Structure of the Energy Landscape of Short Peptides

We have simulated, as a showcase, the pentapeptide Met-enkephalin (Tyr-Gly-Gly-Phe-Met) to visualize the energy landscape and investigate the conformational coverage by the multicanonical method. We have obtained a three-dimensional topographic picture of the whole energy landscape by plotting the histogram with respect to energy(temperature) and the order parameter, which gives the degree of resemblance of any created conformation with the global energy minimum (GEM).Comment: 17 pages, 4 figure

Helix vs. Sheet Formation in a Small Peptide

Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both in gas phase and solvated EKAYLRT forms an $\alpha$-helix when not interacting with other molecules. However, in the vicinity of a $\beta$-strand, the peptide forms a $\beta$-strand. Because of this change in secondary structure our peptide may provide a simple model for the $\alpha \to \beta$ transition that is supposedly related to the outbreak of Prion diseases and similar illnesses.Comment: to appear in Physical Review

Partition Function Zeros and Finite Size Scaling of Helix-Coil Transitions in a Polypeptide

We report on multicanonical simulations of the helix-coil transition of a polypeptide. The nature of this transition was studied by calculating partition function zeros and the finite-size scaling of various quantities. Estimates for critical exponents are presented.Comment: RevTex, 4 eps-files; to appear in Phys. Rev. Le

Multi-Overlap Simulations for Transitions between Reference Configurations

We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows one to overcome free energy barriers in the overlap variable. Subsequently, we generalize the approach to deal with the overlaps with respect to two reference configurations so that transitions between them are induced. We illustrate our approach by simulations of the brainpeptide Met-enkephalin with the ECEPP/2 energy function using the global-energy-minimum and the second lowest-energy states as reference configurations. The free energy is obtained as functions of the dihedral and the root-mean-square distances from these two configurations. The latter allows one to identify the transition state and to estimate its associated free energy barrier.Comment: 12 pages, (RevTeX), 14 figures, Phys. Rev. E, submitte

Reconstructing the Density of States by History-Dependent Metadynamics

We present a novel method for the calculation of the energy density of states D(E) for systems described by classical statistical mechanics. The method builds on an extension of a recently proposed strategy that allows the free energy profile of a canonical system to be recovered within a pre-assigned accuracy,[A. Laio and M. Parrinello, PNAS 2002]. The method allows a good control over the error on the recovered system entropy. This fact is exploited to obtain D(E) more efficiently by combining measurements at different temperatures. The accuracy and efficiency of the method are tested for the two-dimensional Ising model (up to size 50x50) by comparison with both exact results and previous studies. This method is a general one and should be applicable to more realistic model systems

Atomic and itinerant effects at the transition metal x-ray absorption K-pre-edge exemplified in the case of V2_2O3_3

X-ray absorption spectroscopy is a well established tool for obtaining information about orbital and spin degrees of freedom in transition metal- and rare earth-compounds. For this purpose usually the dipole transitions of the L- (2p to 3d) and M- (3d to 4f) edges are employed, whereas higher order transitions such as quadrupolar 1s to 3d in the K-edge are rarely studied in that respect. This is due to the fact that usually such quadrupolar transitions are overshadowed by dipole allowed 1s to 4p transitions and, hence, are visible only as minor features in the pre-edge region. Nonetheless, these features carry a lot of valuable information, similar to the dipole L-edge transition, which is not accessible in experiments under pressure due to the absorption of the diamond anvil pressurecell. We recently performed a theoretical and experimental analysis of such a situation for the metal insulator transition of (V(1-x)Crx)2O3. Since the importance of the orbital degrees of freedom in this transition is widely accepted, a thorough understanding of quadrupole transitions of the vanadium K-pre-edge provides crucial information about the underlying physics. Moreover, the lack of inversion symetry at the vanadium site leads to onsite mixing of vanadium 3d- and 4p- states and related quantum mechanical interferences between dipole and quadrupole transitions. Here we present a theoretical analysis of experimental high resolution x-ray absorption spectroscopy at the V pre-K edge measured in partial fluorescence yield mode for single crystals. We carried out density functional as well as configuration interaction calculations in order to capture effects coming from both, itinerant and atomic limits

Partnership, ownership and control: the impact of corporate governance on employment relations

Prevailing patterns of dispersed share ownership and rules of corporate governance for UK listed companies appear to constrain the ability of managers to make credible, long-term commitments to employees of the kind needed to foster effective labour-management partnerships. We present case study evidence which suggests that such partnerships can nevertheless emerge where product market conditions and the regulatory environment favour a stakeholder orientation. Proactive and mature partnerships may also be sustained where the board takes a strategic approach to mediating between the claims of different stakeholder groups, institutional investors are prepared to take a long-term view of their holdings, and strong and independent trade unions are in a position to facilitate organisational change

Determining the crystal-field ground state in rare earth Heavy Fermion materials using soft-x-ray absorption spectroscopy

We infer that soft-x-ray absorption spectroscopy is a versatile method for the determination of the crystal-field ground state symmetry of rare earth Heavy Fermion systems, complementing neutron scattering. Using realistic and universal parameters, we provide a theoretical mapping between the polarization dependence of Ce $M_{4,5}$ spectra and the charge distribution of the Ce $4f$ states. The experimental resolution can be orders of magnitude larger than the $4f$ crystal field splitting itself. To demonstrate the experimental feasibility of the method, we investigated CePd$_2$Si$_2$, thereby settling an existing disagreement about its crystal-field ground state

Inequivalent routes across the Mott transition in V2O3 explored by X-ray absorption

The changes in the electronic structure of V2O3 across the metal-insulator transition induced by temperature, doping and pressure are identified using high resolution x-ray absorption spectroscopy at the V pre K-edge. Contrary to what has been taken for granted so far, the metallic phase reached under pressure is shown to differ from the one obtained by changing doping or temperature. Using a novel computational scheme, we relate this effect to the role and occupancy of the a1g orbitals. This finding unveils the inequivalence of different routes across the Mott transition in V2O

Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble

A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of the self-overlap is controlled in a similar manner as the multicanonical ensemble. As a consequence, the ensemble --the multi-self-overlap ensemble-- contains adequate portions of self-overlapping conformations as well as higher energy ones. It is shown that the multi-self-overlap ensemble algorithm reproduce correctly the canonical averages at finite temperatures of the HP model of lattice proteins. Moreover, it outperforms massively a standard multicanonical algorithm for a difficult example of a polymer with 8-stickers. Alternative algorithm based on exchange Monte Carlo method is also discussed.Comment: 5 Pages, 4 Postscript figures, uses epsf.st