arXiv subjects

Han-Yu Jiang

Publications and source records attributed to Han-Yu Jiang.

9 recordsLinked to original sources

arXiv2025

A Novel Nonlinear IP$_3$R State Transition Model and Calcium Oscillation

We present a novel nonlinear state transition model for inositol 1,4,5-trisphosphate receptors (IP$_3$Rs) that incorporates a pre-activated state, as suggested by electron microscopy observations. Our model provides a theoretical framework for the biphasic Ca$^{2+}$ dependence of IP$_3$Rs and accurately reproduces their experimentally observed state distribution under saturating IP$_3$ conditions. By integrating receptor dynamics with cytoplasmic and endoplasmic reticulum (ER) calcium exchange, we simulate IP$_3$R-mediated Ca$^{2+}$ oscillations governed by six key conformational states. A pivotal finding is that IP$_3$ regulates these oscillations in a switch-like manner: once a critical IP$_3$ concentration is reached, the system abruptly transitions to sustained, constant-amplitude oscillations that quickly terminate when the concentration exceeds a secondary threshold. These results underscore the crucial role of the pre-activated state in modulating calcium signaling.

physics.bio-ph↗

arXiv2025

Formation and Regulation of Calcium Sparks on a Nonlinear Spatial Network of Ryanodine Receptors

Accurate regulation of calcium release is essential for cellular signaling, with the spatial distribution of ryanodine receptors (RyRs) playing a critical role. In this study, we present a nonlinear spatial network model that simulates RyR spatial organization to investigate calcium release dynamics by integrating RyR behavior, calcium buffering, and calsequestrin (CSQ) regulation. The model successfully reproduces calcium sparks, shedding light on their initiation, duration, and termination mechanisms under clamped calcium conditions. Our simulations demonstrate that RyR clusters act as on-off switches for calcium release, producing short-lived calcium quarks and longer-lasting calcium sparks based on distinct activation patterns. Spark termination is governed by calcium gradients and stochastic RyR dynamics, with CSQ facilitating RyR closure and spark termination. We also uncover the dual role of CSQ as both a calcium buffer and a regulator of RyRs. Elevated CSQ levels prolong calcium release due to buffering effects, while CSQ-RyR interactions induce excessive refractoriness, a phenomenon linked to pathological conditions such as ventricular arrhythmias. Dysregulated CSQ function disrupts the on-off switching behavior of RyRs, impairing calcium release dynamics. These findings provide new insights into RyR-mediated calcium signaling, highlighting CSQ's pivotal role in maintaining calcium homeostasis and its implications for pathological conditions. This work advances the understanding of calcium spark regulation and underscores its significance for cardiomyocyte function.

q-bio.SC↗

arXiv2022

Calcium oscillation on homogeneous and heterogeneous networks of ryanodine receptor

Calcium oscillation is an important calcium homeostasis, imbalance of which is the key mechanism of initiation and progression of many major diseases. The formation and maintenance of calcium homeostasis are closely related to the spatial distribution of calcium channels. In the current paper, a theoretical framework is established by abstracting the spatial distribution of the calcium channels as a nonlinear biological complex network with calcium channels as nodes and Ca$^{2+}$ as edges. A dynamical model for a RyR is adopted to investigate the effect of spatial distribution on calcium oscillation. The mean-field model can be well reproduced from the complete graph and dense Erd\"os-R\'enyi network. The synchronization of RyRs is found important to generate a global calcium oscillation. The clique graph with a cluster structure can not produce a global oscillation due to the failure of synchronization between clusters. A more realistic geometric network is constructed in a two-dimensional plane based on the experimental information about the RyR arrangement of clusters and the frequency distribution of cluster sizes. Different from the clique graph, the global oscillation can be generated with reasonable parameters on the geometric network. The simulation also suggests that existence of small clusters and rogue RyR's plays an important role in the maintenance of global calcium oscillation through keeping synchronization between large clusters. Such results support the heterogeneous distribution of RyR's with different-size clusters, which is helpful to understand recent observations with super resolution nanoscale imaging techniques. The current theoretical framework can also be extent to investigate other phenomena in calcium signal transduction.

q-bio.SC↗

arXiv2021

Molecular states from $D^{()}\bar{D}^{()}/B^{()}\bar{B}^{()}$ and $D^{()}D^{()}/\bar{B}^{()}\bar{B}^{()}$ interactions

In this work, we preform a systematic investigation about hidden heavy and doubly heavy molecular states from the $D^{(*)}\bar{D}^{(*)}/B^{(*)}\bar{B}^{(*)}$ and $D^{(*)}D^{(*)}/\bar{B}^{(*)}\bar{B}^{(*)}$ interactions in the quasipotential Bethe-Salpeter equation (qBSE) approach. With the help of Lagrangians with heavy quark and chiral symmetries, interaction potentials are constructed within the one-boson-exchange model in which we include the $π$, $η$, $ρ$, $ω$ and $σ$ exchanges, as well as $J/ψ$ or $Υ$ exchange. Possible bound states from the interactions considered are searched for as the pole of scattering amplitude. The results suggest that experimentally observed states, $Z_c(3900)$, $Z_c(4020)$, $Z_b(10610)$, and $Z_b(10650)$, can be related to the $D\bar{D}^{*}$, $D^*\bar{D}^{*}$, $B\bar{B}^{*}$, and $B^*\bar{B}^{*}$ interactions with quantum numbers $I^G(J^P)=1^+(1^{+})$, respectively. The $D\bar{D}^{*}$ interaction is also attractive enough to produce a pole with $0^+(0^+)$ which is related to the $X(3872)$. Within the same theoretical frame, the existence of $D\bar{D}$ and $B\bar{B}$ molecular states with $0(0^+)$ are predicted. The possible $D^*\bar{D}^*$ molecular states with $0(0^+, 1^+, 2^+)$ and $1(0^+)$ and their bottom partners are also suggested by the calculation. In the doubly heavy sector, no bound state is produced from the $DD/\bar{B}\bar{B}$ interaction while a bound state is found with $0(1^+)$ from $DD^*/\bar{B}\bar{B}^*$ interaction. The $D^*D^*/\bar{B}^*\bar{B}^*$ interaction produces three molecular states with $0(1^+)$, $0(2^+)$ and $1(2^+)$.

hep-ph↗

arXiv2021

Hidden and doubly heavy molecular states from interactions $D^{()}_{(s)}{\bar{D}}^{()}_{s}$/$B^{()}_{(s)}{\bar{B}}^{()}_{s}$ and ${D}^{()}_{(s)}D_{s}^{()}$/${B}^{()}_{(s)}B_{s}^{()}$

In this work, we perform a systematical investigation about the possible hidden and doubly heavy molecular states with open and hidden strangeness from interactions of $D^{(*)}{\bar{D}}^{(*)}_{s}$/$B^{(*)}{\bar{B}}^{(*)}_{s}$, ${D}^{(*)}_{s}{\bar{D}}^{(*)}_{s}$/${B}^{(*)}_{s}{\bar{B}}^{(*)}_{s}$, ${D}^{(*)}D_{s}^{(*)}$/${B}^{(*)}B_{s}^{(*)}$, and $D_{s}^{(*)}D_{s}^{(*)}$/$B_{s}^{(*)}B_{s}^{(*)}$ in a quasipotential Bethe-Salpeter equation approach. The interactions of the systems considered are described within the one-boson-exchange model, which includes exchanges of light mesons and $J/ψ/Υ$ meson. Possible molecular states are searched for as poles of scattering amplitudes of the interactions considered. The results suggest that recently observed $Z_{cs}(3985)$ can be assigned as a molecular state of $D^*\bar{D}_s+D\bar{D}^*_s$, which is a partner of $Z_c(3900)$ state as a $D\bar{D}^*$ molecular state. The calculation also favors the existence of hidden heavy states $D_s\bar{D}_s/B_s\bar{B}_s$ with spin parity $J^P=0^+$, $D_s\bar{D}^*_s/B_s\bar{B}^*_s$ with $1^{+}$, and $D^*_s\bar{D}^*_s/B^*_s\bar{B}^*_s$ with $0^+$, $1^+$, and $2^+$. In the doubly heavy sector, the bound states can be found from the interactions $(D^*D_s+DD^*_s)/(B^*B_s+BB^*_s)$ with $1^+$, $D_s\bar{D}_s^*/B_s\bar{B}_s^*$ with $1^+$, $D^*D^*_s/B^*B^*_s$ with $1^+$ and $2^+$, and $D^*_sD^*_s/B^*_sB^*_s$ with $1^+$ and $2^+$. Some other interactions are also found attractive, but may be not strong enough to produce a bound state. The results in this work are helpful for understanding the $Z_{cs}(3985)$, and future experimental search for the new molecular states.

hep-ph↗

arXiv2021

Nonlinear signal transduction network with multistate

Signal transduction is an important and basic mechanism to cell life activities. The stochastic state transition of receptor induces the release of signaling molecular, which triggers the state transition of other receptors. It constructs a nonlinear sigaling network, and leads to robust switchlike properties which are critical to biological function. Network architectures and state transitions of receptor affect the performance of this biological network. In this work, we perform a study of nonlinear signaling on biological polymorphic network by analyzing network dynamics of the Ca$^{2+}$ induced Ca$^{2+}$ release mechanism, where fast and slow processes are involved and the receptor has four conformational states. Three types of networks, Erd\"os-R\'enyi network, Watts-Strogatz network and BaraB\'asi-Albert network, are considered with different parameters. The dynamics of the biological networks exhibit different patterns at different time scales. At short time scale, the second open state is essential to reproduce the quasi-bistable regime, which emerges at a critical strength of connection for all three states involved in the fast processes and disappears at another critical point. The pattern at short time scale is not sensitive to the network architecture. At long time scale, only monostable regime is observed, and difference of network architectures affects the results more seriously. Our finding identifies features of nonlinear signaling networks with multistate that may underlie their biological function.

q-bio.MN↗

arXiv2021

Functional annotation of creeping bentgrass protein sequences based on convolutional neural network

Background: Creeping bentgrass (Agrostis soionifera) is a perennial grass of Gramineae, belonging to cold season turfgrass, but has poor disease resistance. Up to now, little is known about the induced systemic resistance (ISR) mechanism, especially the relevant functional proteins, which is important to disease resistance of turfgrass. Achieving more information of proteins of infected creeping bentgrass is helpful to understand the ISR mechanism. Results: With BDO treatment, creeping bentgrass seedlings were grown, and the ISR response was induced by infecting Rhizoctonia solani. High-quality protein sequences of creeping bentgrass seedlings were obtained. Some of protein sequences were functionally annotated according to the database alignment while a large part of the obtained protein sequences was left non-annotated. To treat the non-annotated sequences, a prediction model based on convolutional neural network was established with the dataset from Uniport database in three domains to acquire good performance, especially the higher false positive control rate. With established model, the non-annotated protein sequences of creeping bentgrass were analyzed to annotate proteins relevant to disease-resistance response and signal transduction. Conclusions: The prediction model based on convolutional neural network was successfully applied to select good candidates of the proteins with functions relevant to the ISR mechanism from the protein sequences which cannot be annotated by database alignment. The waste of sequence data can be avoided, and research time and labor will be saved in further research of protein of creeping bentgrass by molecular biology technology. It also provides reference for other sequence analysis of turfgrass disease-resistance research.

q-bio.GN↗

arXiv2020

Three-dimensional cytoplasmic calcium propagation with boundaries

Ca$^{2+}$ plays an important role in cell signal transduction. Its intracellular propagation is the most basic process of Ca$^{2+}$ signaling, such as calcium wave and double messenger system. In this work, with both numerical simulation and mean field ansatz, the 3-dimensional probability distribution of Ca$^{2+}$, which is read out by phosphorylation, is studied in two scenarios with boundaries. The coverage of distribution of Ca$^{2+}$ is found at an order of magnitude of $μ$m, which is consistent with experimental observed calcium spike and wave. Our results suggest that the double messenger system may occur in the ER-PM junction to acquire great efficiency. The buffer effect of kinase is also discussed by calculating the average position of phosphorylations and free Ca$^{2+}$. The results are helpful to understand the mechanism of Ca$^{2+}$ signaling.

physics.bio-ph↗

arXiv2020

Possible molecular states from the $NΔ$ interaction

Recently, a hint for dibaryon $NΔ(D_{21})$ was observed at WASA-AT-COSY with a mass about $30\pm10$ MeV below the $NΔ$ threshold. It has a relatively small binding energy compared with the $d^*(2380)$ and a width close to the width of the $Δ$ baryon, which suggests that it may be a dibaryon in a molecular state picture. In this work, we study the possible $S$-wave molecular states from the $NΔ$ interaction within the quasipotential Bethe-Salpeter equation approach. The interaction is described by exchanging $π$, $ρ$, and $ω$ mesons. With reasonable parameters, a $D_{21}$ bound state can be produced from the interaction. The results also suggest that there may exist two more possible $D_{12}$ and $D_{22}$ states with smaller binding energies. The $π$ exchange is found to play the most important role to bind two baryons to form the molecular states. An experimental search for possible $NΔ(D_{12})$ and $NΔ(D_{22})$ states will be helpful for understanding the hint of the dibaryon $NΔ(D_{21})$.

nucl-th↗