Folding thermodynamics of three beta-sheet peptides: A model study

We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic attraction. The native populations obtained for these three sequences are in good agreement with experimental data. We also show that the apparent native population depends on which observable is studied; the hydrophobicity energy and the number of native hydrogen bonds give different results. The magnitude of this dependence matches well with the results obtained in two different experiments on the beta-hairpin.Comment: 17 pages, 7 figures, to appear in Protein

Stability of the Kauffman Model

Random Boolean networks, the Kauffman model, are revisited by means of a novel decimation algorithm, which reduces the networks to their dynamical cores. The average size of the removed part, the stable core, grows approximately linearly with N, the number of nodes in the original networks. We show that this can be understood as the percolation of the stability signal in the network. The stability of the dynamical core is investigated and it is shown that this core lacks the well known stability observed in full Kauffman networks. We conclude that, somewhat counter-intuitive, the remarkable stability of Kauffman networks is generated by the dynamics of the stable core. The decimation method is also used to simulate large critical Kauffman networks. For networks up to N=32 we perform full enumeration studies. Strong evidence is provided for that the number of limit cycles grows linearly with N. This result is in sharp contrast to the often cited $\sqrt{N}$ behavior.Comment: 12 pages, 4 figure

Hydrogen Bonds, Hydrophobicity Forces and the Character of the Collapse Transition

We study the thermodynamic behavior of a model protein with 54 amino acids that 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 character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix sequence.Comment: 14 pages, 8 figure

‘I had a lump in my stomach’: Swedish gay and lesbian students' experiences of their time in school

Objectives: Gay and lesbian youth can experience ignorance and a lack of acknowledgement surrounding their sexual orientation during their time in school. This qualitative interview study describes how Swedish gay and lesbian students experience their secondary school years on the basis that society has heteronormative values. Methods: The data is based on eight telephone interviews with gay and lesbian young adults, aged 18–25 and was analysed using a qualitative narrative approach. Findings: The findings presented four themes: not fitting into the norm of heterosexuality, lacking confirmation of their own homosexuality, finding courage, seeing the school as a supportive or a non-supportive environment. Conclusions: A way to normalise homosexuality can be to discuss sexual development and attraction from a health-promoting perspective. Professionals working in school need to feel comfortable with issues such as sexuality in order to create a situation of confidence for the student

Training young engineers to see

This case study in the professional education of engineers is based on a Talent Programme at Combitech in Sweden, in association with the Royal Institute of Technology. The approach is based on use of the Dialogue Seminar Method. © 2011 The Author(s).</p

Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space

We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors approximately local deformations of the chain. The degree of bias is controlled by a parameter b. The method is tested on a reduced model protein with 54 amino acids and the Ramachandran torsion angles as its only degrees of freedom, for different b. Without excessive fine tuning, we find that the effective step size can be increased by a factor of three compared to the unbiased b=0 case. The method may be useful for kinetic studies, too.Comment: 14 pages, 4 figure

Effect of blood plasma collected after adrenocorticotropic hormone administration during the preovulatory period in the sow on oocyte in vitro maturation

Reproduction may be affected by stressful events changing the female endocrine or metabolic profile. An altered environment during oocyte development could influence the delicate process of oocyte maturation. Here, the effect of simulated stress by media supplementation with blood plasma from sows after adrenocorticotropic hormone (ACTH) administration during the preovulatory period was assessed. Oocytes were matured for 46 h in the presence of plasma from ACTH-treated sows, or plasma from NaCl-treated control sows, or medium without plasma (BSA group). The plasma used had been collected at 36 h and 12 h (± 2 h) before ovulation (for the first 24 h + last 22 h of maturation, respectively). Subsequent fertilisation and embryo development were evaluated. Actin cytoskeleton and mitochondrial patterns were studied by confocal microscopy both in the oocytes and the resulting blastocysts. Nuclear maturation did not differ between treatments. Subtle differences were observed in the actin microfilaments in oocytes; however, mitochondrial patterns were associated with the treatment (P<0.001). These differences in mitochondrial patterns were not reflected by in vitro outcomes, which were similar in all groups. In conclusion, an altered hormonal environment provided by a brief exposure to plasma from ACTH-treated sows during in vitro oocyte maturation, could induce alterations in actin cytoskeleton and mitochondrial patterns in oocytes. However, these changes might not hamper the subsequent in vitro embryo development

The Greenhouse Gas Emission from Portland Cement Concrete Pavement Construction in China.

This study proposes an inventory analysis method to evaluate the greenhouse gas (GHG) emissions from Portland cement concrete pavement construction, based on a case project in the west of China. The concrete pavement construction process was divided into three phases, namely raw material production, concrete manufacture and pavement onsite construction. The GHG emissions of the three phases are analyzed by a life cycle inventory method. The CO₂e is used to indicate the GHG emissions. The results show that for 1 km Portland cement concrete pavement construction, the total CO₂e is 8215.31 tons. Based on the evaluation results, the CO₂e of the raw material production phase is 7617.27 tons, accounting for 92.7% of the total GHG emissions; the CO₂e of the concrete manufacture phase is 598,033.10 kg, accounting for 7.2% of the total GHG emissions. Lastly, the CO₂e of the pavement onsite construction phase is 8396.59 kg, accounting for only 0.1% of the total GHG emissions. The main greenhouse gas is CO₂ in each phase, which accounts for more than 98% of total emissions. N₂O and CH₄ emissions are relatively insignificant

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

Life Cycle Assessment of Concrete

Detta är en studie på betong som följer metodiken för en livscykelanalys (LCA). Studien är gjord för två typer av betong, vanlig husbyggnadsbetong och frostbehändig betong som används vid brobygge. Speciellt fokus läggs på det flyttillsatsmedel som tillsätts i betongen. Användningsfasen är inte medtagen i studien på grund av att det inte är specificerat vilken typ av betongkonstruktion som betongen används i och betongen antas även vara inert under denna fas.Resultaten visar att det är råmaterialproduktionen och transporterna som är de största bidragande orsakerna till betongens totala miljöpåverkan. Den process i råmaterialproduktionen som bidrar mest till miljöpåverkan är cementproduktionen. Inom transporterna så är det transporten av betong, följt av transporten av cement till depå som bidrar mest. Miljöpåverkan från frostbehändig betong är mellan 24 - 41 % högre än den från normal betong. Orsaken till detta är att den frostbehändiga betongen innehåller mer cement. Flyttillsatsmedel bidrar med mellan 0.4 - 10.4 % av betongens totala miljöpåverkan, minst till växthuspotentialen (GWP) och mest till potentialen för bildningen av fotokemiska oxidanter (POCP). Även toxiciteten hos flyttillsatsmedel har bedömts och slutsatsen är att det låga läckage av flyttillsatsmedel som sker från betong sannolikt inte orsakar någon risk för varken miljö eller människor