169 research outputs found
Scaling in many-body systems and proton structure function
The observation of scaling in processes in which a weakly interacting probe
delivers large momentum to a many-body system simply reflects the
dominance of incoherent scattering off target constituents. While a suitably
defined scaling function may provide rich information on the internal dynamics
of the target, in general its extraction from the measured cross section
requires careful consideration of the nature of the interaction driving the
scattering process. The analysis of deep inelastic electron-proton scattering
in the target rest frame within standard many-body theory naturally leads to
the emergence of a scaling function that, unlike the commonly used structure
functions and , can be directly identified with the intrinsic proton
response.Comment: 11 pages, 4 figures. Proceedings of the 11th Conference on Recent
Progress in Many-Body Theories, Manchester, UK, July 9-13 200
Momentum distributions in ^3He-^4He liquid mixtures
We present variational calculations of the one-body density matrices and
momentum distributions for ^3He-^4He mixtures in the zero temperature limit, in
the framework of the correlated basis functions theory. The ground-state wave
function contains two- and three-body correlations and the matrix elements are
computed by (Fermi)Hypernetted Chain techniques. The dependence on the ^3He
concentration (x_3) of the ^4He condensate fraction and of the
^3He pole strength (Z_F) is studied along the P=0 isobar. At low ^3He
concentration, the computed ^4He condensate fraction is not significantly
affected by the ^3He statistics. Despite of the low x_3 values, Z_F is found to
be quite smaller than that of the corresponding pure ^3He because of the strong
^3He-^4He correlations and of the overall, large total density \rho. A small
increase of along x_3 is found, which is mainly due to the decrease
of \rho respect to the pure ^4He phase.Comment: 23 pages, 7 postscript figures, Revte
Description of recent large- neutron inclusive scattering data from liquid He
We report dynamical calculations for large- structure functions of liquid
He at =1.6 and 2.3 K and compare those with recent MARI data. We extend
those calculations far beyond the experimental range q\le 29\Ain in order to
study the approach of the response to its asymptotic limit for a system with
interactions having a strong short-range repulsion. We find only small
deviations from theoretical behavior, valid for smooth . We repeat an
extraction by Glyde et al of cumulant coefficients from data. We argue that
fits determine the single atom momentum distribution, but express doubt as to
the extraction of meaningful Final State Interaction parameters.Comment: 37 pages, 13 postscript fig
Momentum distribution of liquid helium
We have obtained the one--body density matrix and the momentum distribution
of liquid He at K from Diffusion Monte Carlo (DMC)
simulations, using trial functions optimized via the Euler Monte Carlo (EMC)
method. We find a condensate fraction smaller than in previous calculations.
Though we do not explicitly include long--range correlations in our
calculations, we get a momentum distribution at long wavelength which is
compatible with the presence of long--range correlations in the exact wave
function. We have also studied He, using fixed--node DMC, with nodes and
trial functions provided by the EMC. In particular, we analyze the momentum
distribution with respect to the discontinuity as well as the
singular behavior, at the Fermi surface. We also show that an approximate
factorization of the one-body density matrix
holds, with and respectively the density matrix of the
ideal Fermi gas and the density matrix of a Bose He.Comment: 10 pages, REVTeX, 12 figure
Energetic Components of Cooperative Protein Folding
A new lattice protein model with a four-helix bundle ground state is analyzed
by a parameter-space Monte Carlo histogram technique to evaluate the effects of
an extensive variety of model potentials on folding thermodynamics. Cooperative
helical formation and contact energies based on a 5-letter alphabet are found
to be insufficient to satisfy calorimetric and other experimental criteria for
two-state folding. Such proteinlike behaviors are predicted, however, by models
with polypeptide-like local conformational restrictions and
environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press
Single-molecule experiments in biological physics: methods and applications
I review single-molecule experiments (SME) in biological physics. Recent
technological developments have provided the tools to design and build
scientific instruments of high enough sensitivity and precision to manipulate
and visualize individual molecules and measure microscopic forces. Using SME it
is possible to: manipulate molecules one at a time and measure distributions
describing molecular properties; characterize the kinetics of biomolecular
reactions and; detect molecular intermediates. SME provide the additional
information about thermodynamics and kinetics of biomolecular processes. This
complements information obtained in traditional bulk assays. In SME it is also
possible to measure small energies and detect large Brownian deviations in
biomolecular reactions, thereby offering new methods and systems to scrutinize
the basic foundations of statistical mechanics. This review is written at a
very introductory level emphasizing the importance of SME to scientists
interested in knowing the common playground of ideas and the interdisciplinary
topics accessible by these techniques. The review discusses SME from an
experimental perspective, first exposing the most common experimental
methodologies and later presenting various molecular systems where such
techniques have been applied. I briefly discuss experimental techniques such as
atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers
(MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I
then present several applications of SME to the study of nucleic acids (DNA,
RNA and DNA condensation), proteins (protein-protein interactions, protein
folding and molecular motors). Finally, I discuss applications of SME to the
study of the nonequilibrium thermodynamics of small systems and the
experimental verification of fluctuation theorems. I conclude with a discussion
of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond.
Matt
An Estimate of the Numbers and Density of Low-Energy Structures (or Decoys) in the Conformational Landscape of Proteins
The conformational energy landscape of a protein, as calculated by known potential energy functions, has several minima, and one of these corresponds to its native structure. It is however difficult to comprehensively estimate the actual numbers of low energy structures (or decoys), the relationships between them, and how the numbers scale with the size of the protein.We have developed an algorithm to rapidly and efficiently identify the low energy conformers of oligo peptides by using mutually orthogonal Latin squares to sample the potential energy hyper surface. Using this algorithm, and the ECEPP/3 potential function, we have made an exhaustive enumeration of the low-energy structures of peptides of different lengths, and have extrapolated these results to larger polypeptides.We show that the number of native-like structures for a polypeptide is, in general, an exponential function of its sequence length. The density of these structures in conformational space remains more or less constant and all the increase appears to come from an expansion in the volume of the space. These results are consistent with earlier reports that were based on other models and techniques
Calculation of the Free Energy and Cooperativity of Protein Folding
Calculation of the free energy of protein folding and delineation of its pre-organization are of foremost importance for understanding, predicting and designing biological macromolecules. Here, we introduce an energy smoothing variant of parallel tempering replica exchange Monte Carlo (REMS) that allows for efficient configurational sampling of flexible solutes under the conditions of molecular hydration. Its usage to calculate the thermal stability of a model globular protein, Trp cage TC5b, achieves excellent agreement with experimental measurements. We find that the stability of TC5b is attained through the coupled formation of local and non-local interactions. Remarkably, many of these structures persist at high temperature, concomitant with the origin of native-like configurations and mesostates in an otherwise macroscopically disordered unfolded state. Graph manifold learning reveals that the conversion of these mesostates to the native state is structurally heterogeneous, and that the cooperativity of their formation is encoded largely by the unfolded state ensemble. In all, these studies establish the extent of thermodynamic and structural pre-organization of folding of this model globular protein, and achieve the calculation of macromolecular stability ab initio, as required for ab initio structure prediction, genome annotation, and drug design
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