My research focuses on the development and use of condensed phase, molecular simulation methods to investigate chemical problems. An understanding of the fundamental physical laws governing the interactions between atoms and molecules can be used to describe complex biological systems.

The ideas I am pursuing are united by a common theme: Unraveling the structure, dynamics, and thermodynamics of complex chemical systems such as proteins, molecular liquids, and lipid bilayers.

Great success has been achieved using molecular mechanics to describe the behavior and structure of biological molecules, and ever-increasing computational power allows for larger and more complex systems to be investigated. Theoretical chemistry, chemical physics and computational chemistry, as applied to model biological systems, is a powerful combination for a research program addressing interesting and timely questions in biology and chemistry.

My current research focus on the molecular dynamics simulation of lipid bilayers, membrane proteins such as ion channels and the spectroscopy of molecular liquids. We use simulation and collaborations with experimentalists, to interrogate the structure, dynamics and interactions of these chemically and biologically complex problems. Some of the projects I am currently working on include the:

• nicotinic acetylcholine receptor
• potassium ion channel

and interfacial systems, such as:

• lipid bilayers
• protein - lipid interactions

My research also includes the development and application of new computer modeling techniques. For example, we continue to develop our state-of-the-art, parallel molecular dynamics code. This code takes full advantage of recent algorithmic developments and new parallel computer technology, which allows us to investigate ever larger and more complex systems.

‡ Undergraduate Student
* Graduate Student

Perry A, Neipert C, Space B, and Moore PB, "Theoretical Modeling of Interface Specific Vibrational Spectroscopy: Methods and Applications to Aqueous Interfaces", Chemical Reviews 106(4), 1234-1258 (2006).

Napoleon RL‡ and Moore PB, "Structural Characterization of Interfacial n-Octanol and 3-Octanol Using Molecular Dynamic Simulations", J. Physical Chemistry B 110(8), 3666-3673 (2006).

Srinivas G, Nielsen SO, Moore PB, Klein ML, "Molecular Dynamics Simulations of Surfactant Self-Organization at a Solid-Liquid Interface", J. Amer. Chem. Soc 128(3), 848-853 (2006).

Perry A, Neipert C, Kasprzyk CR, Green T, Space B, and Moore PB, "A Theoretical Description of the Polarization Dependence of the Sum Frequency Generation Spectroscopy of the Water/Vapor Interface", J. Chemical Physics 123(14), Article # 144705 (2005).

Perry A, Neipert C, Ridley C, Space B, and Moore PB, "Identification of a Wagging Vibrational Mode of Water Molecules at the Water/Vapor Interface', Physical Review E 71(5), Article # 050601(2005).

Nielsen SO, Ensing B, Ortiz V, Moore PB, and Klein ML, "Lipid Bilayer Perturbations Around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study", Biophysical J. 88(6), 3822-3828 (2005).

Lopez CF, Nielsen SO, Ensing B, Moore PB, and Klein ML, "Structure and Dynamics of Model Pore Insertion into a Membrane" Biophysical J. 88(5), 3083-3094 (2005).

Nielsen, Steve O.; Lopez, Carlos F.; Ivanov, Ivaylo; Moore, Preston B.; Shelley, John C.; and Klein, Michael L., "Transmembrane Peptide-Induced Lipid Sorting and Mechanism of La-to-Inverted Phase Transition Using Coarse-Grain Molecular Dynamics", Biophysical Journal, 87(4), 2107-2115 (2004).

Lopez, Carlos F.; Nielsen, Steve O.; Klein, Michael L.; Moore, Preston B., "Hydrogen Bonding Structure and Dynamics of Water at the Dimyristoylphosphatidylcholine Lipid Bilayer Surface from a Molecular Dynamics Simulation", Journal of Physical Chemistry B, 108(21), 6603-6610 (2004).

Roney, Alfred B.; Space, Brian; Castner, Edward W.; Napoleon, Raeanne L.‡; Moore, Preston B., "A Molecular Dynamics Study of Aggregation Phenomena in Aqueous n-Propanol", Journal of Physical Chemistry B, 108(22), 7389-7401 (2004).

Lopez, Carlos F.; Nielsen, Steve O.; Moore, Preston B.; Klein, Michael L., "Understanding Nature's Design for a Nanosyringe", Proceedings National Academy of Sciences, 101(13), 4431-4434 (2004).

S.O. Nielsen, C.F. Lopez, P.B. Moore, J.C. Shelley, M.L. Klein, "Molecular Dynamics Investigations of Lipid Langmuir Monolayers Using a Coarse-Grain Model", J. Phys. Chem. B, 107, 13911-13917 (2003).

R. DeVane, C. Ridley. R.W. Larsen, B. Space, P.B. Moore and S.I. Chan, "A Molecular Dynamics Method for Calculating Molecular Volume Changes Appropriate for Biomolecular Simulation", Biophys J., 85, 2801-2807 (2003).

A. Perry, H. Ahlborn, B. Space, and P.B. Moore, "A Combined Time Correlation Function and Instantaneous Normal Mode Study of the Sum Frequency Generation Spectroscopy of the Water/Vapor Interface", J. Chem. Phys., 118, 8411-8419 (2003).

CF Lopez, M Montal, JK Blasie, ML Klein, and PB Moore, "Molecular Dynamics Investigation of Membrane-Bound Bundles of the Channel Forming Transmembrane Domain of Viral Protein U from the Human Immunodeficiency Virus HIV-1", Biophys J., 83, 1259-1267 2002.

C.F. Lopez, P.B. Moore, J.C. Shelley, M.Y. Shelley and M.L. Klein, "Computer Simulation Studies of Biomembranes Using a Coarse Grain Model", Comp. Phys. Comm., 147, 1-6 2002.

C.F. Lopez, S.O. Nielsen, P.B. Moore, J.C. Shelley and M.L. Klein, "Self-Assembly of a Phospholipid Langmuir Monolayer Using Coarse-Grained Molecular Dynamics Simulations", J. Phys.: Condensed Matter, 14, 9431-9444 2002.

PB Moore, CF Lopez and ML Klein, "Dynamical Properties of a Dimiristoylphosphatidylcholine Fully Hydrated Bilayer from a Multinanosecond Molecular Dynamics Simulation", Biophysical J., 81, 2484-2494 2001.

JC Shelley, MY Shelley, RC Reeder, S Bandyopadhyay, PB Moore, ML Klein, "Simulations of Phospholipids Using a Coarse Grain Model", J. Phys Chem. B., 105, 9785-9792 2001.

XD Ji, H Ahlborn, B Space, PB Moore, "A Theoretical Investigation of the Temperature Dependence of the Optical Kerr Effect and Raman Spectroscopy of Liquid CS₂", J. Chem. Phys., 113, 8693-8699 2000.

PB Moore, Q Zhong, T Husslein and ML Klein, "Simulation of the HIV-1 Vpu Transmembrane Domain as a Pentameric Bundle", FEBS Letters, 431, 143-148 1998.