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  • 11
    Electronic Resource
    Electronic Resource
    Rotational Relaxation of a Spherocylinder and a Semirigid Molecule in Concentrated Solutions (1994)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 9265-9269 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100088a029
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  • 12
    Electronic Resource
    Electronic Resource
    Response to "Comment on a proposed method for finding barrier height distributions'' [J. Chem. Phys. 103, 1235 (1995)] (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 1237-1238 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A rebuttal is given to a criticism of an approximate method for the determination of the distribution of energy barrier heights in liquids and proteins. It is argued that the one-dimensional counterexample used in the critique violates clearly stated assumptions in the derivation, which also appear to hold in nature. The method is shown to be accurate in a more appropriate one-dimensional test.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469785
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  • 13
    Electronic Resource
    Electronic Resource
    A mean-field model for semiflexible chains (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 9408-9412 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We derive a mean-field model for a semiflexible chain using a functional integral approach. The resulting model satisfies the global constraint 〈u2(s)〉=1 rather than the hard constraint that u2(s)=1 for all s. The function u(s) is the tangent vector ∂r/∂s, where r(s) represents the conformation of the chain and s is the arc length. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470001
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  • 14
    Electronic Resource
    Electronic Resource
    Semiflexible chains under tension (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 4243-4247 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A functional integral formalism is used to derive the extension of a stiff chain subject to an external force. The force versus extension curves are calculated using a mean-field approach in which the hard constraint u2(s)=1 is replaced by a global constraint 〈u2(s)〉=1 where u(s) is the tangent vector describing the chain and s is the arclength. The theory quantitatively reproduces the experimental results for DNA that is subject to a constant force. We also treat the problems of semiflexible chain in a nematic field. In the limit of weak nematic field strength our treatment reproduces the exact results for chain expansion parallel to the director. When the strength of the nematic field is large, a situation in which there are two equivalent minima in the free energy, the intrinsically mean-field approach yields incorrect results for the dependence of the persistence length on the nematic field. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.473128
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  • 15
    Electronic Resource
    Electronic Resource
    Dynamics of collapse of flexible polyampholytes (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 5126-5129 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We provide a theory for the dynamics of collapse of flexible polyampholytes (PAs) using Langevin equation. Metastable pearl-necklace structures form in a time scale proportional to N4/5 (N is the number of monomers). In the late stage of collapse the pearls merge with the largest one growing at the expense of smaller ones (Lifshitz–Slyozov mechanism). The time scale for this process is τcoll∼N. Counterion-mediated collapse of strongly charged polyelectrolytes (PEs) follow a similar route to the globular state. Simulations support the proposed collapse mechanism for PAs and PEs. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1312267
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  • 16
    Electronic Resource
    Electronic Resource
    Electrostatic Persistence Length of a Polyelectrolyte Chain (1995)
    s.l. : American Chemical Society
    Macromolecules 28 (1995), S. 577-581 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma00106a023
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  • 17
    Electronic Resource
    Electronic Resource
    On the Simulation of Quantum Systems: Path Integral Methods (1986)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physical Chemistry 37 (1986), S. 401-424 
    Details
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.pc.37.100186.002153
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  • 18
    Electronic Resource
    Electronic Resource
    EARLY EVENTS IN RNA FOLDING (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physical Chemistry 52 (2001), S. 751-762 
    Details
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM). According to KPM a small fraction of molecules folds rapidly to the native state whereas the remaining fraction is kinetically trapped in a low free-energy non-native state. This model provides a unified description of the way RNA and proteins fold. Single-molecule experiments on Tetrahymena ribozyme, which directly validate our theory, are analyzed using KPM. We also describe the earliest events that occur on microsecond time scales in RNA folding. These must involve collapse of RNA molecules that are mediated by counterion-condensation. Estimates of time scales for the initial events in RNA folding are provided for the Tetrahymena ribozyme.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.physchem.52.1.751
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  • 19
    Electronic Resource
    Electronic Resource
    Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 4119-4125 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to describe the potentials between nearest neighbor nonbonded beads. We show that, under the simulation conditions when the native basin of attraction (NBA) is the most stable, there is an excellent correlation between folding times τF and the dimensionless parameter σT=(Tθ−TF)/Tθ, where Tθ is the collapse temperature and TF is the folding transition temperature. There is also a significant correlation between τF and another dimensionless quantity Z=(EN−Ems)/δ, where EN is the energy of the native state, Ems is the average energy of the ensemble of misfolded structures, and δ is the dispersion in the contact energies. In contrast, there is no significant correlation between τF and the Z-score gap ΔZ=EN−Ems. An approximate relationship between σT and the Z-score is derived, which explains the superior correlation seen between τF and σT. For two state folders τF is linked to the free energy difference (not simply energy gap, however it is defined) between the unfolded states and the NBA. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.477012
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  • 20
    Electronic Resource
    Electronic Resource
    Path integral Monte Carlo study of the hydrated electron (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 86 (1987), S. 6404-6418 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The structure of an excess electron in water at room temperature is investigated using the Feynman path integral technique. The interaction potential between the electron and water is modeled by an effective potential, made up of three terms: a static potential, a repulsive potential, and a polarization potential. The polarization part is treated in two different ways: approximated as pairwise additive, and exactly with the many body polarization effects treated self-consistently. It is shown that the excess electron forms a cavity with the radius of the electron being 2.24 A(ring) for pairwise additive polarization and 2.11 A(ring) for the self-consistent treatment of the polarization. There is no sharp geometrical coordination number of water molecules around the electron. The water molecules within a distance of about 3.5 A(ring) from the center of the electronic change distribution point their OH bonds towards the electron, and form only three hydrogen bonds. It is also found that the pair correlation function of the solvent molecules close to the electron are considerably different from the corresponding quantities calculated in the bulk. The electron, therefore, is shown to modify the local density to a large extent. There are important structural differences between the many body polarization model and the two body polarization model. It is concluded that for a quantitative description of the structure of the hydrated electron, the self-consistent treatment of the long range (many body) polarization effects are important.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.452429
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