Fitting a function to time-dependent ensemble averaged data

Time-dependent ensemble averages, i.e., trajectory-based averages of some observable, are of importance in many fields of science. A crucial objective when interpreting such data is to fit these averages (for instance, squared displacements) with a function and extract parameters (such as diffusion constants). A commonly overlooked challenge in such function fitting procedures is that fluctuations around mean values, by construction, exhibit temporal correlations. We show that the only available general purpose function fitting methods, correlated chi-square method and the weighted least squares method (which neglects correlation), fail at either robust parameter estimation or accurate error estimation. We remedy this by deriving a new closed-form error estimation formula for weighted least square fitting. The new formula uses the full covariance matrix, i.e., rigorously includes temporal correlations, but is free of the robustness issues, inherent to the correlated chi-square method. We demonstrate its accuracy in four examples of importance in many fields: Brownian motion, damped harmonic oscillation, fractional Brownian motion and continuous time random walks. We also successfully apply our method, weighted least squares including correlation in error estimation (WLS-ICE), to particle tracking data. The WLS-ICE method is applicable to arbitrary fit functions, and we provide a publically available WLS-ICE software.Comment: 47 pages (main text: 15 pages, supplementary: 32 pages

Folding in two-dimenensional off-lattice models of proteins

Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that the rank-ordering-based scheme of the assignment of contact energies typically fails in off-lattice models even though it generates high stability of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in which the interaction potentials are restricted to the native contacts in a target shape, gives rise to good folding properties. Involving other contacts deteriorates these properties.Comment: REVTeX, 9 pages, 8 EPS figure

Three-helix-bundle Protein in a Ramachandran Model

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.Comment: 15 pages, 7 figure

The Crumpling Transition Revisited

The ``crumpling" transition, between rigid and crumpled surfaces, has been object of much discussion over the past years. The common lore is that such transition should be of second order. However, some lattice versions of the rigidity term on fixed connectivity surfaces seem to suggest that the transition is of higher order instead. While some models exhibit what appear to be lattice artifacts, others are really indistiguishable from models where second order transitions have been reported and yet appear to have third order transitions.Comment: Contribution to Lattice 92. 4 pages. espcrc2.sty file included. 6 figures upon request. UB-ECM-92/30 and UAB-FT-29

Disordered Heteropolymers with Crosslinks - Phase Diagram and Conformational Transitions

We study the phase behavior of random heteropolymers (RHPs) with quenched cross-links, a novel polymer class of technological and biological relevance, and show the possible occurrence of freezing with few chain conformations sampled. The sensitivity of the frozen phase microstructure to the disorder components is elucidated at positive solubility parameter values; at low T's segregated microphases form, while at a finite T, a first order conformational transition occurs, and is attributed to statistical matching of large microphases bounded by cross-links. The end of the symmetry broken regime stabilization by cross-links occurs at a higher T by a second order conformational transition. \\icrophases form, while at a finite T, a first order conformational transition occurs, and is attributed to statistical matching of large microphases bounded by cross-links. The end of the symmetry broken regime stabilization by cross-links occurs at a higher T by a second order conformational transition.Comment: 5 pages, 2 ps. figures. submitted to Chem. Phys. Let

The Relevant Scale Parameter in the High Temperature Phase of QCD

We introduce the running coupling constant of QCD in the high temperature phase, $\tilde{g}^2(T)$, through a renormalization scheme where the dimensional reduction is optimal at the one-loop level. We then calculate the relevant scale parameter, $\Lambda_T$, which characterizes the running of $\tilde{g}^2(T)$ with $T$, using the background field method in the static sector. It is found that $\Lambda_T/\Lambda_{\overline{\text{MS}}} =e^{(\gamma_E+1/22)}/(4\pi)\approx 0.148$. We further verify that the coupling $\tilde{g}^2(T)$ is also optimal for lattice perturbative calculations. Our result naturally explains why the high temperature limit of QCD sets in at temperatures as low as a few times the critical temperature. In addition, our $\Lambda_T$ agrees remarkably well with the scale parameter determined from the lattice measurement of the spatial string tension of the SU(2) gauge theory at high $T$.Comment: 13 pages, RevTeX 3.0, no figures. Full postscript version available via anonymous ftp (192.84.132.4) at ftp://risc0.ca.infn.it/pub/private/lissia/infnca-th-94-24.p

Use of the Metropolis algorithm to simulate the dynamics of protein chains

The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a simplified protein model, it is possible to show that setting a threshold of 1 degree on the movement of the dihedrals of the protein backbone in a single Monte Carlo step, the mean quantities associated with the off-equilibrium dynamics (e.g., energy, RMSD, etc.) are well reproduced, while the good description of higher moments requires smaller moves. An important result is that the time duration of a Monte Carlo step depends linearly on the temperature, something which should be accounted for when doing simulations at different temperatures.Comment: corrections to the text and to the figure

Parity breaking at high temperature and density

We investigate the question of parity breaking in three-dimensional Euclidean SU(2) gauge-Higgs theory by Monte Carlo simulations. We observe no sign of spontaneous parity breaking in the behaviour of both local and non-local gauge invariant operators. However, the presence of parity odd terms in the action can induce a phase transition to a parity odd ground state which is characterized by a Chern-Simons like condensate. The implications for various proposed scenarios of fermion number non-conservation is discussed.Comment: 20 pages, 13 figures not included, sorr

The Instanton Density at Finite Temperatures

For {\it low} T new strict results for the instanton density n(T) are reported. Using the PCAC methods, we express n(T) in terms of {\it vacuum} average values of certain operators, times their {\it calculated} T-dependence. At high T, we discuss the {\it applicability} limits of the perturbative results. We further speculate about possible behaviour of n(T) at $T\sim T_c$

Viscosities of Quark-Gluon Plasmas

The quark and gluon viscosities are calculated in quark-gluon plasmas to leading orders in the coupling constant by including screening. For weakly interaction QCD and QED plasmas dynamical screening of transverse interactions and Debye screening of longitudinal interactions controls the infrared divergences. For strongly interacting plasmas other screening mechanisms taken from lattice calculations are employed. By solving the Boltzmann equation for quarks and gluons including screening the viscosity is calculated to leading orders in the coupling constant. The leading logarithmic order is calculated exactly by a full variational treatment. The next to leading orders are found to be very important for sizable coupling constants as those relevant for the transport properties relevant for quark-gluon plasmas created in relativistic heavy ion collisions and the early universe.Comment: 12 pages + 6 figures, report LBL-3492