Markov modeling of peptide folding in the presence of protein crowders

We use Markov state models (MSMs) to analyze the dynamics of a $\beta$-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin inhibitor (BPTI) and GB1]. In these systems, at the temperature used, the peptide can be folded or unfolded and bound or unbound to crowder molecules. Four or five major free-energy minima can be identified. To estimate the dominant MC relaxation times of the peptide, we build MSMs using a range of different time resolutions or lag times. We show that stable relaxation-time estimates can be obtained from the MSM eigenfunctions through fits to autocorrelation data. The eigenfunctions remain sufficiently accurate to permit stable relaxation-time estimation down to small lag times, at which point simple estimates based on the corresponding eigenvalues have large systematic uncertainties. The presence of the crowders have a stabilizing effect on the peptide, especially with BPTI crowders, which can be attributed to a reduced unfolding rate $k_\text{u}$, while the folding rate $k_\text{f}$ is left largely unchanged.Comment: 18 pages, 6 figure

Assembling a toolkit for computational dissection of dense protein systems

The cellular interior is a dense environment. Understanding how such an environment impacts the properties of proteins and other macromolecules, as well as how weak, non-specific interactions drive processes such as protein droplet formation through liquid-liquid phase separation, is a major challenge in biological physics. The complexity of this environment often makes experimental studies extremely challenging, leaving an important niche to be filled by simulation studies. Simulations do, however, have their own set of challenges, and to use them to their full potential, a suitable set of computational tools must be developed. Such a toolset must include accurate yet computationally affordable force fields, computationally efficient simulation algorithms, and analysis tools that allow for the extraction of meaningful information from the simulation results.In this thesis, a number of tools for all three areas are developed and/or evaluated. We present an atom level, implicit solvent force field, as well as a coarse-grained continuous HP model which we use for droplet formation studies. We investigate sampling issues in field theory simulations with the complex Langevin equation. We use finite-size scaling analysis to analyse simulations of liquid-liquid phase separation, and Markov state modeling to analyse crowding simulations

Exit choice in fire emergencies - Influencing choice of exit with flashing lights

Fire accidents and evacuation experiments have revealed that people often use familiar exits in fire emergencies. However, the design of emergency exits has also been shown to impact people’s choice of exit. In the present research, the use of flashing lights to direct people to emergency exits is explored in a series of experiments in both buildings and road tunnels. Recommendations concerning how the system should be designed are developed based on the results. In addition, a framework (Theory of Affordances) is used to explain and interpret the empirical findings and a research strategy for testing and developing evacuation systems is proposed

Rigid Calabi-Yau threefolds, Picard Eisenstein series and instantons

Type IIA string theory compactified on a rigid Calabi-Yau threefold gives rise to a classical moduli space that carries an isometric action of U(2,1). Various quantum corrections break this continuous isometry to a discrete subgroup. Focussing on the case where the intermediate Jacobian of the Calabi-Yau admits complex multiplication by the ring of quadratic imaginary integers O_d, we argue that the remaining quantum duality group is an arithmetic Picard modular group PU(2,1;O_d). Based on this proposal we construct an Eisenstein series invariant under this duality group and study its non-Abelian Fourier expansion. This allows the prediction of non-perturbative effects, notably the contribution of D2- and NS5-brane instantons. The present work extends our previous analysis in 0909.4299 which was restricted to the special case of the Gaussian integers O_1=Z[i].Comment: 8 pages, for the proceedings of Quantum Theories and Symmetries V

Traffic Information Signs, Colour Scheme of Emergency Exit Portals and Acoustic Systems for Road Tunnel Emergency Evacuations

This work presents a literature review and a questionnaire study with 62 participants aimed at providing recommendations on the design of a set of evacuation systems for road tunnels: 1) Traffic Information Sign (TIS) - message and size of the sign (large or small), colour scheme, and use of pictograms and/or flashing lights, 2) Emergency exit portal layout - colour scheme, 3) Acoustic systems - voice message and/or warning signals. The TIS is recommended to include the use of two panels which present text (in amber) and flashing lights in one panel and the emergency exit pictorial symbol in green in the other panel. An increased size of the panels has a positive effect on capturing participants’ attention. The recommended colour scheme for the emergency exit portal is safety green for the portal and a “green darker than the safety green” for the door. Vocal messages are not recommended since they may be quite difficult to perceive in tunnels. The use of a warning signal (F_SAW signal) based on British Standards is recommended

Custom Lossless Compression and High-Quality Lossy Compression of White Blood Cell Microscopy Images for Display and Machine Learning Applications

This master's thesis investigates both custom lossless compression and high-quality lossy compression of microscopy images of white blood cells produced by CellaVision's blood analysis systems. A number of different compression strategies have been developed and evaluated, all of which are taking advantage of the specific color filter array used in the sensor in the cameras in the analysis systems. Lossless compression has been the main focus of this thesis. The lossless compression method, of those developed, that gave best result is based on a statistical autoregressive model. A model is constructed for each color channel with external information from the other color channels. The difference between the predictions from the statistical model and the original is further Huffman coded. The method achieves an average bit-rate of 3.0409 bits per pixel on the test set consisting of 604 images. The proposed lossy method is based on taking the difference between the image compressed with an ordinary lossy compression method, JPEG 2000, and the original image. The JPEG 2000 image is saved, as well as the differences at the foreground (i.e. locations with cells), in order to keep the cells identical to the cells in the original image, but allow loss of information for the, not so important, background. This method achieves a bit-rate of 2.4451 bits per pixel, with a peak signal-to-noise-ratio (PSNR) of 48.05 dB

Interim Report: Flashing Lights for Road Tunnel Emergency Exit Portals - A Virtual Reality Experiment

A virtual reality (VR) experiment with 96 participants was carried out to provide recommendations on the design of flashing lights on emergency exit portals for road tunnel emergency evacuation. The experiment was carried out in a Cave Automatic Virtual Environment (CAVE) laboratory at Lund University. A set of variables has been investigated, namely 1) Colour of flashing lights, 2) Flashing rate, 3) The type of light source, 4) the number and layout of the lights on the portal (1 light on top of the exit door, 3 lights of which 1 on top and 2 on the sides of the exit door, or 2 bars on the sides of the exit door). An additional portal design variable has also been investigated, i.e. 5) the use of a window vs a painted running man on the exit door. Participants were immersed in a VR road tunnel emergency evacuation scenario and they were then asked to rank different portal designs using a questionnaire based on the Theory of Affordances. Results show that green or white flashing lights perform better than blue lights in the emergency exit portals. Flashing rate of 1 Hz and 4 Hz performed better than flashing rates at 0.5 Hz. A LED light source performed better than single and double strobe lights. Although the three layouts of the lights under consideration performed similarly, the use of a higher number of lights is deemed to be beneficial. If the door is visible (i.e., if no smoke is taken into consideration in the emergency scenario), the scenario with the running man painted on the door provides equal results than a door with a window. Nevertheless, the use of the window is recommended since it allows seeing behind the door (including the possibility to see the traffic), and reduce people’s hesitation

Profitability of Crop Cultivation in Small Arable Fields When Taking Economic Values of Ecosystem Services into Account

Small arable fields are beneficial with regard to ecosystem services, e.g., concerning biodiversity. By selecting appropriate crops and cultivation practices, arable fields can also be used as carbon sinks. The objectives of this study were to investigate what impact field conditions (e.g., field size and shape) and payments (subsidies) for environmental benefits have on profitability. A dynamic simulation model was used to simulate machine operations in fields of two different shapes and five different sizes (from 0.75 to 12.00 ha). A wide range of crops cultivated in Sweden were investigated (fallow land and plantation of Norway spruce were also included). A perimeter-based subsidy was suggested in order to conserve and promote biodiversity, and an area- and crop-based subsidy was suggested in order to promote sequestration of soil organic carbon (SOC). The results showed that, without financial support and from a purely economic point of view, most field types investigated should be planted with Norway spruce. With currently available subsidies, e.g., EU Common Agricultural Policy (CAP) direct payments, hybrid aspen, poplar, fallow, and extensive ley cultivation are the most profitable crops. Perimeter-based subsidies favoured the net gain for small fields. As expected, a subsidy for sequestration of SOC favoured cultivation of specific SOC-sequestering crops such as ley, willow, and poplar. Our recommendation for future studies is to investigate a well-balanced combination of perimeter-based support and SOC sequestration support that benefits biodiversity and climate under different cultivation conditions

The Effects of Increasing the Minimum Wage on Prices: Analyzing the Incidence of Policy Design and Context

We analyze the price pass-through effect of the minimum wage and use the results to provide insight into the competitive structure of low-wage labor markets. Using monthly price series, we find that the pass-through effect is entirely concentrated on the month that the minimum wage change goes into effect, and is much smaller than what the canonical literature has found. We then discuss why our results differ from that literature, noting the impact of series interpolation in generating most of the previous results. We then use the variation in the size of the minimum wage change to evaluate the competitive nature of low-wage labor markets. Finally, we exploit the rich variation in minimum wage policy of the last 10–15 years—including the rise of state and city-level minimum wage changes and the increased use of indexation—to investigate how the extent of price pass-through varies by policy context. This paper contributes to the literature by clarifying our understanding of the dynamics and magnitude of the pass-through effect and enriching the discussion of how different policies may shape the effect that minimum wage hikes have on prices