Abstract:
The phase transition in a model for vortex lines in high temperature superconductors with columnar defects, i.e., linearly correlated quenched random disorder, is studied with finite size scaling and Monte Carlo simulations. Previous studies of critical properties have mainly focused on the limit of strongly screened vortex line interactions. Here the opposite limit of weak screening is considered. The simulation results provide evidence for a new universality class, with new critical exponents that differ from the case of strong screening of the vortex interaction. In particular, scaling is anisotropic and characterized by a nontrivial value of the anisotropy exponent $\zeta=\nu_\parallel/\nu_\perp$. The exponents we find, $\zeta = 1.25 \pm 0.1, \nu_\perp=1.0 \pm 0.1, z = 1.95 \pm 0.1$, are similar to certain experimental results on YBCO.

Abstract:
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation where non-native interactions are ignored. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root-mean-square deviation of 1.8 A from the native structure. The sequence-dependent part of our potential is pairwise additive. Our calculations suggest that fine-tuning this potential by parameter optimization is of limited use.

Abstract:
We study the vortex glass transition in disordered high temperature superconductors using Monte Carlo simulations. We use a random pinning model with strong point-correlated quenched disorder, a net applied magnetic field, longrange vortex interactions, and periodic boundary conditions. From a finite size scaling study of the helicity modulus, the RMS current, and the resistivity, we obtain critical exponents at the phase transition. The new exponents differ substantially from those of the gauge glass model, but are consistent with those of the pure three-dimensional XY model.

Abstract:
We study the thermodynamic behavior of a model protein with 54 amino acids that is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix sequence.

Abstract:
ZSPA-1 is an engineered protein that binds to its parent, the three-helix-bundle Z domain of staphylococcal protein A. Uncomplexed ZSPA-1 shows a reduced helix content and a melting behavior that is less cooperative, compared with the wild-type Z domain. Here we show that the difference in folding behavior between these two sequences can be partly understood in terms of an off-lattice model with 5-6 atoms per amino acid and a minimalistic potential, in which folding is driven by backbone hydrogen bonding and effective hydrophobic attraction.

Abstract:
We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid and has the Ramachandran torsional angles $\phi_i$, $\psi_i$ as its degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. For a suitable choice of the relative strength of these interactions, we find that the three-helix-bundle protein undergoes an abrupt folding transition from an expanded state to the native state. Also shown is that the corresponding one- and two-helix segments are less stable than the three-helix sequence.

Abstract:
We discuss the angular momentum blockade in small d-wave superconducting grains in an external field. We find that abrupt changes in angular momentum state of the condensate, angular momentum blockade, occur as a result of changes in the angular momentum of the condensate in an external magnetic field. The effect rep- resents a direct analogy with the Coulomb blockade. We use the Ginzburg-Landau formalism to illustrate how a magnetic field induces a deviation from the d-wave symmetry which is described by a (d + id')-order parameter. We derive the behavior of the volume magnetic susceptibility as a function of the magnetic field, and corresponding magnetization jumps at critical values of the field that should be experimentally observable in superconducting grains.

Abstract:
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good approximation can be described by a simple two-state model, with parameters that are in reasonable quantitative agreement with experimental data. Despite the apparent two-state character of the melting curves, the energy distributions are found to lack a clear bimodal shape, which is discussed in some detail. We also perform a Monte Carlo-based kinetic study and find, in accord with experimental data, that the alpha-helix forms faster than the beta-hairpin.

Abstract:
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described in terms of a simple two-state system, and that the relaxation behavior is close to single exponential. The motion along individual reaction coordinates is roughly diffusive on timescales beyond the reconfiguration time for an individual helix. A simple estimate based on diffusion in a square-well potential predicts the relaxation time within a factor of two.

Abstract:
The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate, i.e. the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work.