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

Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002

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

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

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

Metropolis simulations of Met-Enkephalin with solvent-accessible area parameterizations

We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300$K$. For the energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied. The simulations are compared with one another, with simulations with a distance dependent electrostatic permittivity $\epsilon (r)$, and with vacuum simulations ($\epsilon =2$). Parallel tempering and the biased Metropolis techniques RM$_1$ are employed and their performance is evaluated. The measured observables include energy and dihedral probability densities (pds), integrated autocorrelation times, and acceptance rates. Two of the ASP sets turn out to be unsuitable for these simulations. For all other systems selected configurations are minimized in search of the global energy minima, which are found for the vacuum and the $\epsilon(r)$ system, but for none of the ASP models. Other observables show a remarkable dependence on the ASPs. In particular, we find three ASP sets for which the autocorrelations at 300$$K are considerably smaller than for vacuum simulations.Comment: 10 pages and 8 figure

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