Universality and non-universality of mobility in heterogeneous single-file systems and Rouse chains

We study analytically the tracer particle mobility in single-file systems with distributed friction constants. Our system serves as a prototype for non-equilibrium, heterogeneous, strongly interacting Brownian systems. The long time dynamics for such a single-file setup belongs to the same universality class as the Rouse model with dissimilar beads. The friction constants are drawn from a density $\varrho(\xi)$ and we derive an asymptotically exact solution for the mobility distribution $P[\mu_0(s)]$, where $\mu_0(s)$ is the Laplace-space mobility. If $\varrho$ is light-tailed (first moment exists) we find a self-averaging behaviour: $P[\mu_0(s)]=\delta[\mu_0(s)-\mu(s)]$ with $\mu(s)\propto s^{1/2}$. When $\varrho(\xi)$ is heavy-tailed, $\varrho(\xi)\simeq \xi^{-1-\alpha} \ (0<\alpha<1)$ for large $\xi$ we obtain moments $\langle [\mu_s(0)]^n\rangle \propto s^{\beta n}$ where $\beta=1/(1+\alpha)$ and no self-averaging. The results are corroborated by simulations.Comment: 8 pages, 4 figures, REVTeX, to appear in Physical Review

Stochastic approach to DNA breathing dynamics

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups.Comment: 7 pages, 6 figures, epl.cl

Applying a potential across a biomembrane: electrostatic contribution to the bending rigidity and membrane instability

We investigate the effect on biomembrane mechanical properties due to the presence an external potential for a non-conductive non-compressible membrane surrounded by different electrolytes. By solving the Debye-Huckel and Laplace equations for the electrostatic potential and using the relevant stress-tensor we find: in (1.) the small screening length limit, where the Debye screening length is smaller than the distance between the electrodes, the screening certifies that all electrostatic interactions are short-range and the major effect of the applied potential is to decrease the membrane tension and increase the bending rigidity; explicit expressions for electrostatic contribution to the tension and bending rigidity are derived as a function of the applied potential, the Debye screening lengths and the dielectric constants of the membrane and the solvents. For sufficiently large voltages the negative contribution to the tension is expected to cause a membrane stretching instability. For (2.) the dielectric limit, i.e. no salt (and small wavevectors compared to the distance between the electrodes), when the dielectric constant on the two sides are different the applied potential induces an effective (unscreened) membrane charge density, whose long-range interaction is expected to lead to a membrane undulation instability.Comment: 16 pages, 3 figures, some revisio

Resonant coupling between localized plasmons and anisotropic molecular coatings in ellipsoidal metal nanoparticles

We present an analytic theory for the optical properties of ellipsoidal plasmonic particles covered by anisotropic molecular layers. The theory is applied to the case of a prolate spheroid covered by chromophores oriented parallel and perpendicular to the metal surface. For the case that the molecular layer resonance frequency is close to being degenerate with one of the particle plasmon resonances strong hybridization between the two resonances occur. Approximate analytic expressions for the hybridized resonance frequencies, their extinction cross section peak heights and widths are derived. The strength of the molecular - plasmon interaction is found to be strongly dependent on molecular orientation and suggest that this sensitivity could be the basis for novel nanoparticle based bio/chemo-sensing applications.Comment: 11 pages, 5 figure

Fitting a function to time-dependent ensemble averaged data

Time-dependent ensemble averages, i.e., trajectory-based averages of some observable, are of importance in many fields of science. A crucial objective when interpreting such data is to fit these averages (for instance, squared displacements) with a function and extract parameters (such as diffusion constants). A commonly overlooked challenge in such function fitting procedures is that fluctuations around mean values, by construction, exhibit temporal correlations. We show that the only available general purpose function fitting methods, correlated chi-square method and the weighted least squares method (which neglects correlation), fail at either robust parameter estimation or accurate error estimation. We remedy this by deriving a new closed-form error estimation formula for weighted least square fitting. The new formula uses the full covariance matrix, i.e., rigorously includes temporal correlations, but is free of the robustness issues, inherent to the correlated chi-square method. We demonstrate its accuracy in four examples of importance in many fields: Brownian motion, damped harmonic oscillation, fractional Brownian motion and continuous time random walks. We also successfully apply our method, weighted least squares including correlation in error estimation (WLS-ICE), to particle tracking data. The WLS-ICE method is applicable to arbitrary fit functions, and we provide a publically available WLS-ICE software.Comment: 47 pages (main text: 15 pages, supplementary: 32 pages

Strain-level bacterial typing directly from patient samples using optical DNA mapping

For bacterial infections, it is important to rapidly and accurately identify and characterize the type of bacteria involved so that optimal antibiotic treatment can be given quickly to the patient. However, current diagnostic methods are sometimes slow and cannot be used for mixtures of bacteria. We have, therefore, developed a method to identify bacteria directly from patient samples. The method was tested on two common species of disease-causing bacteria - Escherichia coli and Klebsiella pneumoniae - and it could correctly identify the bacterial strain or subtype in both urine samples and mixtures. Hence, the method has the potential to provide fast diagnostic information for choosing the most suited antibiotic, thereby reducing the risk of death and suffering. Nyblom, Johnning et al. develop an optical DNA mapping approach for bacterial strain typing of patient samples. They demonstrate rapid identification of clinically relevant E. coli and K. pneumoniae strains, without the need for cultivation. BackgroundIdentification of pathogens is crucial to efficiently treat and prevent bacterial infections. However, existing diagnostic techniques are slow or have a too low resolution for well-informed clinical decisions.MethodsIn this study, we have developed an optical DNA mapping-based method for strain-level bacterial typing and simultaneous plasmid characterisation. For the typing, different taxonomical resolutions were examined and cultivated pure Escherichia coli and Klebsiella pneumoniae samples were used for parameter optimization. Finally, the method was applied to mixed bacterial samples and uncultured urine samples from patients with urinary tract infections.ResultsWe demonstrate that optical DNA mapping of single DNA molecules can identify Escherichia coli and Klebsiella pneumoniae at the strain level directly from patient samples. At a taxonomic resolution corresponding to E. coli sequence type 131 and K. pneumoniae clonal complex 258 forming distinct groups, the average true positive prediction rates are 94% and 89%, respectively. The single-molecule aspect of the method enables us to identify multiple E. coli strains in polymicrobial samples. Furthermore, by targeting plasmid-borne antibiotic resistance genes with Cas9 restriction, we simultaneously identify the strain or subtype and characterize the corresponding plasmids.ConclusionThe optical DNA mapping method is accurate and directly applicable to polymicrobial and clinical samples without cultivation. Hence, it has the potential to rapidly provide comprehensive diagnostics information, thereby optimizing early antibiotic treatment and opening up for future precision medicine management

Data: A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings

<p>Data for publication: A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings, Plos One 2014, by Charleston Noble, Adam N. Nilsson, Camilla Freitag, Jason P. Beech, Jonas O. Tegenfeldt, Tobias Ambjornsson</p> <p> </p