Searcharxiv⌕ Search

arXiv subjects

Z. Rapti

Publications and source records attributed to Z. Rapti.

16 recordsLinked to original sources
arXiv2024

Practical identifiability and parameter estimation of compartmental epidemiological models

Practical parameter identifiability in ODE-based epidemiological models is a known issue, yet one that merits further study. It is essentially ubiquitous due to noise and errors in real data. In this study, to avoid uncertainty stemming from data of unknown quality, simulated data with added noise are used to investigate practical identifiability in two distinct epidemiological models. Particular emphasis is placed on the role of initial conditions, which are assumed unknown, except those that are directly measured. Instead of just focusing on one method of estimation, we use and compare results from various broadly used methods, including maximum likelihood and Markov Chain Monte Carlo (MCMC) estimation. Among other findings, our analysis revealed that the MCMC estimator is overall more robust than the point estimators considered. Its estimates and predictions are improved when the initial conditions of certain compartments are fixed so that the model becomes globally identifiable. For the point estimators, whether fixing or fitting the that are not directly measured improves parameter estimates is model-dependent. Specifically, in the standard SEIR model, fixing the initial condition for the susceptible population S(0) improved parameter estimates, while this was not true when fixing the initial condition of the asymptomatic population in a more involved model. Our study corroborates the change in quality of parameter estimates upon usage of pre-peak or post-peak time-series under consideration. Finally, our examples suggest that in the presence of significantly noisy data, the value of structural identifiability is moot.

stat.ME↗
arXiv2022

The role of mobility in the dynamics of the COVID-19 epidemic in Andalusia

Metapopulation models have been a popular tool for the study of epidemic spread over a network of highly populated nodes (cities, provinces, countries) and have been extensively used in the context of the ongoing COVID-19 pandemic. In the present work, we revisit such a model, bearing a particular case example in mind, namely that of the region of Andalusia in Spain during the period of the summer-fall of 2020 (i.e., between the first and second pandemic waves). Our aim is to consider the possibility of incorporation of mobility across the province nodes focusing on mobile-phone time dependent data, but also discussing the comparison for our case example with a gravity model, as well as with the dynamics in the absence of mobility. Our main finding is that mobility is key towards a quantitative understanding of the emergence of the second wave of the pandemic and that the most accurate way to capture it involves dynamic (rather than static) inclusion of time-dependent mobility matrices based on cell-phone data. Alternatives bearing no mobility are unable to capture the trends revealed by the data in the context of the metapopulation model considered herein.

physics.soc-ph↗
arXiv2022

Backcasting COVID-19: A Physics-Informed Estimate for Early Case Incidence

It is widely accepted that the number of reported cases during the first stages of the COVID-19 pandemic severely underestimates the number of actual cases. We leverage delay embedding theorems of Whitney and Takens and use Gaussian Process regression to estimate the number of cases during the first 2020 wave based on the second wave of the epidemic in several European countries, South Korea, and Brazil. We assume that the second wave was more accurately monitored and hence that it can be trusted. We then construct a manifold diffeomorphic to that of the implied original dynamical system, using fatalities or hospitalizations only. Finally, we restrict the diffeomorphism to the reported cases coordinate of the dynamical system. Our main finding is that in the European countries studied, the actual cases are under-reported by as much as 50\%. On the other hand, in South Korea -- which had an exemplary and proactive mitigation approach -- a far smaller discrepancy between the actual and reported cases is predicted, with an approximately 17\% predicted under-estimation. We believe that our backcasting framework is applicable to other epidemic outbreaks where (due to limited or poor quality data) there is uncertainty around the actual cases.

q-bio.QM↗
arXiv2020

Reaction-diffusion spatial modeling of COVID-19: Greece and Andalusia as case examples

We examine the spatial modeling of the outbreak of COVID-19 in two regions: the autonomous community of Andalusia in Spain and the mainland of Greece. We start with a 0D compartmental epidemiological model consisting of Susceptible, Exposed, Asymptomatic, (symptomatically) Infected, Hospitalized, Recovered, and deceased populations. We emphasize the importance of the viral latent period and the key role of an asymptomatic population. We optimize model parameters for both regions by comparing predictions to the cumulative number of infected and total number of deaths via minimizing the $\ell^2$ norm of the difference between predictions and observed data. We consider the sensitivity of model predictions on reasonable variations of model parameters and initial conditions, addressing issues of parameter identifiability. We model both pre-quarantine and post-quarantine evolution of the epidemic by a time-dependent change of the viral transmission rates that arises in response to containment measures. Subsequently, a spatially distributed version of the 0D model in the form of reaction-diffusion equations is developed. We consider that, after an initial localized seeding of the infection, its spread is governed by the diffusion (and 0D model "reactions") of the asymptomatic and symptomatically infected populations, which decrease with the imposed restrictive measures. We inserted the maps of the two regions, and we imported population-density data into COMSOL, which was subsequently used to solve numerically the model PDEs. Upon discussing how to adapt the 0D model to this spatial setting, we show that these models bear significant potential towards capturing both the well-mixed, 0D description and the spatial expansion of the pandemic in the two regions. Veins of potential refinement of the model assumptions towards future work are also explored.

q-bio.PE↗
arXiv2009

Soliton Dynamics in Linearly Coupled Discrete Nonlinear Schrödinger Equations

We study soliton dynamics in a system of two linearly coupled discrete nonlinear Schrödinger equations, which describe the dynamics of a two-component Bose gas, coupled by an electromagnetic field, and confined in a strong optical lattice. When the nonlinear coupling strengths are equal, we use a unitary transformation to remove the linear coupling terms, and show that the existing soliton solutions oscillate from one species to the other. When the nonlinear coupling strengths are different, the soliton dynamics is numerically investigated and the findings are compared to the results of an effective two-mode model. The case of two linearly coupled Ablowitz-Ladik equations is also investigated.

nlin.PS↗
arXiv2008

Rabi switch of condensate wavefunctions in a multicomponent Bose gas

Using a time-dependent linear (Rabi) coupling between the components of a weakly interacting multicomponent Bose-Einstein condensate (BEC), we propose a protocol for transferring the wavefunction of one component to the other. This "Rabi switch" can be generated in a binary BEC mixture by an electromagnetic field between the two components, typically two hyperfine states. When the wavefunction to be transfered is - at a given time - a stationary state of the multicomponent Hamiltonian, then, after a time delay (depending on the Rabi frequency), it is possible to have the same wavefunction on the other condensate. The Rabi switch can be used to transfer also moving bright matter-wave solitons, as well as vortices and vortex lattices in two-dimensional condensates. The efficiency of the proposed switch is shown to be 100% when inter-species and intra-species interaction strengths are equal. The deviations from equal interaction strengths are analyzed within a two-mode model and the dependence of the efficiency on the interaction strengths and on the presence of external potentials is examined in both 1D and 2D settings.

cond-mat.other↗
arXiv2007

Solitary Waves Under the Competition of Linear and Nonlinear Periodic Potentials

In this paper, we study the competition of linear and nonlinear lattices and its effects on the stability and dynamics of bright solitary waves. We consider both lattices in a perturbative framework, whereby the technique of Hamiltonian perturbation theory can be used to obtain information about the existence of solutions, and the same approach, as well as eigenvalue count considerations, can be used to obtained detailed conditions about their linear stability. We find that the analytical results are in very good agreement with our numerical findings and can also be used to predict features of the dynamical evolution of such solutions.

nlin.PS↗
arXiv2006

Healing Length and Bubble Formation in DNA

We have recently suggested that the probability for the formation of thermally activated DNA bubbles is, to a very good approximation, proportional to the number of soft AT pairs over a length L(n) that depend on the size $n$ of the bubble and on the temperature of the DNA. Here we clarify the physical interpretation of this length by relating it to the (healing) length that is required for the effect of a base-pair defect to become neligible. This provides a simple criteria to calculate L(n) for bubbles of arbitrary size and for any temperature of the DNA. We verify our findings by exact calculations of the equilibrium statistical properties of the Peyrard-Bishop-Dauxois model. Our method permits calculations of equilibrium thermal openings with several order of magnitude less numerical expense as compared with direct evaluations.

cond-mat.soft↗
arXiv2005

Lengthscales and Cooperativity in DNA Bubble Formation

It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in specific regions with lengths which at physiological temperatures are of the order of (but not equal to) the size of the bubble. The analysis is based on the Peyrard- Bishop-Dauxois model, whose equilibrium statistical properties have been accurately calculated here with a transfer integral approach.

cond-mat.soft↗
arXiv2004

On the modulational stability of Gross-Pitaevskii type equations in 1+1 dimensions

The modulational stability of the nonlinear Schr{ö}dinger (NLS) equation is examined in the case with a quadratic external potential. This study is motivated by recent experimental studies in the context of matter waves in Bose-Einstein condensates (BECs). The theoretical analysis invokes a lens-type transformation that converts the Gross-Pitaevskii into a regular NLS equation with an additional growth term. This analysis suggests the particular interest of a specific time-varying potential ((t+t*)^{-2}). We examine both this potential, as well as the time independent one numerically and conclude by suggesting experiments for the production of solitonic wave-trains in BEC.

cond-mat.soft↗
arXiv2004

Modulational Instability in Bose-Einstein Condensates under Feshbach Resonance Management

We investigate the modulational instability of nonlinear Schr{ö}dinger equations with periodic variation of their coefficients. In particular, we focus on the case of the recently proposed, experimentally realizable protocol of Feshbach Resonance Management for Bose-Einstein condensates. We derive the corresponding linear stability equation analytically and we show that it can be reduced to a Kronig-Penney model, which allows the determination of the windows of instability. The results are tested numerically in the absence, as well as in the presence of the magnetic trapping potential.

cond-mat.soft↗
arXiv2004

On the modulational stability of Gross-Pittaevskii type equations in 1+1 dimensions

The modulational stability of the nonlinear Schr{ö}dinger (NLS) equation is examined in the cases with linear and quadratic external potential. This study is motivated by recent experimental studies in the context of matter waves in Bose-Einstein condensates. The linear case can be examined by means of the Tappert transformation and can be mapped to the NLS in the appropriate (constant acceleration) frame. The quadratic case can be examined by using a lens-type transformation that converts it into a regular NLS with an additional linear growth term.

cond-mat.soft↗
arXiv2004

Modulational and Parametric Instabilities of the Discrete Nonlinear Schrödinger Equation

We examine the modulational and parametric instabilities arising in a non-autonomous, discrete nonlinear Schr{ö}dinger equation setting. The principal motivation for our study stems from the dynamics of Bose-Einstein condensates trapped in a deep optical lattice. We find that under periodic variations of the heights of the interwell barriers (or equivalently of the scattering length), additionally to the modulational instability, a window of parametric instability becomes available to the system. We explore this instability through multiple-scale analysis and identify it numerically. Its principal dynamical characteristic is that, typically, it develops over much larger times than the modulational instability, a feature that is qualitatively justified by comparison of the corresponding instability growth rates.

cond-mat.soft↗
arXiv2004

Variational Approach to the Modulational Instability

We study the modulational stability of the nonlinear Schrödinger equation (NLS) using a time-dependent variational approach. Within this framework, we derive ordinary differential equations (ODEs) for the time evolution of the amplitude and phase of modulational perturbations. Analyzing the ensuing ODEs, we re-derive the classical modulational instability criterion. The case (relevant to applications in optics and Bose-Einstein condensation) where the coefficients of the equation are time-dependent, is also examined.

cond-mat.soft↗
arXiv2004

On the Modulational Instability of the Nonlinear Schrödinger Equation with Dissipation

The modulational instability of spatially uniform states in the nonlinear Schrödinger equation is examined in the presence of higher-order dissipation. The study is motivated by results on the effects of three-body recombination in Bose-Einstein condensates, as well as by the important recent work of Segur et al. on the effects of linear damping in NLS settings. We show how the presence of even the weakest possible dissipation suppresses the instability on a longer time scale. However, on a shorter scale, the instability growth may take place, and a corresponding generalization of the MI criterion is developed. The analytical results are corroborated by numerical simulations. The method is valid for any power-law dissipation form, including the constant dissipation as a special case.

cond-mat.soft↗