arXiv subjects

Tommy A. Byrd

Publications and source records attributed to Tommy A. Byrd.

7 recordsLinked to original sources

arXiv2020

Cell-to-cell information at a feedback-induced bifurcation point

A ubiquitous way that cells share information is by exchanging molecules. Yet, the fundamental ways that this information exchange is influenced by intracellular dynamics remain unclear. Here we use information theory to investigate a simple model of two interacting cells with internal feedback. We show that cell-to-cell molecule exchange induces a collective two-cell critical point and that the mutual information between the cells peaks at this critical point. Information can remain large far from the critical point on a manifold of cellular states, but scales logarithmically with the correlation time of the system, resulting in an information-correlation time tradeoff. This tradeoff is strictly imposed, suggesting the correlation time as a proxy for the mutual information.

physics.bio-ph↗

arXiv2019

Biochemical feedback and its application to immune cells II: dynamics and critical slowing down

Near a bifurcation point, the response time of a system is expected to diverge due to the phenomenon of critical slowing down. We investigate critical slowing down in well-mixed stochastic models of biochemical feedback by exploiting a mapping to the mean-field Ising universality class. This mapping allows us to quantify critical slowing down in experiments where we measure the response of T cells to drugs. Specifically, the addition of a drug is equivalent to a sudden quench in parameter space, and we find that quenches that take the cell closer to its critical point result in slower responses. We further demonstrate that our class of biochemical feedback models exhibits the Kibble-Zurek collapse for continuously driven systems, which predicts the scaling of hysteresis in cellular responses to more gradual perturbations. We discuss the implications of our results in terms of the tradeoff between a precise and a fast response.

physics.bio-ph↗

arXiv2019

Universality of biochemical feedback and its application to immune cells

We map a class of well-mixed stochastic models of biochemical feedback in steady state to the mean-field Ising model near the critical point. The mapping provides an effective temperature, magnetic field, order parameter, and heat capacity that can be extracted from biological data without fitting or knowledge of the underlying molecular details. We demonstrate this procedure on fluorescence data from mouse T cells, which reveals distinctions between how the cells respond to different drugs. We also show that the heat capacity allows inference of absolute molecule number from fluorescence intensity. We explain this result in terms of the underlying fluctuations and demonstrate the generality of our work.

physics.bio-ph↗

arXiv2016

Dynamic sampling and information encoding in biochemical networks

Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate the dynamic encoding of information in the ATP-induced calcium responses of fibroblast cells, using a vectorial, or multi-time-point, measure from information theory. We find that the amount of extracted information depends on physiological constraints such as the sampling rate and memory capacity of the downstream network, and is affected differentially by intrinsic vs. extrinsic noise. By comparing to a minimal physical model, we find, surprisingly, that the information is often insensitive to the detailed structure of the underlying dynamics, and instead the decoding mechanism acts as a simple low-pass filter. These results demonstrate the mechanisms and limitations of dynamic information storage in cells.

q-bio.CB↗

arXiv2015

Matter, Energy, and Heat Transfer in a Classical Ballistic Atom Pump

A ballistic atom pump is a system containing two reservoirs of neutral atoms or molecules and a junction connecting them containing a localized time-varying potential. Atoms move through the pump as independent particles. Under certain conditions, these pumps can create net transport of atoms from one reservoir to the other. While such systems are sometimes called "quantum pumps," they are also models of classical chaotic transport, and their quantum behavior cannot be understood without study of the corresponding classical behavior. Here we examine classically such a pump's effect on energy and temperature in the reservoirs, in addition to net particle transport. We show that the changes in particle number, of energy in each reservoir, and of temperature in each reservoir vary in unexpected ways as the incident particle energy is varied.

cond-mat.quant-gas↗

arXiv2015

Ballistic atom pumps

We examine a classically-chaotic system consisting of two reservoirs of particles connected by a channel containing oscillating potential-energy barriers. We investigate whether such a system can preferentially pump particles from one reservoir to the other, a process often called "quantum pumping." We show how to make a "particle diode" which under specified conditions permits net particle pumping in only one direction. Then we examine systems having symmetric barriers. We find that if all initial particle energies are considered, a system with symmetric barriers cannot preferentially pump particles. However, if only finite initial energy bands are considered, the system can create net particle transport in either direction. We study the system classically, semiclassically, and quantum mechanically, and find that the quantum description cannot be fully understood without the insight gained from classical and semiclassical analysis.

cond-mat.quant-gas↗

arXiv2012

Scattering by an oscillating barrier: quantum, classical, and semiclassical comparison

We present a detailed study of scattering by an amplitude-modulated potential barrier using three distinct physical frameworks: quantum, classical, and semiclassical. Classical physics gives bounds on the energy and momentum of the scattered particle, while also providing the foundation for semiclassical theory. We use the semiclassical approach to selectively add quantum-mechanical effects such as interference and diffraction. We find good agreement between the quantum and semiclassical momentum distributions. Our methods and results can be used to understand quantum and classical aspects of transport mechanisms involving time-varying potentials, such as quantum pumping.

cond-mat.quant-gas↗