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

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

Could a different management routine that strengthens the mother-offspring bond contribute to a more efficient organic piglet production?

In current Swedish organic piglet production full reproductive potential of the sows and growth potential of piglets are not achieved. The efficiency is held back by occurrence of lactational oestrus, low litter weight and large weight variation within litter. Therefore it is critical that these obstacles are reduced in a way that is easy to adapt in practice and does not contradict the ideas behind organic animal husbandry. This project aims to an improvement of the conditions needed to efficiently produce organic piglets in a batch wise manner. The batch wise breeding will reduce production costs and increase disease control. Our preliminary results indicate that the sow’s weaning to oestrus interval can be affected by the time spent in individual farrowing pen during the lactational period

Kinematic and spermatic recovery after selection by centrifugation in colloid solutions of ovine cryopreserved semen

ABSTRACT Frozen and thawed ovine semen undergo morphological and functional changes that prevent or decrease the efficiency of fertilization. Sperm selection methods seek to improve the quality and viability of the fertilizing materials. Four sperm selection methods were employed, using two silica colloidal solutions coated with silane (silica colloidal-silane) or by polyvinylpyrrolidone (silica colloidal-PVP), and varying the volume of colloidal solution. Sperm kinematic and sperm recovery were evaluated by means of CASA. The protocols using silica colloidal-silane showed higher total motility (TM), progressive motility (PM) and percentage of rapid sperm (%RAP) compared to the methods employing silica colloidal-PVP and to the samples prior to sperm selection. The silica colloidal-PVP had greater sperm recovery compared to the silica colloidal-silane. Only the method using 4mL of silica colloidal-PVP was not efficient in selecting samples with better quality compared to the samples analyzed prior to sperm selection. The methods using lower volumes of colloidal solution did not differ from those using higher volumes and the best results were shown by the method with 1mL silica colloidal-silane. The results found in the study indicated greater efficiency of the silica colloidal-silane solution for sperm selection of thawed ovine semen when compared to selection using silica colloidal-PVP. The method using 1mL of silica colloidal-silane was equally efficient to the method with higher volume, presenting itself as an alternative to process samples with lower sperm concentration

Investigation of an IC Engine Intake Flow Based on Highly Resolved LES and PIV

To reduce emissions and fuel consumption, the current generation of gasoline engines uses technologies such as direct injection, downsizing and supercharging. All of them require a strong vortical in-cylinder charge motion, usually described as “tumble”, to improve fuel-air mixing and enhance flame propagation. The tumble development strongly depends on the flow field during the intake stroke. This flow field is dominated by the intake jet, which has to be captured well in the simulation. This work investigates the intake jet on a steady-state flow bench, especially in the vicinity of the intake valve. At first, the general flow dynamics of the intake jet for three different valve lifts and three different mass flows were investigated experimentally. For the smallest valve lift (3 mm), flow-field measurements using Particle Image Velocimetry (PIV) show that the orientation of the intake jet significantly depends on the air flow rate, attaching to the pent roof for low flow rates. This phenomenon is less pronounced for higher valve lifts. An intermediate valve lift and flow rate were chosen for further investigations by scale-resolving simulations. Three different meshes (coarse, medium and fine) and two turbulence models (Sigma and Detached Eddy Simulation-Shear Stress Transport (DES-SST)) are applied to consider their effect on the numerical results. An ad-hoc post-processing methodology based on the ensemble-averaged velocity field is presented capturing the jet centerline’s mean velocity and velocity fluctuations as well as its orientation, curvature and penetration depth. The simulation results are compared to each other as well as to measurements by PIV