Final state effects on superfluid 4^{\bf 4}He in the deep inelastic regime

A study of Final State Effects (FSE) on the dynamic structure function of superfluid $^4$He in the Gersch--Rodriguez formalism is presented. The main ingredients needed in the calculation are the momentum distribution and the semidiagonal two--body density matrix. The influence of these ground state quantities on the FSE is analyzed. A variational form of $\rho_2$ is used, even though simpler forms turn out to give accurate results if properly chosen. Comparison to the experimental response at high momentum transfer is performed. The predicted response is quite sensitive to slight variations on the value of the condensate fraction, the best agreement with experiment being obtained with $n_0=0.082$. Sum rules of the FSE broadening function are also derived and commented. Finally, it is shown that Gersch--Rodriguez theory produces results as accurate as those coming from other more recent FSE theories.Comment: 20 pages, RevTex 3.0, 11 figures available upon request, to be appear in Phys. Rev.

Beyond the binary collision approximation for the large-qq response of liquid 4^4He

We discuss corrections to the linear response of a many-body system beyond the binary collision approximation. We first derive for smooth pair interactions an exact expression of the response $\propto 1/q^2$, considerably simplifying existing forms and present also the generalization for interactions with a strong, short-range repulsion. We then apply the latter to the case of liquid $^4$He. We display the numerical influence of the $1/q^2$ correction around the quasi-elastic peak and in the low-intensity wings of the response, far from that peak. Finally we resolve an apparent contradiction in previous discussions around the fourth order cumulant expansion coefficient. Our results prove that the large-$q$ response of liquid $^4$He can be accurately understood on the basis of a dynamical theory.Comment: 19 p. Figs. available on reques

Description of recent large-qq neutron inclusive scattering data from liquid 4^4He

We report dynamical calculations for large-$q$ structure functions of liquid $^4$He at $T$=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 $1/q$ behavior, valid for smooth $V$. 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 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 $(n_0^{(4)})$ 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 $n_0^{(4)}$ 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

Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.Comment: Proceedings of the National Academy of Science, 2002, Vol.99. 685-69

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

Momentum distribution of liquid helium

We have obtained the one--body density matrix and the momentum distribution $n(p)$ of liquid $^4$He at $T=3D0^o$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 $^3$He, using fixed--node DMC, with nodes and trial functions provided by the EMC. In particular, we analyze the momentum distribution $n(p)$ with respect to the discontinuity $Z$ as well as the singular behavior, at the Fermi surface. We also show that an approximate factorization of the one-body density matrix $\rho(r)\simeq \rho_0(r)\rho_B(r)$ holds, with $\rho_0(r)$ and $\rho_B(r)$ respectively the density matrix of the ideal Fermi gas and the density matrix of a Bose $^3$He.Comment: 10 pages, REVTeX, 12 figure

The role of a disulfide bridge in the stability and folding kinetics of Arabidopsis thaliana cytochrome c6A

Cytochrome c 6A is a eukaryotic member of the Class I cytochrome c family possessing a high structural homology with photosynthetic cytochrome c 6 from cyanobacteria, but structurally and functionally distinct through the presence of a disulfide bond and a heme mid-point redox potential of + 71 mV (vs normal hydrogen electrode). The disulfide bond is part of a loop insertion peptide that forms a cap-like structure on top of the core α-helical fold. We have investigated the contribution of the disulfide bond to thermodynamic stability and (un)folding kinetics in cytochrome c 6A from Arabidopsis thaliana by making comparison with a photosynthetic cytochrome c 6 from Phormidium laminosum and through a mutant in which the Cys residues have been replaced with Ser residues (C67/73S). We find that the disulfide bond makes a significant contribution to overall stability in both the ferric and ferrous heme states. Both cytochromes c 6A and c 6 fold rapidly at neutral pH through an on-pathway intermediate. The unfolding rate for the C67/73S variant is significantly increased indicating that the formation of this region occurs late in the folding pathway. We conclude that the disulfide bridge in cytochrome c 6A acts as a conformational restraint in both the folding intermediate and native state of the protein and that it likely serves a structural rather than a previously proposed catalytic role. © 2011 Elsevier B.V. All rights reserved

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