. Sci. USA, 93, 8951-8955.

A. Pohorille and M. A. Wilson, (1996) Excess chemical potential of small solutes across water—membrane and water—hexane interfaces, J. Chem. Phys. 104, 3760-3773.

M. A. Wilson and A. Pohorille, (1996) Mechanism of Unassisted Ion Transport across Membrane Bilayers, J. Am. Chem. Soc. 118, 6580-6587.

Chipot, C.; Wilson, M. A.; Pohorille, A., (1996) Interactions of Anesthetics with the Hexane—water Interface, J. Phys. Chem. B, 101, 782-791.

C. Chipot and A. Pohorille, (1998) Folding and translocation of the undecamer of poly—L—leucine across the water—hexane interface, J. Am. Chem. Soc., 120 11912-11924.

Chipot, C., Maigret, B. and Pohorille, A. (1999) Early events in the folding of an amphipatic peptide: a multinanosecond molecular dynamics study. Proteins: Struct. Funct. Gen. 36, 383-399.

Pohorille, A., New, M. H., Schweighofer, K. & Wilson, M. A. (1999) Insights from Computer Simulations into the interactions of small molecules with lipid membranes. Curr. Topics in Membranes, 48:50-76.

Eger, E.I., Ionescu, P., Laster, M.J., Gong, D., Hudlicky, T., Kendig, J.J., Harris, R.A., Trudell, J.R., & Pohorille, A. (1999) Minimum alveolar anesthetic concentration of fluorinated alkanols in rats: relevance to theories of narcosis. Anesth. Analg. 88, 867-76.

Schweighofer, K. & Pohorille, A. (2000), Computer simulations of ion channel gating: the M2 channel of Influenza A virus. Biophys. J. 78, 150-163.

New, M. H. & Pohorille, A. (2000), An Inherited Efficiencies Model of non-genomic evolution. Simulation Practice and Theory 8, 99-108.

Sokolowska, J. and Pohorille, A. (2000) Models of risk and choice: challenge or danger, Acta Psych. 104, 339-369.

Lanyi, J. K. and Pohorille, A. (2001) Proton pumps: mechanism of action and applications, Trends Biotechnol., 19:140-144.

Pohorille, A., From molecules in space to the origin of life and back, Adv. Space Sci., 30: 1509-1520.

Darve, E. and Pohorille, A. (2001) Calculating free energies using average force, J. Chem. Phys., 115:9169-9183.

Pohorille A. and Deamer, D. (2001) Artificial cells: Prospects for biotechnology, Trends Biotechnol., 20:123-128.

Pratt, L. R. and Pohorille, A. (2002) Hydrophobic effects and modeling of biophysical aqueous interfaces, Chem. Rev. 102: 2671-2692.

Bay, S. D., Shrager, J., Pohorille, A. and Langley, P. (2002) Revising regulatory networks: from expression data to causal models, J. Biomed. Informatics, 35: 289-97.

Pohorille, A., Wilson, M. A. and Chipot, C. (2003) Membrane peptides and their role in protobiological evolution, Orig. Life Evol. Biosphere, 33: 173-197.

Bay, S.D., Chrisman, L., Pohorille, A. and Shrager, J. (2004) Temporal aggregation bias and inference of causal regulatory networks. J Comput Biol., 11: 971-85.

Rodriguez-Gomez, D., Darve, E. and Pohorille, A. (2004) Assessing the efficiency of free energy calculation methods, J. Chem. Phys., 120: 3563-3570.

Pohorille, A., Schweighofer, K. and Wilson, M. A. (2005 ) The origin and early evolution of membrane channels, Astrobiology, 5: 1-17.

Henin, J., Pohorille, A. and Chipot, C. (2005) Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A, J. Am. Chem. Soc., 127: 8478-84.

A. Pohorille, Protocells as Universal Ancestors of Living Systems. In Protocells: Bridging Nonliving and Living Matter, S. Rasmussen, M. Bedau, L. Chen, D. Deamer, D. Krakauer, N. Packard, and P. Shuster, Eds.. MIT Press, Cambridge, MA., 2008.

Pohorille, A. and Darve E. (2006) A Bayesian approach to calculating free energies in chemical and biological systems, in Bayesian Inference and Maximum Entropy Methods in Science and Engineering. American Institute of Physics, Melville, NY.

E. Darve, D. Rodriguez-Gomez and A. Pohorille. Adaptive Biasing Force method for scalar and vector free energy calculations, J. Chem. Phys., in press.

Free Energy Calculations. Theory and Applications to Chemistry and Biology, C. Chipot and A. Pohorille, Eds., Springer Verlag, Berlin, 2007.

NB: This is just a sample of what this section will look like.