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Register a new userOptimizing experimental parameters for tracking of diffusing particles
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Added by
Christian Lyngby Vestergaard
Publication date
2015
fields
Physics
and research's language is
English
Authors
Christian L. Vestergaard
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We describe how a single-particle tracking experiment should be designed in order for its recorded trajectories to contain the most information about a tracked particles diffusion coefficient. The precision of estimators for the diffusion coefficient is affected by motion blur, limited photon statistics, and the length of recorded time-series. We demonstrate for a particle undergoing free diffusion that precision is negligibly affected by motion blur in typical experiments, while optimizing photon counts and the number of recorded frames is the key to precision. Building on these results, we describe for a wide range of experimental scenarios how to choose experimental parameters in order to optimize the precision. Generally, one should choose quantity over quality: experiments should be designed to maximize the number of frames recorded in a time-series, even if this means lower information content in individual frames.
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A measure called Physical Complexity is established and calculated for a population of sequences, based on statistical physics, automata theory, and information theory. It is a measure of the quantity of information in an organisms genome. It is based on Shannons entropy, measuring the information in a population evolved in its environment, by using entropy to estimate the randomness in the genome. It is calculated from the difference between the maximal entropy of the population and the actual entropy of the population when in its environment, estimated by counting the number of fixed loci in the sequences of a population. Up to now, Physical Complexity has only been formulated for populations of sequences with the same length. Here, we investigate an extension to support variable length populations. We then build upon this to construct a measure for the efficiency of information storage, which we later use in understanding clustering within populations. Finally, we investigate our extended Physical Complexity through simulations, showing it to be consistent with the original.
The totally asymmetric simple exclusion process (TASEP), which describes the stochastic dynamics of interacting particles on a lattice, has been actively studied over the past several decades and applied to model important biological transport processes. Here we present a software package, called EGGTART (Extensive GUI gives TASEP-realization in real time), which quantifies and visualizes the dynamics associated with a generalized version of the TASEP with an extended particle size and heterogeneous jump rates. This computational tool is based on analytic formulas obtained from deriving and solving the hydrodynamic limit of the process. It allows an immediate quantification of the particle density, flux, and phase diagram, as a function of a few key parameters associated with the system, which would be difficult to achieve via conventional stochastic simulations. Our software should therefore be of interest to biophysicists studying general transport processes, and can in particular be used in the context of gene expression to model and quantify mRNA translation of different coding sequences.
This chapter describes gene expression analysis by Singular Value Decomposition (SVD), emphasizing initial characterization of the data. We describe SVD methods for visualization of gene expression data, representation of the data using a smaller number of variables, and detection of patterns in noisy gene expression data. In addition, we describe the precise relation between SVD analysis and Principal Component Analysis (PCA) when PCA is calculated using the covariance matrix, enabling our descriptions to apply equally well to either method. Our aim is to provide definitions, interpretations, examples, and references that will serve as resources for understanding and extending the application of SVD and PCA to gene expression analysis.
Nuclear Reaction Analysis with ${}^{3}$He holds the promise to measure Deuterium depth profiles up to large depths. However, the extraction of the depth profile from the measured data is an ill-posed inversion problem. Here we demonstrate how Bayesian Experimental Design can be used to optimize the number of measurements as well as the measurement energies to maximize the information gain. Comparison of the inversion properties of the optimized design with standard settings reveals huge possible gains. Application of the posterior sampling method allows to optimize the experimental settings interactively during the measurement process.
A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as yet unexplored fashion. Our analysis of the complete Protein Data Bank reveals several new knots which, along with previously discovered ones, can shed light on such connections. In particular, we identify the most complex knot discovered to date in human ubiquitin hydrolase, and suggest that its entangled topology protects it against unfolding and degradation by the proteasome. Knots in proteins are typically preserved across species and sometimes even across kingdoms. However, we also identify a knot which only appears in some transcarbamylases while being absent in homologous proteins of similar structure. The emergence of the knot is accompanied by a shift in the enzymatic function of the protein. We suggest that the simple insertion of a short DNA fragment into the gene may suffice to turn an unknotted into a knotted structure in this protein.
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