arXiv subjects

Sean X. Sun

Publications and source records attributed to Sean X. Sun.

7 recordsLinked to original sources

arXiv2020

On the Transcriptomic Signature and General Stress State Associated with Aneuploidy

Whether aneuploid cells with diverse karyotypes have any properties in common has a been a subject of intense interest. A recent study by Terhorst et al. (1) reinvestigated the common aneuploidy gene expression (CAGE), disputing the conclusion of our recent work (2). In this short article, which has been submitted to PNAS as a Letter to the Editor, we explain our major concerns about Terhorst et al. and why we believe that our previous conclusion stands valid.

q-bio.GN↗

arXiv2018

Building the Space Elevator: Lessons from Biological Design

One of the biggest perceived challenges in building megastructures, such as the space elevator, is the unavailability of materials with sufficient tensile strength. The presumed necessity of very strong materials stems from a design paradigm which requires structures to operate at a small fraction of their maximum tensile strength (usually, 50% or less). This criterion limits the probability of failure by giving structures sufficient leeway in handling stochastic components, such as variability in material strength and/or external forces. While reasonable for typical engineering structures, low working stress ratios --- defined as operating stress as a fraction of ultimate tensile strength --- in the case of megastructures are both too stringent and unable to adequately control the failure probability. We draw inspiration from natural biological structures, such as bones, tendons and ligaments, which are made up of smaller substructures and exhibit self-repair, and suggest a design that requires structures to operate at significantly higher stress ratios, while maintaining reliability through a continuous repair mechanism. We outline a mathematical framework for analysing the reliability of structures with components exhibiting probabilistic rupture and repair that depend on their time-in-use (age). Further, we predict time-to-failure distributions for the overall structure. We then apply this framework to the space elevator and find that a high degree of reliability is achievable using currently existing materials, provided it operates at sufficiently high working stress ratios, sustained through an autonomous repair mechanism, implemented via, e.g., robots.

physics.space-ph↗

arXiv2018

Erg(r)odicity: Hidden Bias and the Growthrate Gain

Many single-cell observables are highly heterogeneous. A part of this heterogeneity stems from age-related phenomena: the fact that there is a nonuniform distribution of cells with different ages. This has led to a renewed interest in analytic methodologies including use of the "von Foerster equation" for predicting population growth and cell age distributions. Here we discuss how some of the most popular implementations of this machinery assume a strong condition on the ergodicity of the cell cycle duration ensemble. We show that one common definition for the term ergodicity, "a single individual observed over many generations recapitulates the behavior of the entire ensemble" is implied by the other, "the probability of observing any state is conserved across time and over all individuals" in an ensemble with a fixed number of individuals but that this is not true when the ensemble is growing. We further explore the impact of generational correlations between cell cycle durations on the population growth rate. Finally, we explore the "growth rate gain" - the phenomenon that variations in the cell cycle duration lead to an improved population-level growth rate - in this context. We highlight that, fundamentally, this effect is due to asymmetric division.

q-bio.QM↗

arXiv2017

Inertia and Prediction in the Response to External Perturbation of Noisy Variables

For most stochastic dynamical systems, variables which are tightly regulated tend to respond slowly to external changes. This idea is often discussed for applicable systems, within a linear response regime, through the Fluctuation Dissipation Theorem (FDT). In a previous paper, we proposed a phenomenological model for the response of the cell cycle duration distribution to environmental changes which correlated the width of this distribution to response efficiency when FDT was not applicable. Here we emphasize how that model may be used to illustrate this general principle, that the stochasticity of a variable while inversely proportional to stability is often directly proportional to lability. Comparisons are made between this discrete-time model and the simple harmonic oscillator. We then consider a simple continuous dynamical system, the 'Active Oscillator', which illustrates this principle in another fashion.

physics.gen-ph↗

arXiv2016

"Inchworm Filaments": Motility and Pattern Formation

In a previous paper, we examined a class of possible conformations for helically patterned filaments in contact with a bonding surface. In particular, we investigated geometries where contact between the pattern and the surface was improved through a periodic twisting and lifting of the filament. A consequence of this lifting is that the total length of the filament projected onto the surface decreases after bonding. When the bonding character of the surface is actuated, this phenomenon can lead to both lifelike "inchworm" behavior of the filaments and ensemble movement. We illustrate, through simulation, how pattern formation may be achieved through this mechanism.

q-bio.SC↗

arXiv2016

To Grow is Not Enough: Impact of Noise on Cell Environmental Response and Fitness

Quantitative single cell measurements have shown that cell cycle duration (the time between cell divisions) for diverse cell types is a noisy variable. The underlying distribution is mean scalable with a universal shape for many cell types in a variety of environments. Here we show through both experiment and theory that increasing the amount of noise in the regulation of the cell cycle negatively impacts the growth rate but positively correlates with improved cellular response to fluctuating environments. Our findings suggest that even non-cooperative cells in exponential growth phase do not optimize fitness through growth rate alone, but also optimize adaptability to changing conditions. In a manner similar to genetic evolution, increasing the noise in biochemical processes correlates with improved response of the system to environmental changes.

q-bio.CB↗

arXiv2001

Model of a fluid at small and large length scales and the hydrophobic effect

We present a statistical field theory to describe large length scale effects induced by solutes in a cold and otherwise placid liquid. The theory divides space into a cubic grid of cells. The side length of each cell is of the order of the bulk correlation length of the bulk liquid. Large length scale states of the cells are specified with an Ising variable. Finer length scale effects are described with a Gaussian field, with mean and variance affected by both the large length scale field and by the constraints imposed by solutes. In the absence of solutes and corresponding constraints, integration over the Gaussian field yields an effective lattice gas Hamiltonian for the large length scale field. In the presence of solutes, the integration adds additional terms to this Hamiltonian. We identify these terms analytically. They can provoke large length scale effects, such as the formation of interfaces and depletion layers. We apply our theory to compute the reversible work to form a bubble in liquid water, as a function of the bubble radius. Comparison with molecular simulation results for the same function indicates that the theory is reasonably accurate. Importantly, simulating the large length scale field involves binary arithmetic only. It thus provides a computationally convenient scheme to incorporate explicit solvent dynamics and structure in simulation studies of large molecular assemblies.

cond-mat.stat-mech↗