arXiv subjects

Yihan Lin

Publications and source records attributed to Yihan Lin.

21 records · Page 2Linked to original sources

arXiv2017

Analysis and correction of errors in nanoscale particle tracking using the Single-pixel interior filling function (SPIFF) algorithm

Particle tracking, which is an essential tool in many fields of scientific research, uses algorithms that retrieve the centroid of tracked particles with sub-pixel accuracy. However, images in which the particles occupy a small number of pixels on the detector, are in close proximity to other particles or suffer from background noise, show a systematic error in which the particle sub-pixel positions are biased towards the center of the pixel. This pixel locking effect greatly reduces particle tracking accuracy. In this report, we demonstrate the severity of these errors by tracking experimental (and simulated) imaging data of optically trapped silver nanoparticles and single fluorescent proteins. We show that errors in interparticle separation, angle and mean square displacement are significantly reduced by applying the corrective Single- pixel interior filling function (SPIFF) algorithm. Our work demonstrates the potential ubiquity of such errors and the general applicability of SPIFF correction to many experimental fields.

cond-mat.soft↗

arXiv2014

Scaling laws governing stochastic growth and division of single bacterial cells

Uncovering the quantitative laws that govern the growth and division of single cells remains a major challenge. Using a unique combination of technologies that yields unprecedented statistical precision, we find that the sizes of individual Caulobacter crescentus cells increase exponentially in time. We also establish that they divide upon reaching a critical multiple ($\approx$1.8) of their initial sizes, rather than an absolute size. We show that when the temperature is varied, the growth and division timescales scale proportionally with each other over the physiological temperature range. Strikingly, the cell-size and division-time distributions can both be rescaled by their mean values such that the condition-specific distributions collapse to universal curves. We account for these observations with a minimal stochastic model that is based on an autocatalytic cycle. It predicts the scalings, as well as specific functional forms for the universal curves. Our experimental and theoretical analysis reveals a simple physical principle governing these complex biological processes: a single temperature-dependent scale of cellular time governs the stochastic dynamics of growth and division in balanced growth conditions.

physics.bio-ph↗

arXiv2012

Phase resetting reveals network dynamics underlying a bacterial cell cycle

Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS).

q-bio.MN↗