arXiv subjects

Patrick Murphy

Publications and source records attributed to Patrick Murphy.

10 recordsLinked to original sources

arXiv2024

Role of Non-Exponential Reversal times in Aggregation Models of Bacterial Populations

In this paper, we consider 1D agent-based and kinetic models of aggregation with reversals. In particular, we fit a Gamma distribution to represent the run times in myxobacteria and analyze numerically the importance of non-exponential reversal times. We demonstrate that non-exponential reversal times aid aggregation and result in tighter aggregates. We compare and contrast the behavior of agent-based and kinetic models, and also consider kinetic models with aggregation driven by chemotaxis. Thus, incorporating non-exponential reversal times into models of aggregation can be particularly important for reproducing experimental data, such as aggregate persistence and dispersal.

physics.bio-ph↗

arXiv2024

Annihilation dynamics during spiral defect chaos revealed by particle models

Pair-annihilation events are ubiquitous in a variety of spatially extended systems and are often studied using computationally expensive simulations. Here we develop an approach in which we simulate the pair-annihilation of spiral wave tips in cardiac models using a computationally efficient particle model. Spiral wave tips are represented as particles with dynamics governed by diffusive behavior and short-ranged attraction. The parameters for diffusion and attraction are obtained by comparing particle motion to the trajectories of spiral wave tips in cardiac models during spiral defect chaos. The particle model reproduces the annihilation rates of the cardiac models and can determine the statistics of spiral wave dynamics, including its mean termination time. We show that increasing the attraction coefficient sharply decreases the mean termination time, making it a possible target for pharmaceutical intervention

q-bio.TO↗

arXiv2024

Existence of weak solutions for the kinetic models of motion of myxobacteria with alignment and reversals

In this paper, we consider three non-linear kinetic partial differential equations that emerge in the modeling of motion of rod-shaped cells such as myxobacteria. This motion is characterized by nematic alignment with neighboring cells, orientation reversals from cell polarity switching, orientation diffusion, and transport driven by chemotaxis. Our primary contribution lies in establishing the existence of weak solutions for these equations. Our analytical approach is based on the application of the classical averaging lemma from the kinetic theory, augmented by a novel version where the transport operator is substituted with a uni-directional diffusion operator.

math.AP↗

arXiv2023

Breakdown of Boltzmann-type Models for the Alignment of Self-propelled Rods

Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann's hypothesis of "molecular chaos", that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of self-propelled rods where rod reorientation occurs upon binary collisions. We examine the accuracy of the kinetic model by comparing numerical solutions of the continuous equations to an agent-based model that implements the underlying rules governing microscopic alignment. Even for the simplest case considered, our comparison demonstrates that the kinetic model fails to replicate the discrete dynamics due to the formation of rod clusters that violate statistical independence. Additionally, we show that introducing noise to limit cluster formation helps improve the agreement between the analytical model and agent simulations but does not restore agreement completely. These results highlight the need to both develop and disseminate improved moment-closure methods for modeling biological and active matter systems.

physics.bio-ph↗

arXiv2022

A mean-field model for nematic alignment of self-propelled rods

In this paper we develop a model for nematic alignment of self-propelled rods interacting through binary collisions. We avoid phenomenological descriptions of rod interaction in favor of rigorously using a set of microscopic-level rules. Under the assumption that each collision results in a small change to a rod's orientation, we derive the Fokker-Planck equation for the evolution of the kinetic density function. Using analytical and numerical methods, we study the emergence of the nematic order from a homogeneous, uniform steady-state of the mean-field equation.

physics.bio-ph↗

arXiv2020

The Zwicky Transient Facility: Observing System

The Zwicky Transient Facility (ZTF) Observing System (OS) is the data collector for the ZTF project to study astrophysical phenomena in the time domain. ZTF OS is based upon the 48-inch aperture Schmidt-type design Samuel Oschin Telescope at the Palomar Observatory in Southern California. It incorporates new telescope aspheric corrector optics, dome and telescope drives, a large-format exposure shutter, a flat-field illumination system, a robotic bandpass filter exchanger, and the key element: a new 47-square-degree, 600 megapixel cryogenic CCD mosaic science camera, along with supporting equipment. The OS collects and delivers digitized survey data to the ZTF Data System (DS). Here, we describe the ZTF OS design, optical implementation, delivered image quality, detector performance, and robotic survey efficiency.

astro-ph.IM↗

arXiv2019

The Zwicky Transient Facility: System Overview, Performance, and First Results

The Zwicky Transient Facility (ZTF) is a new optical time-domain survey that uses the Palomar 48-inch Schmidt telescope. A custom-built wide-field camera provides a 47 deg$^2$ field of view and 8 second readout time, yielding more than an order of magnitude improvement in survey speed relative to its predecessor survey, the Palomar Transient Factory (PTF). We describe the design and implementation of the camera and observing system. The ZTF data system at the Infrared Processing and Analysis Center provides near-real-time reduction to identify moving and varying objects. We outline the analysis pipelines, data products, and associated archive. Finally, we present on-sky performance analysis and first scientific results from commissioning and the early survey. ZTF's public alert stream will serve as a useful precursor for that of the Large Synoptic Survey Telescope.

astro-ph.IM↗

arXiv2019

The Zwicky Transient Facility: Science Objectives

The Zwicky Transient Facility (ZTF), a public-private enterprise, is a new time domain survey employing a dedicated camera on the Palomar 48-inch Schmidt telescope with a 47 deg$^2$ field of view and 8 second readout time. It is well positioned in the development of time domain astronomy, offering operations at 10% of the scale and style of the Large Synoptic Survey Telescope (LSST) with a single 1-m class survey telescope. The public surveys will cover the observable northern sky every three nights in g and r filters and the visible Galactic plane every night in g and r. Alerts generated by these surveys are sent in real time to brokers. A consortium of universities which provided funding ("partnership") are undertaking several boutique surveys. The combination of these surveys producing one million alerts per night allows for exploration of transient and variable astrophysical phenomena brighter than r $\sim$ 20.5 on timescales of minutes to years. We describe the primary science objectives driving ZTF including the physics of supernovae and relativistic explosions, multi-messenger astrophysics, supernova cosmology, active galactic nuclei and tidal disruption events, stellar variability, and Solar System objects.

astro-ph.IM↗

arXiv2011

Design, Implementation and Characterization of a Cooperative Communications System

Cooperative communications is a class of techniques which seek to improve reliability and throughput in wireless systems by pooling the resources of distributed nodes. While cooperation can occur at different network layers and time scales, physical layer cooperation at symbol time scales offers the largest benefit in combating losses due to fading. However, symbol level cooperation poses significant implementation challenges, especially in synchronizing the behaviors and carrier frequencies of distributed nodes. We present the implementation and characterization of a complete, real-time cooperative physical layer transceiver built on the Rice Wireless Open-Access Research Platform (WARP). In our implementation autonomous nodes employ physical layer cooperation without a central synchronization source, and are capable of selecting between non-cooperative and cooperative communication per packet. Cooperative transmissions use a distributed Alamouti space-time block code and employ either amplify-and-forward or decode-and-forward relaying. We also present experimental results of our transceiver's real-time performance under a variety of topologies and propagation conditions. Our results clearly demonstrate significant performance gains (more than 40x improvement in PER in some topologies) provided by physical layer cooperation, even when subject to the constraints of a real-time implementation. We also present methodologies to isolate and understand the sources of performance bottlenecks in our design. As with all our work on WARP, our transceiver design and experimental framework are available via the open-source WARP repository for use by other wireless researchers.

cs.IT↗

arXiv2007

Building a Cooperative Communications System

In this paper, we present the results from over-the-air experiments of a complete implementation of an amplify and forward cooperative communications system. Our custom OFDM-based physical layer uses a distributed version of the Alamouti block code, where the relay sends one branch of Alamouti encoded symbols. First we show analytically and experimentally that amplify and forward protocols are unaffected by carrier frequency offsets at the relay. This result allows us to use a conventional Alamouti receiver without change for the distributed relay system. Our full system implementation shows gains up to 5.5dB in peak power constrained networks. Thus, we can conclusively state that even the simplest form of relaying can lead to significant gains in practical implementations.

cs.IT↗