Solvable Models of Random Hetero-Polymers at Finite Density: I. Statics

We introduce $\infty$-dimensional versions of three common models of random hetero-polymers, in which both the polymer density and the density of the polymer-solvent mixture are finite. These solvable models give valuable insight into the problems related to the (quenched) average over the randomness in statistical mechanical models of proteins, without having to deal with the hard geometrical constraints occurring in finite dimensional models. Our exact solution, which is specific to the $\infty$-dimensional case, is compared to the results obtained by a saddle-point analysis and by the grand ensemble approach, both of which canalso be applied to models of finite dimension. We find, somewhat surprisingly, that the saddle-point analysis can lead to qualitatively incorrect results.Comment: 16 pages, 17 figure

Tyrosine-glycine revisited : resolving the discrepancy between theory and experiment

LFH acknowledges the Engineering and Physical Sciences Research Council for studentship support through the Doctoral Training Account scheme.Energies of 20 conformers of the Tyr-Gly dipeptide were computed using DSD-PBEP86-D3BJ/aug-cc-VTZ, with geometries from M06-2X/6-31+G* and B97-D/6-31+G*. At 0 K, these energies support the earlier finding from MP2/6-31+G*//B3LYP/6-31+G*, that the most stable conformer is folded and H-bonded. However, when free-energy corrections at 400 K are added, non-H-bonded conformers are the most stable. This supports an earlier spectroscopic study in which H-bonded conformers were absent. Of the four most stable conformers at 400 K, two were not matched with spectra in the experimental study, but we argue that all four can in fact be plausibly assigned to the experimental spectra.PostprintPeer reviewe

Swollen-Collapsed Transition in Random Hetero-Polymers

A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139 (1994)]. The transfer matrix technique is used to study various constrained annealed systems which approximate at various degrees of accuracy the original quenched model. For highly hydrophobic chains an ordinary $\theta$-point transition is found from a high temperature swollen phase to a low temperature compact phase. Depending on the type of constrained averages, at very low temperatures a swollen phase or a coexistence between compact and swollen phases are found. The results are carefully compared with the corresponding ones obtained in the continuum limit, and various improvements in the original calculations are discussed.Comment: 13 pages, 8 figures; revised version with minor changes, accepted for publication in European Physical Journal

Climate control of a bulk storage room for foodstuffs

A storage room contains a bulk of potatoes that produce heat due to respiration. A ventilator blows cooled air around to keep the potatoes cool and prevent spoilage. The aim is to design a control law such that the product temperature is kept at a constant, desired level. This physical system is modelled by a set of nonlinear coupled partial differential equations (pde's) with nonlinear input. Due to their complex form, standard control design will not be adequate. A novel modelling procedure is proposed. The input is considered to attain only discrete values. Analysis of the transfer functions of the system in the frequency domain leads to a simplification of the model into a set of static ordinary differential equations ode's). The desired control law is now the optimal time to switch between the discrete input values on an intermediate time interval. The switching time can be written as a symbolic expression of all physical parameters of the system. Finally, a dynamic controller can be designed that regulates the air temperature on a large time interval, by means of adjustment of the switching time

Cluster Derivation of the Parisi Scheme for Disordered Systems

We propose a general quantitative scheme in which systems are given the freedom to sacrifice energy equi-partitioning on the relevant time-scales of observation, and have phase transitions by separating autonomously into ergodic sub-systems (clusters) with different characteristic time-scales and temperatures. The details of the break-up follow uniquely from the requirement of zero entropy for the slower cluster. Complex systems, such as the Sherrington-Kirkpatrick model, are found to minimise their free energy by spontaneously decomposing into a hierarchy of ergodically equilibrating degrees of freedom at different (effective) temperatures. This leads exactly and uniquely to Parisi's replica symmetry breaking scheme. Our approach, which is somewhat akin to an earlier one by Sompolinsky, gives new insight into the physical interpretation of the Parisi scheme and its relations with other approaches, numerical experiments, and short range models. Furthermore, our approach shows that the Parisi scheme can be derived quantitatively and uniquely from plausible physical principles.Comment: 6 pages, 3 figures, proceedings of international conference on "Disordered And Complex Systems", 10-14 July 2000 King's College Londo

Solvable Lattice Gas Models of Random Heteropolymers at Finite Density: II. Dynamics and Transitions to Compact States

In this paper we analyse both the dynamics and the high density physics of the infinite dimensional lattice gas model for random heteropolymers recently introduced in \cite{jort}. Restricting ourselves to site-disordered heteropolymers, we derive exact closed deterministic evolution equations for a suitable set of dynamic order parameters (in the thermodynamic limit), and use these to study the dynamics of the system for different choices of the monomer polarity parameters. We also study the equilibrium properties of the system in the high density limit, which leads to a phase diagram exhibiting transitions between swollen states, compact states, and regions with partial compactification. Our results find excellent verification in numerical simulations, and have a natural and appealing interpretation in terms of real heteropolymers.Comment: 12 pages, 8 eps figures, revised version (to be published in EPJ

Image derived input functions for cerebral PET studies

Lammertsma, A.A. [Promotor]Boellaard, R. [Copromotor]Lubberink, M. [Copromotor