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We consider the dynamics of a one-dimensional system consisting of dissimilar hardcore interacting (bouncy) random walkers. The walkers' (diffusing particles') friction constants ξ(n), where n labels different bouncy walkers, are drawn from a distribution ϱ(ξ(n)). We provide an approximate analytic solution to this recent single-file problem by combining harmonization and effective medium techniqu
Bio-inspired crossover:Natural genomes are affected by various kinds of mutations, manifesting as variations in the genome. This includes modifications to individual base pairs (single nucleotide polymorphism, SNP), but also short insertions and deletions (indels), and variations in the position (translocations) or multiplicity (copy number variations) of genetic sequences. While SNPs are historic
The direct reprogramming of adult skin fibroblasts to neurons is thought to be controlled by a small set of interacting gene regulators. Here, we investigate how the interaction dynamics between these regulating factors coordinate cellular decision making in direct neuronal reprogramming. We put forward a quantitative model of the governing gene regulatory system, supported by measurements of mRNA
This report summarizes the presentations and discussions during the Rapid Reaction Task Force “Dynamics of critical fluctuations: Theory – phenomenology – heavy-ion collisions”, which was organized by the ExtreMe Matter Institute EMMI and held at GSI, Darmstadt, Germany in April 2019. We address the current understanding of the dynamics of critical fluctuations in QCD and their measurement in heav
Hematopoietic stem cell lineage choices are decided by genetic networks that are turned ON/OFF in a switch-like manner. However, prior to lineage commitment, genes are primed at low expression levels. Understanding the underlying molecular circuitry in terms of how it governs both a primed state and, at the other extreme, a committed state is of relevance not only to hematopoiesis but also to deve
We deal with some halos generated by the divergent light from a nearby source. After discussing how the divergent light transforms some halo features, we give an outline of a method of handling the simulation of a divergent-light halo. The simulation method is then successfully tested on some well-documented halo observations. We also present a "simulation atlas" that shows halos produced by cryst
We investigate the mechanical unfolding of the tenth type III domain from fibronectin (FnIII(10)) both at constant force and at constant pulling velocity, by all-atom Monte Carlo simulations. We observe both apparent two-state unfolding and several unfolding pathways involving one of three major, mutually exclusive intermediate states. All three major intermediates lack two of seven native beta-st
Divergent-light halos are halos produced by light from nearby light sources, like street lamps being scattered by small crystals of ice floating in the air. The use of "brute-force" Monte Carlo methods to simulate such halos is extremely inefficient, as most scattered rays will not hit the eye of the observer. I present a new procedure for Monte Carlo simulations of divergent-light halos. This pro
Experimental and theoretical studies of lifetimes and transition probabilities for doubly ionized mercury, Hg III, are reported. Such data are currently of great astrophysical interest because observations with the Goddard high resolution spectrograph on board the Hubble space telescope have shown some 5d(9)6s-5d(9)6p transitions of Hg III in the spectrum of the chemically peculiar star chi Lupi.
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described
We solve a nonequilibrium statistical-mechanics problem exactly, namely, the single-file dynamics of N hard-core interacting particles (the particles cannot pass each other) of size Delta diffusing in a one-dimensional system of finite length L with reflecting boundaries at the ends. We obtain an exact expression for the conditional probability density function rho T(yT,t vertical bar yT,0) that a
Recent studies show that plant organ positioning may be mediated by localized concentrations of the plant hormone auxin. Auxin patterning in the shoot apical meristem is in turn brought about by the subcellular polar distribution of the putative auxin efflux mediator, PIN1. However, the question of what signals determine PIN1 polarization and how this gives rise to regular patterns of auxin concen
An automated peak picking strategy is presented where several peak sets with different signal-to-noise levels are combined to form a more reliable statement on the protein identity. The strategy is compared against both manual peak picking and industry standard automated peak picking on a set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. Th
To assess the value of ECG-gating for the diagnosis of myocardial infarction using myocardial perfusion scintigraphy (MPS) and an artificial neural network. A total of 422 patients referred for MPS were studied using a one day Tc-99m-tetrofosmin protocol. Adenosine stress combined with submaximal dynamic exercise was used. The images were interpreted by one of three experienced clinicians and thes
The tumor suppressor PTEN antagonizes phosphatidylinositol 3-kinase (PI3K), which contributes to tumorigenesis in many cancer types. While PTEN mutations occur in some melanomas, their precise mechanistic consequences have yet to be elucidated. We sought to identify novel downstream effectors of PI3K using a combination of genomic and functional tests. Microarray analysis of 53 melanoma cell lines
Random Boolean networks, the Kauffman model, are revisited by means of a novel decimation algorithm, which removes variables that cannot be relevant to the asymptotic dynamics of the system. The major part of the removed variables have the same fixed state in all limit cycles. These variables are denoted as the stable core of the network and their number grows approximately linearly with N, the nu
We show how to resum neutral propagators to all orders in partially quenched chiral perturbation theory. We calculate the relevant quantities to next-to-next-to-leading order (NNLO). Using these results we show how to extend the proposal by Sharpe and Shoresh for determining the parameters relevant for the eta mass from partially quenched lattice QCD calculations to NNLO.
We present an assay, based on optical DNA mapping in nanochannels that is capable of characterizing the plasmid content of bacterial isolates resistant to antibiotics in a fast an detailed way. In a single experiment we determine the number of different plasmids in each sample, their size, as well as a barcode that can be used for plasmid identification and tracing. In addition we demonstrate that
Background It is important that referring physicians and other treating clinicians properly understand the final reports from diagnostic tests. The aim of the study was to investigate whether referring physicians interpret a final report for a myocardial perfusion scintigraphy (MPS) test in the same way that the reading nuclear medicine physician intended. Methods After viewing final reports conta
