arXiv subjects

C. K. Chan

Publications and source records attributed to C. K. Chan.

14 recordsLinked to original sources

arXiv2024

Dynamics of Information Exchange in Zebrafish: The Role of U-Turns in Visual Communication and Behavior Modulation

Motions of visually coupled zebrafish pairs are studied to understand the effects of information exchange on their behavior as a function of their minimal separation ($d$). We find that when $d$ is small, the pair can display a leader-follower relation (LFR) with trajectories of almost synchronized form. However, with larger $d$, although the same LFR is still maintained, the originally similar trajectories turn into different forms. Detailed analysis of their motion trajectories suggests that the pair might be using U-turns (UTs) to exchange information and to maintain a LFR at the same time. A simulation model based on UTs with inferred and proposed rules is able to reproduce prominent features of observed trajectories; indicating that the transition of trajectories can be understood as the result of a change in information exchange between the fish as $d$ increases. Our finding that UTs as important visual signals is consistent with the fact that UTs can induce a large amount of firings in retinas of observing fish.

physics.bio-ph↗

arXiv2022

Revealing directed effective connectivity of cortical neuronal networks from measurements

In the study of biological networks, one of the major challenges is to understand the relationships between network structure and dynamics. In this paper, we model in vitro cortical neuronal cultures as stochastic dynamical systems and apply a method that reconstructs directed networks from dynamics [Ching and Tam, Phys. Rev. E 95, 010301(R), 2017] to reveal directed effective connectivity, namely the directed links and synaptic weights, of the neuronal cultures from voltage measurements recorded by a multielectrode array. The effective connectivity so obtained reproduces several features of cortical regions in rats and monkeys and has similar network properties as the synaptic network of the nematode C. elegans, the only organism whose entire nervous system has been mapped out as of today. The distribution of the incoming degree is bimodal and the distributions of the average incoming and outgoing synaptic strength are non-Gaussian with long tails. The effective connectivity captures different information from the commonly studied functional connectivity, estimated using statistical correlation between spiking activities. The average synaptic strengths of excitatory incoming and outgoing links are found to increase with the spiking activity in the estimated effective connectivity but not in the functional connectivity estimated using the same sets of voltage measurements. These results thus demonstrate that the reconstructed effective connectivity can capture the general properties of synaptic connections and better reveal relationships between network structure and dynamics.

q-bio.NC↗

arXiv2021

Detection of Anticipatory Dynamics Between a Pair of Zebrafish

Trajectories from a pair of interacting zebrafish are used to test for the existence of anticipatory dynamics in natural systems. Anticipatory dynamics (AD) is unusual in that causal events are not necessarily ordered by their temporal order. However, their causal order can still be established if the direction of information flow (DIF) is known. In order to obtain DIF between trajectories of the two fish, we have made use of the difference of the transfer entropy between the trajectories with a history length established by experiments with known DIF. Our experimental results indicate that AD can be observed much more often in fish pairs of different genders. The use of DIF to determine causal order is further verified by the simulation of two chaotic Lorenz oscillators with anticipatory coupling; mimicking the interaction between the fish. Our simulation results further suggest that the two fish are interacting with their own internal dynamics, not by adaptation.

physics.bio-ph↗

arXiv2021

Information Synergy in the Anticipatory Dynamics of a Retina

Visual perceptions often come with illusions whose physical origin are not well understood yet. The encoding of stochastic light intensity $x(t)$ into spikes with firing rate $r(t)$ at time $t$ is investigated in an experiment with retinas from bullfrogs to understand the mechanism of anticipation. Partial information decomposition of the mutual information between $r$ and the combined state $\{x,\dot x\}$ is found to be consistent with the encoding form: $r(t) \sim (1-λ)x(t) + λ\dot x(t) τ_0$ with $λ$ being a system dependent parameter and $τ_0$ a constant. This form of $r(t)$ indicates that a retina is capable of anticipation based on the synergistic information generation between $x$ and $\dot x$. Our results suggest that illusions such as the anticipation studied here during retinal perception can originate from the recombination of information extracted in the retinal network.

q-bio.NC↗

arXiv2020

Anticipation and Negative Group Delay in a Retina

The mechanism of negative group delay (NGD) is used to understand the anticipatory capability of a retina. Experiments with retinas from bull frogs are performed to compare with the predictions of the NGD model. In particulars, whole field stochastic stimulation with various time correlations are used to probe anticipatory responses from the retina. We find that the NGD model can reproduce essential features of experimental observations characterized by the cross correlations between the stimulation and the retinal responses. The prediction horizon of a retina is found to depend on the correlation time of the stimulation as predicted by the NGD model. Experiments with dark and bright Gaussian light pulses further support the NGD mechanism; but only for the dark pulses indicating that the NGD effect of a retina might originate from its OFF response. Our finding suggests that sensory systems capable of using negative feedback for adaptation can give rise to anticipation as a consequence of the delay in the system.

physics.bio-ph↗

arXiv2019

Astro2020: Training the Future Generation of Computational Researchers

The current disparity in computational knowledge is a critical hindrance to the diversity and success of the field. Recommendations are outlined for policies and funding models to enable the growth and retention of a new generation of computational researchers that reflect the demographics of the undergraduate population in Astronomy and Physics.

astro-ph.IM↗

arXiv2016

Positive Feedback and Synchronized Bursts in Neuronal Cultures

Synchronized bursts (SBs) with complex structures are common in neuronal cultures. Although the origin of SBs is still unclear, they have been studied for their information processing capabilities. Here, we investigate the properties of these SBs in a culture on multi-electrode array system. We find that structures of these SBs are related to the different developmental stages of the cultures. A model based on short term synaptic plasticity, recurrent connections and astrocytic recycling of neurotransmitters has been developed successfully to understand these structures. A phase diagram obtained from this model shows that networks exhibiting SBs are in an oscillatory state due to large enough positive feedback provided by synaptic facilitation and recurrent connections. In this model, the structures of the SBs are the results of intrinsic synaptic interactions; not information stored in the network.

q-bio.NC↗

arXiv2016

Measurement of Anticipative Power of a Retina by Predictive Information

The predictive properties of a retina are studied by measuring the mutual information (MI) between its stimulation and the corresponding firing rates while it is being probed by a train of short pulses with stochastic intervals. Features of the measured MI at various time shifts between the stimulation and the response are used to characterize the predictive properties of the retina. By varying the statistical properties of the pulse train, our experiments show that a retina has the ability to predict future events of the stimulation if the information rate of the stimulation is low enough. Also, this predictive property of the retina occurs at a time scale similar to the well established anticipative phenomenon of omitted stimulus response in a retina. Furthermore, a retina can make use of its predictive ability to distinguish between time series created by an Ornstein--Uhlenbeck and a hidden Markovian process.

q-bio.NC↗

arXiv2016

Propagation and synchronization of reverberatory bursts in developing cultured networks

Developing networks of neural systems can exhibit spontaneous, synchronous activities called neural bursts, which can be important in the organization of functional neural circuits. Before the network matures, the activity level of a burst can reverberate in repeated rise-and-falls in periods of hundreds of milliseconds following an initial wave-like propagation of spiking activity, while the burst itself lasts for seconds. To investigate the spatiotemporal structure of the reverberatory bursts, we culture dissociated, rat cortical neurons on a high-density multi-electrode array to record the dynamics of neural activity over the growth and maturation of the network. We find the synchrony of the spiking significantly reduced following the initial wave and the activities become broadly distributed spatially. The synchrony recovers as the system reverberates until the end of the burst. Using a propagation model we infer the spreading speed of the spiking activity, which increases as the culture ages. We perform computer simulations of the system using a physiological model of spiking networks in two spatial dimensions and find the parameters that reproduce the observed resynchronization of spiking in the bursts. An analysis of the simulated dynamics suggests that the depletion of synaptic resources causes the resynchronization. The spatial propagation dynamics of the simulations match well with observations over the course of a burst and point to an interplay of the synaptic efficacy and the noisy neural self-activation in producing the morphology of the bursts.

q-bio.NC↗

arXiv2015

Adaptive Synchronization and Anticipatory Dynamical System

Many biological systems can sense periodical variations in a stimulus input and produce well-timed, anticipatory responses after the input is removed. Such systems show memory effects for retaining timing information in the stimulus and cannot be understood from traditional synchronization consideration of passive oscillatory systems. To understand this anticipatory phenomena, we consider oscillators built from excitable systems with the addition of an adaptive dynamics. With such systems, well-timed post-stimulus responses similar to those from experiments can be obtained. Furthermore, a well-known model of working memory is shown to possess similar anticipatory dynamics when the adaptive mechanism is identified with synaptic facilitation. The last finding suggests that this type of oscillators can be common in neuronal systems with plasticity.

q-bio.NC↗

arXiv2014

Reconstruction of network structures from repeating spike patterns in simulated bursting dynamics

Repeating patterns of spike sequences from a neuronal network have been proposed to be useful in the reconstruction of the network topology. Reverberations in a physiologically realistic model with various physical connection topologies (from random to scale-free) have been simulated to study the effectiveness of the pattern-matching method in the reconstruction of network topology from network dynamics. Simulation results show that functional networks reconstructed from repeating spike patterns can be quite different from the original physical networks; even global properties, such as the degree distribution, cannot always be recovered. However, the pattern-matching method can be effective in identifying hubs in the network. Since the form of reverberations are quite different for networks with and without hubs, the form of reverberations together with the reconstruction by repeating spike patterns might provide a reliable method to detect hubs in neuronal cultures.

q-bio.NC↗

arXiv2002

Quantum Entanglement of Excitons in Coupled Quantum Dots

Optically-controlled exciton dynamics in coupled quantum dots is studied. We show that the maximally entangled Bell states and Greenberger-Horne-Zeilinger (GHZ) states can be robustly generated by manipulating the system parameters to be at the avoided crossings in the eigenenergy spectrum. The analysis of population transfer is systematically carried out using a dressed-state picture. In addition to the quantum dot configuration that have been discussed by Quiroga and Johnson [Phys. Rev. Lett. \QTR{bf}{83}, 2270 (1999)], we show that the GHZ states also may be produced in a ray of three quantum dots with a shorter generation time.

cond-mat.mes-hall↗

arXiv2002

Dynamics of a two-component atomic Bose-Einstein condensate

The dynamical population oscillations between two internal states of a Bose-Einstein condensate are investigated within the rotating wave approximation. Analytical expressions for the population imbalance in the number states and coherent states have been derived, which predict different revival periods. Thus the true quantum state of the condensates may be unambiguously determined by detecting the atom intensity evolution for one internal state.

cond-mat.mes-hall↗

arXiv2002

Dynamics of spin-2 Bose condensate driven by external magnetic fields

Dynamic response of the F=2 spinor Bose-Einstein condensate (BEC) under the influence of external magnetic fields is studied. A general formula is given for the oscillation period to describe population transfer from the initial polar state to other spin states. We show that when the frequency and the reduced amplitude of the longitudinal magnetic field are related in a specific manner, the population of the initial spin-0 state will be dynamically localized during time evolution. The effects of external noise and nonlinear spin exchange interaction on the dynamics of the spinor BEC are studied. We show that while the external noise may eventually destroy the Rabi oscillations and dynamic spin localization, these coherent phenomena are robust against the nonlinear atomic interaction.

cond-mat.mes-hall↗