arXiv subjects

Ryan T. Kelly

Publications and source records attributed to Ryan T. Kelly.

3 recordsLinked to original sources

arXiv2022

Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments

Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition, and data analysis. Broadly accepted community guidelines and standardized metrics will enhance rigor, data quality, and alignment between laboratories. Here we propose best practices, quality controls, and data reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics.

q-bio.OT↗

arXiv2022

Variable Transformation for Explicit Wall-Shear Stress Formula

We formulate a general variable transformation for existing wall functions that allows for an explicit wall-shear stress term. The proposed transformation aims to enable an explicit expression of wall-shear stress and simplify the implementation of existing wall functions in simulation codes through a simple transformation of variables. The transformation is defined by introducing a new velocity scale allowing the definition of the new wall unit variable $(r^+)$ and the corresponding normalized viscosity $(η_t^+)$. We also demonstrate that the law of the wall in new variables is equivalent to the one expressed in wall-normal variables $(y^+_τ)$ and $(ν_t^+)$. The new form of the law is particularly suitable for implementations in computational fluid dynamics codes as it does not require an iterative procedure to evaluate the wall shear stress. We show how to transform several known and often used expressions of wall functions with and without pressure gradients to allow for an explicit wall-shear stress expression. Finally, we illustrate the new form of wall functions by performing illustrative numerical simulations.

physics.flu-dyn↗

arXiv2021

New views of old proteins: clarifying the enigmatic proteome

All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide provocative projections for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we offer potential futures for a next generation of disruptive approaches to define, quantify and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.

q-bio.BM↗