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We examine contributions of second order physical processes to results of stellar evolution calculations amenable to direct observational testing. In the first paper in the series (Young et al. 2001) we established baseline results using…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of…
This work uncovers the low-dimensional nature the complex dynamics of actuated separated flows. Namely, motivated by the problem of model-based predictive control of separated flows, we identify the requirements on a model-based observer…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…
This paper introduces a new approach for bubble detection based on mixed causal and noncausal autoregressive processes and their tail process representation during an explosive episode. Departing from traditional definitions of bubbles as…
Bayesian change-point detection, together with latent variable models, allows to perform segmentation over high-dimensional time-series. We assume that change-points lie on a lower-dimensional manifold where we aim to infer subsets of…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
We theoretically investigated the temperature fluctuations of DNA close to denaturation and observed a strong enhancement of these fluctuations at the critical temperature. Although in a much lower frequency range, such a sharp increase was…
Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular…
Bubbles released from a needle show shape deformations that depend on the surfactant concentration of the surrounding liquid. We develop a model that predicts the surfactant concentration based on experimental early-stage observations of…
The Scintillating Bubble Chamber collaboration is searching for Weakly Interacting Massive Particles using a novel bubble chamber with intended thresholds as low as 100eV. Existing molecular dynamics simulations of bubble formation in…
When recording the movement of individual animals, cells or molecules one will often observe changes in their diffusive behaviour at certain points in time along their trajectory. In order to capture the different diffusive modes assembled…
While most classic studies of function in experimental neuroscience have focused on the coding properties of individual neurons, recent developments in recording technologies have resulted in an increasing emphasis on the dynamics of neural…
We analyze the properties of naturally formed nano-bubbles in Lennard-Jones molecular dynamics simulations of liquid-to-vapor nucleation in the boiling and the cavitation regimes. The large computational volumes provide a realistic…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
This paper proposes methods to investigate whether the bubble patterns observed in individual series are common to various series. We detect the non-linear dynamics using the recent mixed causal and noncausal models. Both a likelihood ratio…
Despite its fundamental and technological importance, a microscopic understanding of the crystallization process is still elusive. By computer simulations of the hard-sphere model we reveal the mechanism by which thermal fluctuations drive…
The identification and tracking of stellar feedback-driven galaxy bubbles is an important topic in star formation and galactic structure research. However, current observational analysis of bubbles is limited in scope; information on bubble…