Mean first passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding

We have analyzed dynamics on the complex free energy landscape of protein folding in the FOLD-X model, by calculating for each state of the system the mean first passage time to the folded state. The resulting kinetic map of the folding process shows that it proceeds in jumps between well-defined, local free energy minima. Closer analysis of the different local minima allows us to reveal secondary, parallel pathways as well as dead ends.Comment: 7 page

Scale Free Cluster Distributions from Conserving Merging-Fragmentation Processes

We propose a dynamical scheme for the combined processes of fragmentation and merging as a model system for cluster dynamics in nature and society displaying scale invariant properties. The clusters merge and fragment with rates proportional to their sizes, conserving the total mass. The total number of clusters grows continuously but the full time-dependent distribution can be rescaled over at least 15 decades onto a universal curve which we derive analytically. This curve includes a scale free solution with a scaling exponent of -3/2 for the cluster sizes.Comment: 4 pages, 3 figure

Compact phases of polymers with hydrogen bonding

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strength of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling $\beta$-sheets appearing in native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR

Human subjective response to steering wheel vibration caused by diesel engine idle

This study investigated the human subjective response to steering wheel vibration of the type caused by a four-cylinder diesel engine idle in passenger cars. Vibrotactile perception was assessed using sinusoidal amplitude-modulated vibratory stimuli of constant energy level (r.m.s. acceleration, 0.41 m/s(2)) having a carrier frequency of 26 Hz (i.e. engine firing frequency) and modulation frequency of 6.5 Hz (half-order engine harmonic). Evaluations of seven levels of modulation depth parameter m (0.0, 0.1, 0.2, 0.4, 0.6, 0.8, and 1.0) were performed in order to define the growth function of human perceived disturbance as a function of amplitude modulation depth. Two semantic descriptors were used (unpleasantness and roughness) and two test methods (the Thurstone paired-comparison method and the Borg CR-10 direct evaluation scale) for a total of four tests. Each test was performed using an independent group of 25 individuals. The results suggest that there is a critical value of modulation depth m = 0.2 below which human subjects do not perceive differences in amplitude modulation and above which the stimulus-response relationship increases monotonically with a power function. The Stevens power exponents suggest that the perceived unpleasantness is non-linearly dependent on modulation depth m with an exponent greater than 1 and that the perceived roughness is dependent with an exponent close to unity

Using engineering design tools in multidisciplinary distributed student teams

Collaborative design practice in distributed student teams is becoming more popular as technology makes it easier to communicate ideas with others that are geographically distant. However, a challenge for students is to use design tools which they are not familiar with. These design tools usually differ from each other and engineers may find it much more difficult to share their ideas. This could make the whole design process longer and less successful. Each year the University of Malta, City University London and University of Strathclyde organise a joint collaborative design project, involving engineering students with different disciplines and cultural backgrounds. In this paper, the patterns of use of design tools by students to collaborate with each other are investigated. Based on survey results of students, this paper proposes an approach which can be utilised by engineering students to enhance collaboration in multidisciplinary distributed design teams

Retinal metric: a stimulus distance measure derived from population neural responses

The ability of the organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this "neural metric" tells us how distinguishable a pair of stimulus clips is to the retina, given the noise in the neural population response. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the SVM-like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.Comment: 5 pages, 4 figures, to appear in Phys Rev Let

Peacock Bundles: Bundle Coloring for Graphs with Globality-Locality Trade-off

Bundling of graph edges (node-to-node connections) is a common technique to enhance visibility of overall trends in the edge structure of a large graph layout, and a large variety of bundling algorithms have been proposed. However, with strong bundling, it becomes hard to identify origins and destinations of individual edges. We propose a solution: we optimize edge coloring to differentiate bundled edges. We quantify strength of bundling in a flexible pairwise fashion between edges, and among bundled edges, we quantify how dissimilar their colors should be by dissimilarity of their origins and destinations. We solve the resulting nonlinear optimization, which is also interpretable as a novel dimensionality reduction task. In large graphs the necessary compromise is whether to differentiate colors sharply between locally occurring strongly bundled edges ("local bundles"), or also between the weakly bundled edges occurring globally over the graph ("global bundles"); we allow a user-set global-local tradeoff. We call the technique "peacock bundles". Experiments show the coloring clearly enhances comprehensibility of graph layouts with edge bundling.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

SEM-EDS analyses of small craters in stardust aluminium foils: implications for the Wild-2 dust distribution

Implications for the Wild-2 dust distribution of the statistical results obtained by SEM-EDS from nearly 300 impact craters on aluminium foils of the Stardust sample tray assembly

Allelic loss at chromosome 13q12-q13 is associated with poor prognosis in familial and sporadic breast cancer.

Loss of heterozygosity (LOH) was analysed in 84 primary tumours from sporadic, familial and hereditary breast cancer using five microsatellite markers spanning the chromosomal region 13q12-q13 which harbours the BRCA2 breast cancer susceptibility gene, and using one other marker located within the RBI tumour-suppressor gene at 13q14. LOH at the BRCA2 region was found in 34% and at RBI in 27% of the tumours. Selective LOH at BRCA2 occurred in 7% of the tumours, whereas selective LOH at RBI was observed in another 7%. Moreover, a few tumours demonstrated a restricted deletion pattern, suggesting the presence of additional tumour-suppressor genes both proximal and distal of BRCA2. LOH at BRCA2 was significantly correlated to high S-phase values, low oestrogen and progesterone receptor content and DNA non-diploidy. LOH at BRCA2 was also associated, albeit non-significantly, with large tumour size and the ductal and medullar histological types. No correlation was found with lymph node status, patient age or a family history of breast cancer. A highly significant and independent correlation existed between LOH at BRCA2 and early recurrence and death. LOH at RBI was not associated with the above mentioned factors or prognosis. The present study does not provide conclusive evidence that BRCA2 is the sole target for deletions at 13q12-q13 in breast tumours. However, the results suggest that inactivation of one or several tumour-suppressor genes in the 13q12-q13 region confer a strong tumour growth potential and poor prognosis in both familial and sporadic breast cancer