206 citations · 556 across the 17 of their papers we have counts for
17 papers
Extreme first passage times for populations of identical rare events
James MacLaurin, Jay M. Newby
A collection of identical and independent rare event first passage times is considered. The problem of finding the fastest out of such events to occur is called an extreme firs…
Measurement Error Correction in Particle Tracking Microrheology
Yun Ling, Martin Lysy, Ian Seim +4
In diverse biological applications, particle tracking of passive microscopic species has become the experimental measurement of choice -- when either the materials are of limited v…
Limited processivity of single motors improves overall transport flux of self-assembled motor-cargo complexes
Keshav B. Patel, Shengtan Mao, M. Gregory Forest +2
Single kinesin molecular motors can processively move along a microtubule (MT) a few micrometers on average before dissociating. However, cellular length scales over which transpor…
Evidence that self-similar microrheology of highly entangled polymeric solutions scales robustly with, and is tunable by, polymer concentration
Ian Seim, Jeremy A. Cribb, Jay M. Newby +4
We report observations of a remarkable scaling behavior with respect to concentration in the passive microbead rheology of two highly entangled polymeric solutions, polyethylene ox…
Convolutional neural networks automate detection for tracking of submicron scale particles in 2D and 3D
Jay M. Newby, Alison M. Schaefer, Phoebe T. Lee +2
Particle tracking is a powerful biophysical tool that requires conversion of large video files into position time series, i.e. traces of the species of interest for data analysis.…
Uniform asymptotic approximation of diffusion to a small target: generalized reaction models
Sam Isaacson, Ava Mauro, Jay Newby
The diffusion of a reactant to a binding target plays a key role in many biological processes. The reaction-radius at which the reactant and target may interact is often a small pa…
First-passage time to clear the way for receptor-ligand binding in a crowded environment
Jay Newby, Jun Allard
Certain biological reactions, such as receptor-ligand binding at cell-cell interfaces and macromolecules binding to biopolymers, require many smaller molecules crowding a reaction…
The Dynamics of Bistable Switching Behavior in Limit Cycle Systems with Additive Noise
Michael A. Schwemmer, Jay M. Newby
Additive noise is known to produce counter-intuitive behaviors in nonlinear dynamical systems. Previously, it was shown that systems with a deterministic limit cycle can display bi…
Asymptotic and numerical methods for metastable events in stochastic gene networks
Jay Newby
A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA t…
Bistable switching asymptotics for the self regulating gene
Jay Newby
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bi…
Spontaneous excitability in the Morris--Lecar model with ion channel noise
Jay Newby
Noise induced excitability is studied in type I and II Morris-Lecar neurons subject to constant sub threshold input, where fluctuations arise from sodium and potassium ion channels…
Effects of moderate noise on a limit cycle oscillator: Counter rotation and bistability
Jay M. Newby, Michael A. Schwemmer
The effects of noise on the dynamics of nonlinear systems is known to lead to many counter-intuitive behaviors. Using simple planar limit cycle oscillators, we show that the additi…
Metastability in a stochastic neural network modeled as a velocity jump Markov process
Paul C. Bressloff, Jay M. Newby
One of the major challenges in neuroscience is to determine how noise that is present at the molecular and cellular levels affects dynamics and information processing at the macros…
Metastable behavior in Markov processes with internal states
Jay Newby, Jon Chapman
A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise…
Breakdown of fast-slow analysis in an excitable system with channel noise
Jay M. Newby, Paul C. Bressloff, James P. Keener
We consider a stochastic version of an excitable system based on the Morris-Lecar model of a neuron, in which the noise originates from stochastic Sodium and Potassium ion channels…
Uniform asymptotic approximation of diffusion to a small target
Samuel A. Isaacson, Jay Newby
The problem of the time required for a diffusing molecule, within a large bounded domain, to first locate a small target is prevalent in biological modeling. Here we study this pro…
Isolating intrinsic noise sources in a stochastic genetic switch
Jay Newby
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two…