With a long-term goal to build a practical physics of biological material, our Section on Molecular Biophysics measures, characterizes and codifies the interactions that govern the organization and self-assembly of different kinds of biological molecules. Connected in part with the recent NIH-wide interest in nanotechnology, we are building on our experience with van der Waals fluctuation forces to formulate interactions involving carbon nanotubes not only in their assembly but also and more important as substrates for biopolymers such as DNA. Our undertaking is strengthened by its strong connection with physical theory. Through a series of measurements and analyses of the different kinds of interactions as revealed in vivo, in vitro, and in computation, we are working with DNA assemblies such as those seen in viral capsids and in vitro; polypeptides and polysaccharides in suspension; and lipid/water liquid-crystals. In all these systems, we simultaneously observe the structure of packing as well as measure intermolecular interaction energies. ? - - - - - - - ? ? Van der Waals forces: ? Parsegian, Podgornik; in collaboration with French, Mkrtchian, Rajter, Ching ? ? Despite the fact that van der Waals forces are the dominant interaction that coheres membranes and proteins, the source of the powerful surface tension at membrane interfaces, as well as the attraction that creates membrane multilayers or allows membranes to adhere to artificial surfaces, they are only now being studied in a systematic collaboration between quantum physicists and biophysicists. The greatest adventure this year has been to use the quantum mechanical density functional theory (DFT) solved for several carbon nanotubes so as to compute the forces that cause them to cohere as well as serve as a substrate for many materials. It is remarkable that quantum chemistry combined with our expertise on macromolecular interactions is allowing us to see properties such as torque as well as force between carbon nanotubes. ? ? The key has been to begin with the elements of physical theory that relate the polarizability of materials to the fluctuations of charges within them. From this we have been able to design experiments that show how macromolecular organization responds to deliberate changes in solution properties. Progress is thus through a tight coupling of modern quantum theory of structured materials coupled with experiments and measurements that reveal electromagnetic properties. ? ? In the present instance, we have teamed with groups that measure absorption spectra in order to formulate and to compute van der Waals forces involving lipids, water, and ions, as well as synthetic structures such as carbon nanotubes. The results have shown how charge fluctuation forces conferred by ions in solution can modify forces between lipid membranes. We have measured those forces as well as computed van der Waals charge fluctuation forces in those same systems. ? ? We also progressed in extending the Lifshitz theory of van der Waals interactions in stratified media like lipid multilamellar systems to be able to compute forces between bodies with extended interfaces. These can range from the practical the composite media of electric insulators to the biological the action of extended polymer layers on biological membranes.? ? - - - - - - - ? Molecular assembly in vitro and in viro ? Bezrukov, Harries, Parsegian, Petrache, Podgornik, Rau, Stanley, Todd; Gelbart, Knobler, Zemb? ? Beginning with direct measurements of forces between large molecules, proceeding with observations of molecules under confinement, building on the statistical physics of molecular organization under the action of organizing forces, we have developed new theories and new methods of macromolecular organization. Among these are the observations of DNA under the osmotic stress of large polymers or confined within the hard walls of a virus capsid. ? ? A remarkable number of cellular processes are controlled by the osmotic action of small solutes. These include gating of ionic channels and specific versus non-specific DNAprotein interactions regulating gene expression. Osmotic sensing at the molecular level can probe the forces acting between and within macromolecules. By varying the salt or neutral osmolyte concentration in the bathing solution, we control osmotic pressure.? ? Our most recent adventures have been to observe the ejection of DNA from capsids that subject to different salt conditions. Expansive pressures can vary up to many tens of atmospheres, a pressure that is responsible for initial ejection of DNA. These forces can be varied by ionic conditions. An unrecognized feature of many viruses is that these conditions can penetrate the virus and in fact modify the expansive force within. At one extreme, DNA in simple salts will be under great pressure to expand and be ejected from the capsid; but under other conditions, where DNA condensing ions can enter the capsid, DNA can be under no expansive pressure. We have begun to measure the motion of DNA within capsids subject to different ionic conditions and begun to see how ejection might be controlled by ionic surroundings. Whether these manipulations ultimately affect viral infectivity is a worthwhile and exciting question.

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Cohen, J A; Podgornik, R; Hansen, P L et al. (2009) A phenomenological one-parameter equation of state for osmotic pressures of PEG and other neutral flexible polymers in good solvents. J Phys Chem B 113:3709-14
Munday, J N; Capasso, Federico; Parsegian, V Adrian (2009) Measured long-range repulsive Casimir-Lifshitz forces. Nature 457:170-3
Gurnev, Philip A; Harries, Daniel; Parsegian, V Adrian et al. (2009) The dynamic side of the Hofmeister effect: a single-molecule nanopore study of specific complex formation. Chemphyschem 10:1445-9
Petrache, Horia I; Harries, Daniel; Parsegian, V Adrian (2007) Measurement of lipid forces by X-ray diffraction and osmotic stress. Methods Mol Biol 400:405-19
Galanis, Jennifer; Harries, Daniel; Sackett, Dan L et al. (2006) Spontaneous patterning of confined granular rods. Phys Rev Lett 96:028002
Podgornik, R; French, R H; Parsegian, V A (2006) Nonadditivity in van der Waals interactions within multilayers. J Chem Phys 124:044709
Gondre-Lewis, Marjorie C; Petrache, Horia I; Wassif, Christopher A et al. (2006) Abnormal sterols in cholesterol-deficiency diseases cause secretory granule malformation and decreased membrane curvature. J Cell Sci 119:1876-85
Harries, Daniel; Podgornik, Rudi; Parsegian, V Adrian et al. (2006) Ion induced lamellar-lamellar phase transition in charged surfactant systems. J Chem Phys 124:224702
Petrache, Horia I; Zemb, Thomas; Belloni, Luc et al. (2006) Salt screening and specific ion adsorption determine neutral-lipid membrane interactions. Proc Natl Acad Sci U S A 103:7982-7
Petrache, Horia I; Tristram-Nagle, Stephanie; Harries, Daniel et al. (2006) Swelling of phospholipids by monovalent salt. J Lipid Res 47:302-9

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