Helix Formation and Folding in an Artificial Peptide

We study the relation between $\alpha$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. The free-energy landscape of the peptide is evaluated for various temperatures. Our data indicate that folding of this peptide is a two-step process: in a first step two $\alpha$-helices are formed which afterwards re-arrange themselves into a U-like structure.Comment: 15 pages, with 9 eps 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

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

Generalized Ensemble and Tempering Simulations: A Unified View

From the underlying Master equations we derive one-dimensional stochastic processes that describe generalized ensemble simulations as well as tempering (simulated and parallel) simulations. The representations obtained are either in the form of a one-dimensional Fokker-Planck equation or a hopping process on a one-dimensional chain. In particular, we discuss the conditions under which these representations are valid approximate Markovian descriptions of the random walk in order parameter or control parameter space. They allow a unified discussion of the stationary distribution on, as well as of the stationary flow across each space. We demonstrate that optimizing the flow is equivalent to minimizing the first passage time for crossing the space, and discuss the consequences of our results for optimizing simulations. Finally, we point out the limitations of these representations under conditions of broken ergodicity.Comment: 11 pages Latex, 2 eps figures, revised version, typos corrected, PRE in pres

The role of the spin in quasiparticle interference

Quasiparticle interference patterns measured by scanning tunneling microscopy (STM) can be used to study the local electronic structure of metal surfaces and high temperature superconductors. Here, we show that even in non-magnetic systems the spin of the quasiparticles can have a profound effect on the interference patterns. On Bi(110), where the surface state bands are not spin-degenerate, the patterns are not related to the dispersion of the electronic states in a simple way. In fact, the features which are expected for the spin-independent situation are absent and the observed interference patterns can only be interpreted by taking spin-conserving scattering events into account.Comment: 4 pages, 2 figure

Multicanonical Study of the 3D Ising Spin Glass

We simulated the Edwards-Anderson Ising spin glass model in three dimensions via the recently proposed multicanonical ensemble. Physical quantities such as energy density, specific heat and entropy are evaluated at all temperatures. We studied their finite size scaling, as well as the zero temperature limit to explore the ground state properties.Comment: FSU-SCRI-92-121; 7 pages; sorry, no figures include

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

Monte Carlo simulation and global optimization without parameters

We propose a new ensemble for Monte Carlo simulations, in which each state is assigned a statistical weight $1/k$, where $k$ is the number of states with smaller or equal energy. This ensemble has robust ergodicity properties and gives significant weight to the ground state, making it effective for hard optimization problems. It can be used to find free energies at all temperatures and picks up aspects of critical behaviour (if present) without any parameter tuning. We test it on the travelling salesperson problem, the Edwards-Anderson spin glass and the triangular antiferromagnet.Comment: 10 pages with 3 Postscript figures, to appear in Phys. Rev. Lett

Long Range Order at Low Temperature in Dipolar Spin Ice

Recently it has been suggested that long range magnetic dipolar interactions are responsible for spin ice behavior in the Ising pyrochlore magnets ${\rm Dy_{2}Ti_{2}O_{7}}$ and ${\rm Ho_{2}Ti_{2}O_{7}}$. We report here numerical results on the low temperature properties of the dipolar spin ice model, obtained via a new loop algorithm which greatly improves the dynamics at low temperature. We recover the previously reported missing entropy in this model, and find a first order transition to a long range ordered phase with zero total magnetization at very low temperature. We discuss the relevance of these results to ${\rm Dy_{2}Ti_{2}O_{7}}$ and ${\rm Ho_{2}Ti_{2}O_{7}}$.Comment: New version of the manuscript. Now contains 3 POSTSCRIPT figures as opposed to 2 figures. Manuscript contains a more detailed discussion of the (i) nature of long-range ordered ground state, (ii) finite-size scaling results of the 1st order transition into the ground state. Order of authors has been changed. Resubmitted to Physical Review Letters Contact: [email protected]