Showing papers by "Sebastian Doniach published in 1998"

Protein Denaturation: A Small-Angle X-ray Scattering Study of the Ensemble of Unfolded States of Cytochrome c†

Abstract: Solution X-ray scattering was used to study the equilibrium unfolding of cytochrome c as a function of guanidine hydrochloride concentration at neutral pH. The radius of gyration (Rg) shows a cooperative transition with increasing denaturant with a similar Cm to that observed with circular dichroism. However, the lack of an isoscattering point in the X-ray scattering patterns suggests the equilibrium unfolding is not simply a two-state process. Singular value decomposition (SVD) analysis was applied to the scattering patterns to determine the number of distinct scattering species. SVD analysis reveals the existence of three components, suggesting that at least three equilibrium states of the protein exist. A model was employed to determine the thermodynamic parameters and the scattering profiles of the three equilibrium states. These scattering profiles show that one state is native (N). The other two states (U1, U2) are unfolded, with U2 being fully unfolded and U1 having some residual structure. Using t...

Association-induced folding of globular proteins

Abstract: It has generally been assumed that the aggregation of partially folded intermediates during protein refolding results in the termination of further protein folding. We show here, however, that under some conditions the association of partially folded intermediates can induce additional structure leading to soluble aggregates with many native-like properties. The amount of secondary structure in a monomeric, partially folded intermediate of staphylococcal nuclease was found to double on formation of soluble aggregates at high protein or salt concentrations. In addition, more globularity, as determined from Kratky plots of small-angle x-ray scattering data, was also noted in the associated states.

Metal-insulator transition in NiS 2 − x Se x and the local impurity self-consistent approximation model

Abstract: Angle-resolved photoemission spectroscopy (ARPES) measurements on ${\mathrm{NiS}}_{2\ensuremath{-}x}{\mathrm{Se}}_{x}$ single crystals show the evolution of a narrow band near the Fermi level, which develops in the vicinity of the correlation-driven metal-insulator transition. To model the metal-insulator transition, we use a two-band Hubbard model, which has been studied extensively to describe transition-metal compounds, and use a dynamical mean-field-theory approach. The ARPES data are in striking qualitative agreement with the predictions of the model. Comparison of our data to the calculations suggests a possible mechanism for the metal-insulator transition with Se substitution in which both charge-transfer and hole-doping effects are present.

Multiple time step diffusive Langevin dynamics for proteins.

Abstract: We present an algorithm for simulating the long time scale dynamics of proteins and other macromolecules. Our method applies the concept of multiple time step integration to the diffusive Langevin equation, in which short time scale dynamics are replaced by friction and noise. The macromolecular force field is represented at atomic resolution. Slow motions are modeled by constrained Langevin dynamics with very large time steps, while faster degrees of freedom are kept in local thermal equilibrium. In the limit of a sufficiently large molecule, our algorithm is shown to reduce the CPU time required by two orders of magnitude. We test the algorithm on two systems, alanine dipeptide and bovine pancreatic trypsin inhibitor (BPTI), and find that it accurately calculates a variety of equilibrium and dynamical properties. In the case of BPTI, the CPU time required is reduced by nearly a factor of 60 compared to a conventional, unconstrained Langevin simulation using the same force field. Proteins 30:215–227, 1998. © 1998 Wiley-Liss, Inc.

Metal-insulator transition of the two-band Hubbard model in infinite dimension and its relevance to a strongly correlated electron system: NiS 2 − x Se x

Abstract: We report a study of metal-insulator transition of a strongly correlated two-band Hubbard model using a dynamical mean-field theory approach. We find that the Mott transition appears at half filling even at $T=0$ in contrast to the one-band Hubbard model. The transition is characterized by the development of a ``Kondo-like'' peak near Fermi level. We also find a signature of the coexistence of metallic and antiferromagnetic phases from the study of the single-particle Green's function and the magnetic long-range order due to the superexchange coupling between the correlated electrons. We then suggest the relevance of our results to the metal-insulator transition and the recent angle-resolved photoemission measurements of ${\mathrm{NiS}}_{2\ensuremath{-}x}{\mathrm{Se}}_{x}.$ We also study the effect of carrier doping and the comparison of our findings with the experimental results suggests the possible importance of departures from stoichiometry associated with the Se substitution. The relevance of our results to high-temperature superconductivity is also discussed.

Weakly localized bosons

Abstract: In this paper, we argue that, in two dimensions, the weak localization of bosons, which occurs on the insulating side of the superconductor-insulator transition, is characterized by $\ensuremath{\rho}\ensuremath{\sim}\mathrm{ln}(1/T),$ as compared to $\ensuremath{\sigma}\ensuremath{\sim}\mathrm{ln}T$ for fermions. This unconventional behavior is tied to the diffusion pole of the delocalized (uncondensed) vortices.