Classification framework for partially observed dynamical systems

Shen, Yuan; Tiňo, Peter; Tsaneva-Atanasova, Krasimira

doi:10.1103/physreve.95.043303

Cited by 11 publications

(6 citation statements)

References 22 publications

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“…We note that the linear response formulation assumes Markovian bath dynamics. Recent work has shown additional corrections are required for non-Markovian baths (as also when the initial state has system-bath correlations) [51,52]. We shall neglect such small effects in this work.…”

Section: Linear Response and Absorption Spectrummentioning

confidence: 99%

Single-photon absorption by single photosynthetic light-harvesting complexes

Chan

Gamel

Fleming

et al. 2018

J. Phys. B: At. Mol. Opt. Phys.

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We provide a unified theoretical approach to the quantum dynamics of absorption of single photons and subsequent excitonic energy transfer in photosynthetic light-harvesting complexes. Our analysis combines a continuous mode n -photon quantum optical master equation for the chromophoric system with the hierarchy of equations of motion describing excitonic dynamics in presence of non-Markovian coupling to vibrations of the chromophores and surrounding protein. We apply the approach to simulation of absorption of single-photon coherent states by pigment-protein complexes containing between one and seven chromophores, and compare with results obtained by excitation using a thermal radiation field. We show that the values of excitation probability obtained under single-photon absorption conditions can be consistently related to bulk absorption cross-sections. Analysis of the timescale and efficiency of single-photon absorption by light-harvesting systems within this full quantum description of pigment-protein dynamics coupled to a quantum radiation field reveals a non-trivial dependence of the excitation probability and the excited state dynamics induced by exciton-phonon coupling during and subsequent to the pulse, on the bandwidth of the incident photon pulse. For bandwidths equal to the spectral bandwidth of Chlorophyll a, our results yield an estimation of an average time of ∼0.09 s for a single chlorophyll chromophore to absorb the energy equivalent of one (single-polarization) photon under irradiation by single-photon states at the intensity of sunlight.

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Section: Linear Response and Absorption Spectrummentioning

confidence: 99%

Single-photon absorption by single photosynthetic light-harvesting complexes

Chan

Gamel

Fleming

et al. 2018

J. Phys. B: At. Mol. Opt. Phys.

View full text Add to dashboard Cite

show abstract

“…Although some advances have been made in modelling these interactions [18,26], uncovering the network architecture between these pathways after major surgery and in critical illness has so far not been achieved. To do so will require a larger cohort of patients and a combination of mathematical modelling and machine learning techniques [32].…”

Section: Discussionmentioning

confidence: 99%

Modelling the dynamic interaction of systemic inflammation and the hypothalamic–pituitary–adrenal (HPA) axis during and after cardiac surgery

Galvis

Zavala

Walker

et al. 2022

J. R. Soc. Interface.

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Major surgery and critical illness produce a potentially life-threatening systemic inflammatory response. The hypothalamic–pituitary–adrenal (HPA) axis is one of the key physiological systems that counterbalances this systemic inflammation through changes in adrenocorticotrophic hormone (ACTH) and cortisol. These hormones normally exhibit highly correlated ultradian pulsatility with an amplitude modulated by circadian processes. However, these dynamics are disrupted by major surgery and critical illness. In this work, we characterize the inflammatory, ACTH and cortisol responses of patients undergoing cardiac surgery and show that the HPA axis response can be classified into one of three phenotypes: single-pulse, two-pulse and multiple-pulse dynamics. We develop a mathematical model of cortisol secretion and metabolism that predicts the physiological mechanisms responsible for these different phenotypes. We show that the effects of inflammatory mediators are important only in the single-pulse pattern in which normal pulsatility is lost—suggesting that this phenotype could be indicative of the greatest inflammatory response. Investigating whether and how these phenotypes are correlated with clinical outcomes will be critical to patient prognosis and designing interventions to improve recovery.

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“…Although some advances have been made in modelling these interactions 9,28 , uncovering the network architecture between these pathways after major surgery and in critical illness has so far not been achieved. To do so will require a larger cohort of patients and a combination of mathematical modelling and machine learning techniques 29 .…”

Section: Discussionmentioning

confidence: 99%

The dynamic interaction of systemic inflammation and the hypothalamic-pituitary-adrenal (HPA) axis during and after major surgery

Galvis

Zavala

et al. 2021

Preprint

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Major surgery and critical illness produce a potentially life threatening systemic inflammatory response. The hypothalamic-pituitary-adrenal (HPA) axis is one of the key physiological systems that counterbalances this systemic inflammation through changes in adrenocorticotrophic hormone (ACTH) and cortisol. These hormones normally exhibit highly correlated ultradian pulsatility with an amplitude modulated by circadian processes. However, these dynamics are disrupted by major surgery and critical illness. In this work, we characterise the inflammatory, ACTH and cortisol responses of patients undergoing cardiac surgery and show that the HPA axis response can be classified into one of three phenotypes: single-pulse, two-pulses and multiple-pulses dynamics. We develop a mathematical model of cortisol secretion and metabolism that predicts the physiological mechanisms responsible for these different phenotypes. We show that the effects of inflammatory mediators are important only in the single-pulse pattern in which normal pulsatility is lost – suggesting that this phenotype could be indicative of the greatest inflammatory response. Investigating whether and how these phenotypes are correlated with clinical outcomes will be critical to patient prognosis and designing interventions to improve recovery.

show abstract

Classification framework for partially observed dynamical systems

Cited by 11 publications

References 22 publications

Single-photon absorption by single photosynthetic light-harvesting complexes

Single-photon absorption by single photosynthetic light-harvesting complexes

Modelling the dynamic interaction of systemic inflammation and the hypothalamic–pituitary–adrenal (HPA) axis during and after cardiac surgery

The dynamic interaction of systemic inflammation and the hypothalamic-pituitary-adrenal (HPA) axis during and after major surgery

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