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We study the thermodynamic behavior of a model protein with 54 amino acidsthat is designed to form 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 torsion angles as its only degrees of freedom.The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the charact
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
We study the statistical properties of hydrophobic/polar model sequences with unique native states on the square lattice. It is shown that this ensemble of sequences differs from random sequences in significant ways in terms of both the distribution of hydrophobicity along the chains and total hydrophobicity. Whenever statistically feasible, the analogous calculations are performed for a set of re
BACKGROUND: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplishing this is a nested Monte Carlo where the conformation space is explored over and over again for different fixed sequences; this requires excessive computational demand. Several approximate attempts to remedy this situation
We have developed a simple optimization procedure for assigning binary values to amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The maximization is carried out at fixed composition. For compositions approximately corresponding to an equipartition of the residues, the optimal encoding is found to
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional pr
Background/Objective: A biphasic ceramic bone substitute consisting of calcium sulfate and hydroxyapatite has been reported to give good clinical outcome regarding bone regeneration and may serve as a carrier for antibiotics in the treatment of bone infections. Often, the overlying muscle is in direct contact with the synthetic graft. The dissolving bone substitute induces inflammation, which may
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
This paper presents findings on the role of online traveller information services in regional public transport for olderpeople and people with functional limitations. An explanatory mixed methods design was used. A quantitative questionnairestudy of the target group’s need of traveller information and use of online traveller information services provided the basisfor a qualitative focus group stud
In this work we have investigated face verification based on deep representations from Convolutional Neural Networks (CNNs) to find an accurate and compact face descriptor trained only on a restricted amount of face image data. Transfer learning by fine-tuning CNNs pre-trained on large-scale object recognition has been shown to be a suitable approach to counter a limited amount of target domain da
A well-planned waiting area is crucial for automatic milking systems. In an enclosed waiting area, cows of different rank compete for entering the milking station and they are exposed for a variety of social interactions. Such interactions could increase standing time and delay milking, which may result in stress, lameness, impaired welfare and reduced performance. The aim was to monitor the waiti
Jag avser att redogöra för sambandet, eller förhållandet, mellan formlerna 1+1=♥ och (∀a) (Ǝb) (∀c) [[(cϵa) u λ (c)] → (cϵ b)]. Då den förra formeln är hämtad från ett internetforum för personer diagnostiserade med adhd och deras anhöriga, så är den senare hämtad från den franske filosofen Alain Badious (2005a) mängdteori vari han närmar sig en ontologi om varat. Mitt eget avhandlingsprojekt rör d
BACKGROUND: A mutation found in the BRCA1 or BRCA2 gene of a breast tumor could be either germline or somatically acquired. The prevalence of somatic BRCA1/2 mutations and the ratio between somatic and germline BRCA1/2 mutations in unselected breast cancer patients are currently unclear.PATIENTS AND METHODS: Paired normal and tumor DNA was analyzed for BRCA1/2 mutations by massively parallel seque
Lesions of ERBB2, PTEN, and PIK3CA activate the phosphatidylinositol 3-kinase (PI3K) pathway during cancer development by increasing levels of phosphatidylinositol-3,4,5-triphosphate (PIP(3)). 3-Phosphoinositide-dependent kinase 1 (PDK1) is the first node of the PI3K signal output and is required for activation of AKT. PIP(3) recruits PDK1 and AKT to the cell membrane through interactions with the
The social mechanism program has been successful in sociology and neighboring social science disciplines, such as criminology and political science. However, in our view the literature on social mechanisms is still too preoccupied with intratheoretical and metatheoretical discussions, and we find very few empirical applications. This is surprising since one of the basic aims of the social mechanis
