Fast-variable elimination in stochastic SIRS epidemic model with Itô processes

Journal of the Korean Physical Society · 2025-01-07

Lineage of the SEIRS model and its critical thresholds on social networks

Nonlinear Dynamics · 2025-05-12

General protocol for predicting outbreaks of infectious diseases in social networks

Scientific Reports · 2024-03-12 · 1 citations

Epidemic spreading on social networks with quenched connections is strongly influenced by dynamic correlations between connected nodes, posing theoretical challenges in predicting outbreaks of infectious diseases. The quenched connections introduce dynamic correlations, indicating that the infection of one node increases the likelihood of infection among its neighboring nodes. These dynamic correlations pose significant difficulties in developing comprehensive theories for threshold determination. Determining the precise epidemic threshold is pivotal for diseases control. In this study, we propose a general protocol for accurately determining epidemic thresholds by introducing a new set of fundamental conditions, where the number of connections between individuals of each type remains constant in the stationary state, and by devising a rescaling method for infection rates. Our general protocol is applicable to diverse epidemic models, regardless of the number of stages and transmission modes. To validate our protocol's effectiveness, we apply it to two widely recognized standard models, the susceptible-infected-recovered-susceptible model and the contact process model, both of which have eluded precise threshold determination using existing sophisticated theories. Our results offer essential tools to enhance disease control strategies and preparedness in an ever-evolving landscape of infectious diseases.

A stochastic susceptible-infected-susceptible epidemic model with Stratonovich processes

Journal of the Korean Physical Society · 2023-12-29 · 4 citations

Nonequilibrium phase transitions in metapopulation models of infectious diseases on heterogeneous networks

Journal of Physics A Mathematical and Theoretical · 2023-08-11 · 2 citations

Abstract We study two meta-population models of infectious diseases in heterogeneous networks. We distinguish between asymptomatic and symptomatic infections and these two go through the different courses of infection and recovery. We consider that asymptomatic infections are described by an SIS model and symptomatic infections by an SIR or SIRS model depending on the immunity upon recovery. By introducing the probability of being infected asymptomatically, we combine an SIS model for asymptomatic infections with an SIR or SIRS model for symptomatic infections to obtain the SIS-SIR and SIS-SIRS models. We use a heterogeneous mean-field theory and Monte Carlo simulations to analyze two models and find that both models undergo nonequilibrium continuous phase transitions from the endemic phase to the disease-free phase at certain critical thresholds as we vary the proportion of asymptomatic infections. It suggests that it may be possible to maintain the population in the disease-free phase by controlling the proportion of asymptomatic infections. The SIS-SIRS model shows that asymptomatic infection drives symptomatic infection and vice versa. In addition, the spreading of infections eventually ceases as the population decreases even at a fixed proportion of asymptomatic infections corresponding to the endemic phase. The results provide a theoretical basis for understanding the epidemiological facts that social distancing and reducing asymptomatic infections are important factors in optimizing quarantine measures to prevent the epidemic outbreaks of infectious diseases.

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study

Polymers · 2023 · 3 citations

• Chemical physics
• Chemistry
• Materials science

We studied the translocation of polyelectrolyte (PE) chains driven by an electric field through a pore by means of molecular dynamics simulations of a coarse-grained HP model mimicking high salt conditions. Charged monomers were considered as polar (P) and neutral monomers as hydrophobic (H). We considered PE sequences that had equally spaced charges along the hydrophobic backbone. Hydrophobic PEs were in the globular form in which H-type and P-type monomers were partially segregated and they unfolded in order to translocate through the narrow channel under the electric field. We provided a quantitative comprehensive study of the interplay between translocation through a realistic pore and globule unraveling. By means of molecular dynamics simulations, incorporating realistic force fields inside the channel, we investigated the translocation dynamics of PEs at various solvent conditions. Starting from the captured conformations, we obtained distributions of waiting times and drift times at various solvent conditions. The shortest translocation time was observed for the slightly poor solvent. The minimum was rather shallow, and the translocation time was almost constant for medium hydrophobicity. The dynamics were controlled not only by the friction of the channel, but also by the internal friction related to the uncoiling of the heterogeneous globule. The latter can be rationalized by slow monomer relaxation in the dense phase. The results were compared with those from a simplified Fokker-Planck equation for the position of the head monomer.

Evolutionary dynamics of the island model with stochastic resetting

Journal of the Korean Physical Society · 2022-11-10 · 3 citations

Translocation, Rejection and Trapping of Polyampholytes

Polymers · 2022 · 4 citations

• Physics
• Statistical physics
• Chemistry

= 40 to better demonstrate asymptotic laws. At early times, rejection was mainly controlled by the charge sequence of the head part, but late translocation/rejection was governed by the escape from a trapped state over an antagonistic barrier built up along the sequence. The probability distribution of translocation times from all successful attempts revealed a power-law tail. At finite times, there was a population of trapped sequences that relaxed very slowly (logarithmically) with time. If a subensemble of sequences with prescribed net charge was considered the power-law decay was steeper for a more favorable net charge. Our findings were rationalized by theoretical arguments developed for long chains. We also provided operational criteria for the translocation behavior of a sequence, explaining the selection by the translocation process. From the perspective of protein translocation, our findings can help rationalize the behavior of intrinsically disordered proteins (IDPs), which can be modeled as polyampholytes. Most IDP sequences have a strong net charge favoring translocation. Even for sequences with those large net charges, the translocation times remained very dispersed and the translocation was highly sequence-selective.

The Measurement of Information and Free Energy in Mechanical-Force-Driven Coil–Globule Transitions

The Journal of Physical Chemistry B · 2021-05-11

We study the role of information (the relative entropy) for polymers undergoing coil-globule transitions driven by a time-dependent force. Pulling experiments at various speeds are performed by Brownian dynamics simulations. We obtain the work distributions for the forward and time-reversed backward processes and information stored at the end of the nonequilibrium pulling processes. We present the systematic method to measure the information from the pulling experiments and extract the information by analyzing slowly relaxing modes. When the information is incorporated, the work distributions modified by the information allow access to the proper free energy via the formulation of the generalized fluctuation theorems even if the initial states of the forward and time-reversed backward processes are out of equilibrium. This demonstrates that the work-information conversion works well for a single-molecule system with many degrees of freedom.

Derivation of evolutionary entropy in the steady-state thermodynamics of evolutionary dynamics

Physical review. E · 2021 · 5 citations

• Statistical physics
• Mathematics
• Thermodynamics

We investigate the parallel mutation-selection model with varying population size, which is formulated in terms of individuals undergoing the evolution processes of reproduction and mutation, to derive evolutionary entropy. Under the framework of the steady-state thermodynamics for evolutionary dynamics, the excess growth (the difference between the maximum growth rate and the total growth rate) can be interpreted as the evolutionary entropy defined in terms of the probability distributions characteristic of evolutionary dynamics. The Clausius inequality states that the excess growth is always less than or equal to the entropy difference in evolutionary dynamics. Analytically, by using the genome sequence length L=3, we derive the growth after evolutionary dynamics with the finite number of environmental changes and calculate the entropy difference during this evolutionary dynamics, and we verify the Clausius inequality. Furthermore, by taking the infinite limit of the number of environmental changes, we verify that the equality holds for the quasistatic environmental change. By using the derived evolutionary entropy, we propose the thermodynamic relation between the free fitness and evolutionary entropy, where the free fitness is the maximum growth rate possible. Numerically, we use the Gillespie-type simulations, which provides direct realizations of the master equation governing evolutionary dynamics, to verify the Clausius inequality and we find that the simulation results are in good agreement with the analytic results.