arXiv subjects

Dean Huang

Publications and source records attributed to Dean Huang.

8 recordsLinked to original sources

arXiv2024

Relevance for Human Robot Collaboration

Inspired by the human ability to selectively focus on relevant information, this paper introduces relevance, a novel dimensionality reduction process for human-robot collaboration (HRC). Our approach incorporates a continuously operating perception module, evaluates cue sufficiency within the scene, and applies a flexible formulation and computation framework. To accurately and efficiently quantify relevance, we developed an event-based framework that maintains a continuous perception of the scene and selectively triggers relevance determination. Within this framework, we developed a probabilistic methodology, which considers various factors and is built on a novel structured scene representation. Simulation results demonstrate that the relevance framework and methodology accurately predict the relevance of a general HRC setup, achieving a precision of 0.99, a recall of 0.94, an F1 score of 0.96, and an object ratio of 0.94. Relevance can be broadly applied to several areas in HRC to accurately improve task planning time by 79.56% compared with pure planning for a cereal task, reduce perception latency by up to 26.53% for an object detector, improve HRC safety by up to 13.50% and reduce the number of inquiries for HRC by 80.84%. A real-world demonstration showcases the relevance framework's ability to intelligently and seamlessly assist humans in everyday tasks.

cs.RO↗

arXiv2024

Protein overabundance is driven by growth robustness

Protein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes; whereas overexpression slows growth by increasing the metabolic load. This trade-off naively predicts that cells maximize their fitness by sufficiency, expressing just enough of each essential protein for function. We test this prediction in the naturally-competent bacterium Acinetobacter baylyi by characterizing the proliferation dynamics of essential-gene knockouts at a single-cell scale (by imaging) as well as at a genome-wide scale (by TFNseq). In these experiments, cells proliferate for multiple generations as target protein levels are diluted from their endogenous levels. This approach facilitates a proteome-scale analysis of protein overabundance. As predicted by the Robustness-Load Trade-Off (RLTO) model, we find that roughly 70% of essential proteins are overabundant and that overabundance increases as the expression level decreases, the signature prediction of the model. These results reveal that robustness plays a fundamental role in determining the expression levels of essential genes and that overabundance is a key mechanism for ensuring robust growth.

physics.bio-ph↗

arXiv2023

Koopman Learning with Episodic Memory

Koopman operator theory has found significant success in learning models of complex, real-world dynamical systems, enabling prediction and control. The greater interpretability and lower computational costs of these models, compared to traditional machine learning methodologies, make Koopman learning an especially appealing approach. Despite this, little work has been performed on endowing Koopman learning with the ability to leverage its own failures. To address this, we equip Koopman methods -- developed for predicting non-autonomous time-series -- with an episodic memory mechanism, enabling global recall of (or attention to) periods in time where similar dynamics previously occurred. We find that a basic implementation of Koopman learning with episodic memory leads to significant improvements in prediction on synthetic and real-world data. Our framework has considerable potential for expansion, allowing for future advances, and opens exciting new directions for Koopman learning.

math.DS↗

arXiv2023

Noise robustness and metabolic load determine the principles of central dogma regulation

The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off between metabolic load and growth robustness. The model predicts novel principles of central dogma regulation: Optimal protein expression levels for many genes are in vast overabundance. Essential genes are transcribed above a lower limit of one message per cell cycle. Gene expression is achieved by load balancing between transcription and translation. We present evidence that each of these novel regulatory principles is observed. These results reveal that robustness and metabolic load determine the global regulatory principles that govern gene expression processes, and these principles have broad implications for cellular function.

q-bio.MN↗

arXiv2023

The one-message-per-cell-cycle rule: A conserved minimum transcription level for essential genes

The inherent stochasticity of cellular processes leads to significant cell-to-cell variation in protein abundance. Although this noise has already been characterized and modeled, its broader implications and significance remain unclear. In this paper, we revisit the noise model and identify the number of messages transcribed per cell cycle as the critical determinant of noise. In yeast, we demonstrate that this quantity predicts the non-canonical scaling of noise with protein abundance, as well as quantitatively predicting its magnitude. We then hypothesize that growth robustness requires an upper ceiling on noise for the expression of essential genes, corresponding to a lower floor on the transcription level. We show that just such a floor exists: a minimum transcription level of one message per cell cycle is conserved between three model organisms: Escherichia coli, yeast, and human. Furthermore, all three organisms transcribe the same number of messages per gene, per cell cycle. This common transcriptional program reveals that robustness to noise plays a central role in determining the expression level of a large fraction of essential genes, and that this fundamental optimal strategy is conserved from E. coli to human cells.

physics.bio-ph↗

arXiv2022

The high-resolution in vivo measurement of replication fork velocity and pausing by lag-time analysis

An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell, where a crowded cytoplasm as well as competing and potentially antagonistic processes may significantly affect their rapidity and reliability. To capture these dynamics, we develop a novel method, lag-time analysis, for measuring in vivo dynamics. The approach uses exponential growth as the stopwatch to resolve dynamics in an asynchronous culture and therefore circumvents the difficulties and potential artifacts associated with synchronization or fluorescent labeling. Although lag-time analysis has the potential to be widely applicable to the quantitative analysis of in vivo dynamics, we focus on an important application: characterizing replication dynamics. To benchmark the approach, we analyze replication dynamics in three different species and a collection of mutants. We provide the first quantitative locus-specific measurements of fork velocity, in units of kb per second, as well as replisome-pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In addition to quantitatively characterizing known phenomena, we detect brief, locus-specific pauses at rDNA in wild-type cells for the first time. We also observe temporal fork velocity oscillations in three highly-divergent bacterial species. Lag-time analysis not only has great potential to offer new insights into replication, as demonstrated in the paper, but also has potential to provide quantitative insights into other important processes.

physics.bio-ph↗

arXiv2021

Characterizing stochastic cell cycle dynamics in exponential growth

Two powerful and complementary experimental approaches are commonly used to study the cell cycle and cell biology: One class of experiments characterizes the statistics (or demographics) of an unsynchronized exponentially-growing population, while the other captures cell cycle dynamics, either by time-lapse imaging of full cell cycles or in bulk experiments on synchronized populations. In this paper, we study the subtle relationship between observations in these two distinct experimental approaches. We begin with an existing model: a single-cell deterministic description of cell cycle dynamics where cell states (i.e. periods or phases) have precise lifetimes. We then generalize this description to a stochastic model in which the states have stochastic lifetimes, as described by arbitrary probability distribution functions. Our analyses of the demographics of an exponential culture reveal a simple and exact correspondence between the deterministic and stochastic models: The corresponding state lifetimes in the deterministic model are equal to the exponential mean of the lifetimes in the stochastic model. An important implication is therefore that the demographics of an exponential culture will be well-fit by a deterministic model even if the state timing is stochastic. Although we explore the implications of the models in the context of the Escherichia coli cell cycle, we expect both the models as well as the significance of the exponential-mean lifetimes to find many applications in the quantitative analysis of cell cycle dynamics in other biological systems.

physics.bio-ph↗

arXiv2021

Tesla's fluidic diode and the electronic-hydraulic analogy

Reasoning by analogy is powerful in physics for students and researchers alike, a case in point being electronics and hydraulics as analogous studies of electric currents and fluid flows. Around 100 years ago, Nikola Tesla proposed a flow control device intended to operate similarly to an electronic diode, allowing fluid to pass easily in one direction but providing high resistance in reverse. Here we use experimental tests of Tesla's diode to illustrate principles of the electronic-hydraulic analogy. We design and construct a differential pressure chamber (akin to a battery) that is used to measure flow rate (current) and thus resistance of a given pipe or channel (circuit element). Our results prove the validity of Tesla's device, whose anisotropic resistance derives from its asymmetric internal geometry interacting with high-inertia flows, as quantified by the Reynolds number (here, Re ~ 1e3). Through the design and testing of new fluidic diodes, we explore the limitations of the analogy and the challenges of shape optimization in fluid mechanics. We also provide materials that may be incorporated into lesson plans for fluid dynamics courses, laboratory modules and further research projects.

physics.flu-dyn↗