It has long been known that the three largest subunits in the membrane domain (NuoL, NuoM and NuoN) of complex I are homologous to each other, as well as to two subunits (MrpA and MrpD) from a Na+ /H+ antiporter, Mrp. MrpA and NuoL are more similar to each other and the same is true for MrpD and NuoN. This suggests a functional differentiation which was proven experimentally in a deletion strain m

An implicit water all-atom model is used to study folding, aggregation and mechanical unfolding of small proteins. Physically reasonable results obtained for a variety of applications indicate healthy global properties of the interaction potential.

Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is explored over and over again for different fixed sequences. In this paper we discuss an alternative Monte Carlo approach, multisequence design, where conformation and sequenc

We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the collapse temperature, signalling a possible low-temperature phase transition. The system size dependence at this maximum is investigated both with and without

We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength κ of the local interactions; κ=0 corresponds to the well-known HP model [K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all str

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