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A method for sequence optimization in protein models is presented. The approach, which has inherited its basic philosophy from recent work by Deutsch and Kurosky [Phys. Rev. Lett. 76, 323 (1996)] by maximizing conditional probabilities rather than minimizing energy functions, is based upon a different and very efficient multisequence Monte Carlo scheme. By construction, the method ensures that the
Folding properties of a two-dimensional toy protein model containing only two amino acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entir
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobia and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional protei
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two dimensional and has two different "amino acids." Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level
We develop the hybrid Monte Carlo method for simulations of single off-lattice polymer chains. We discuss implementation and choice of simulation parameters in some detail. The performance of the algorithm is tested on models for homopolymers with short- or long-range self-repulsion, using chains with 16≤N≤512 monomers. Without excessive fine tuning, we find that the computational cost grows as N2
It has been suggested that the modified Steiner action functional has desirble properties for a random surface action. In this paper we investigate the scaling of the string tension and massgap in a variant of this action on dynamically triangulated random surfaces and compare the results with the gaussian plus extrinsic curvature actions that have been used previously.
We study the thermodynamic behaviour of the random chain model proposed by Iori, Marinari and Parisi and how this behaviour depends on the actual sequence of interactions along the chain. The properties of randomly chosen sequences are compared to those of designed sequences obtained through a simulated annealing procedure in sequence space. We show that for designed sequences the transition to th
In some high-profile Swedish cases on violence in intimate relationships, policemen and judges have been blamed for missing important aspects of the victim’s vulnerable situation and the ongoing violence, and indirectly causing the death of the women victims. When these types of cases encounter the criminal justice system, two seemingly opposites are confronted: autonomy and vulnerability. In dete
I denna text lyfter doktoranderna och aktivisterna Emma Söderman och Pouran Djampour fram organiseringen av No Border Musical och Asylstaffetten som exempel för att fråga oss om hur politiskt aktörskap kan göras möjligt i en samhällsordning där medborgarskap ses som en förutsättning för politiskt deltagande.
Phosphor thermometry, a remote temperature sensing technique, is widely implemented to measure the temperature of different combustion engines components. The presence of engine lubricant can influence the behavior of the applied sensor materials, known as thermographic phosphors, and thus leading to erroneous temperature measurements. The effect of two engine lubricants on decay times originating
Sweden's reputation as one of the most encompassing welfare states in the world is maintained by means of a good self-image, not least in relation to refugee policies. At the same time, external authorities have been critical of Sweden's handling of the process of seeking asylum. Drawing on Stanley Cohen's concepts of denial and partial acknowledgment, the article explores how Swedish state offici
On the basis of two points of departure: (1) no state has clean hands and (2) the types of crime a state commits vary with state formations, this article explores cases where the Swedish state and its agencies have been held responsible for some form of wrongdoing. Drawing on a total of 8,561 judgments issued against the state by agencies of control (the Parliamentary Ombudsman, the Chancellor of
We investigate the workings of an early eighteenth century instrument for predicting eclipses described by the French astronomer de la Hire in his book Tabulae Astronomicae.Two Burmese eclipse calculations, one lunar and one solar, are analysed using examples from a Burmese manuscript. The fundamental parameters are with some important exceptions the same as in the Suryasiddhanta, but the handling of, for instance, parallax in the solar eclipse is different and much simplified. Specific to Burma are also the shadow calculations.
