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  1. Article ; Online: Forecasting the outcome and estimating the epidemic model parameters from the fatality time series in COVID-19 outbreaks.

    Vattay, Gábor

    Physical biology

    2020  Volume 17, Issue 6, Page(s) 65002

    Abstract: In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. ... ...

    Abstract In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. Detailed epidemic models may contain a large number of empirical parameters, which cannot be determined with sufficient accuracy. In this paper, we show that the cumulative number of deaths can be regarded as a master variable, and the parameters of the epidemic such as the basic reproduction number, the size of the susceptible population, and the infection rate can be determined. In the SIR model, we derive an explicit single variable differential equation for the evolution of the cumulative number of fatalities. We show that the epidemic in Spain, Italy, and Hubei Province, China follows this master equation closely. We discuss the relationship with the logistic growth model, and we show that it is a good approximation when the basic reproduction number is less than 2.3. This condition is valid for the outbreak in Hubei, but not for the outbreaks in Spain, Italy, and New York. The difference is in the shorter infectious period in China, probably due to the separation policy of the infected. For more complex models, with more internal variables, such as the SEIR model, the equations derived from the SIR model remain valid approximately, due to the separation of timescales.
    MeSH term(s) Basic Reproduction Number ; COVID-19/epidemiology ; COVID-19/mortality ; Disease Outbreaks ; Forecasting ; Humans ; Models, Statistical ; SARS-CoV-2/isolation & purification
    Keywords covid19
    Language English
    Publishing date 2020-09-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2133216-2
    ISSN 1478-3975 ; 1478-3967
    ISSN (online) 1478-3975
    ISSN 1478-3967
    DOI 10.1088/1478-3975/abac69
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Relaxation of the Ising spin system coupled to a bosonic bath and the time dependent mean field equation.

    Veszeli, Máté Tibor / Vattay, Gábor

    PloS one

    2022  Volume 17, Issue 2, Page(s) e0264412

    Abstract: The Ising model does not have strictly defined dynamics, only a spectrum. There are different ways to equip it with time dependence, e.g., the Glauber or the Kawasaki dynamics, which are both stochastic, but it means there is a master equation that can ... ...

    Abstract The Ising model does not have strictly defined dynamics, only a spectrum. There are different ways to equip it with time dependence, e.g., the Glauber or the Kawasaki dynamics, which are both stochastic, but it means there is a master equation that can also describe their dynamics. These equations can be derived from the Redfield equation, where the spin system is weakly coupled to a bosonic bath. In this paper, we investigate the temperature dependence of the relaxation time of a Glauber-type master equation, especially in the case of the fully connected, uniform Ising model. The finite-size effects were analyzed with a reduced master equation and the thermodynamic limit with a time-dependent mean field equation.
    MeSH term(s) Computer Simulation ; Models, Chemical
    Language English
    Publishing date 2022-02-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0264412
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Mean field approximation for solving QUBO problems.

    Veszeli, Máté Tibor / Vattay, Gábor

    PloS one

    2022  Volume 17, Issue 8, Page(s) e0273709

    Abstract: The Quadratic Unconstrained Binary Optimization (QUBO) problem is NP-hard. Some exact methods like the Branch-and-Bound algorithm are suitable for small problems. Some approximations like stochastic simulated annealing for discrete variables or mean- ... ...

    Abstract The Quadratic Unconstrained Binary Optimization (QUBO) problem is NP-hard. Some exact methods like the Branch-and-Bound algorithm are suitable for small problems. Some approximations like stochastic simulated annealing for discrete variables or mean-field annealing for continuous variables exist for larger ones, and quantum computers based on the quantum adiabatic annealing principle have also been developed. Here we show that the mean-field approximation of the quantum adiabatic annealing leads to equations similar to those of thermal mean-field annealing. However, a new type of sigmoid function replaces the thermal one. The new mean-field quantum adiabatic annealing can replicate the best-known cut values on some of the popular benchmark Maximum Cut problems.
    MeSH term(s) Algorithms ; Computers
    Language English
    Publishing date 2022-08-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0273709
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Forecasting the outcome and estimating the epidemic model parameters from the fatality time series in COVID-19 outbreaks

    Vattay, Gábor

    Physical Biology

    2020  Volume 17, Issue 6, Page(s) 65002

    Keywords Biophysics ; Cell Biology ; Molecular Biology ; Structural Biology ; covid19
    Publisher IOP Publishing
    Publishing country uk
    Document type Article ; Online
    ZDB-ID 2133216-2
    ISSN 1478-3975 ; 1478-3967
    ISSN (online) 1478-3975
    ISSN 1478-3967
    DOI 10.1088/1478-3975/abac69
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Relaxation of the Ising spin system coupled to a bosonic bath and the time dependent mean field equation

    Máté Tibor Veszeli / Gábor Vattay

    PLoS ONE, Vol 17, Iss

    2022  Volume 2

    Abstract: The Ising model does not have strictly defined dynamics, only a spectrum. There are different ways to equip it with time dependence, e.g., the Glauber or the Kawasaki dynamics, which are both stochastic, but it means there is a master equation that can ... ...

    Abstract The Ising model does not have strictly defined dynamics, only a spectrum. There are different ways to equip it with time dependence, e.g., the Glauber or the Kawasaki dynamics, which are both stochastic, but it means there is a master equation that can also describe their dynamics. These equations can be derived from the Redfield equation, where the spin system is weakly coupled to a bosonic bath. In this paper, we investigate the temperature dependence of the relaxation time of a Glauber-type master equation, especially in the case of the fully connected, uniform Ising model. The finite-size effects were analyzed with a reduced master equation and the thermodynamic limit with a time-dependent mean field equation.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Predicting the ultimate outcome of the COVID-19 outbreak in Italy

    Vattay, Gabor

    Abstract: During the COVID-19 outbreak, it is essential to monitor the effectiveness of measures taken by governments on the course of the epidemic. Here we show that there is already a sufficient amount of data collected in Italy to predict the outcome of the ... ...

    Abstract During the COVID-19 outbreak, it is essential to monitor the effectiveness of measures taken by governments on the course of the epidemic. Here we show that there is already a sufficient amount of data collected in Italy to predict the outcome of the process. We show that using the proper metric, the data from Hubei Province and Italy has striking similarity, which enables us to calculate the expected number of confirmed cases and the number of deaths by the end of the process. Our predictions will improve as new data points are generated day by day, which can help to make further public decisions. The method is based on the data analysis of logistic growth equations describing the process on the macroscopic level. At the time of writing of the first version, the number of fatalities in Italy was expected to be 6000, and the predicted end of the crisis was April 15, 2020. In this new version, we discuss what changed in the two weeks which passed since then. The trend changed drastically on March 17, 2020, when the Italian health system reached its capacity limit. Without this limit, probably 3500 more people would have died. Instead, due to the limitations, 17.000 people are expected to die now, which is a five-fold increase. The predicted end of the crisis now shifted to May 8, 2020.
    Keywords covid19
    Publisher ArXiv
    Document type Article
    Database COVID19

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  7. Article: Forecasting the outcome and estimating the epidemic model parameters from the fatality time series in COVID-19 outbreaks

    Vattay, Gabor

    Phys. biol

    Abstract: In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. ... ...

    Abstract In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. Detailed epidemic models may contain a large number of empirical parameters, which cannot be determined with sufficient accuracy. In this paper, we show that the cumulative number of deaths can be regarded as a master variable, and the parameters of the epidemic such as the basic reproduction number, the size of the susceptible population, and the infection rate can be determined. In the SIR model, we derive an explicit single variable differential equation for the evolution of the cumulative number of fatalities. We show that the epidemic in Spain, Italy, and Hubei Province, China follows this master equation closely. We discuss the relationship with the logistic growth model, and we show that it is a good approximation when the basic reproduction number is less than $2.3$. This condition is valid for the outbreak in Hubei, but not for the outbreaks in Spain, Italy, and New York. The difference is in the shorter infectious period in China, probably due to the separation policy of the infected. For more complex models, with more internal variables, such as the SEIR model, the equations derived from the SIR model remain valid approximately, due to the separation of timescales.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #696869
    Database COVID19

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  8. Book ; Online: Predicting the ultimate outcome of the COVID-19 outbreak in Italy

    Vattay, Gabor

    2020  

    Abstract: During the COVID-19 outbreak, it is essential to monitor the effectiveness of measures taken by governments on the course of the epidemic. Here we show that there is already a sufficient amount of data collected in Italy to predict the outcome of the ... ...

    Abstract During the COVID-19 outbreak, it is essential to monitor the effectiveness of measures taken by governments on the course of the epidemic. Here we show that there is already a sufficient amount of data collected in Italy to predict the outcome of the process. We show that using the proper metric, the data from Hubei Province and Italy has striking similarity, which enables us to calculate the expected number of confirmed cases and the number of deaths by the end of the process. Our predictions will improve as new data points are generated day by day, which can help to make further public decisions. The method is based on the data analysis of logistic growth equations describing the process on the macroscopic level. At the time of writing of the first version, the number of fatalities in Italy was expected to be 6000, and the predicted end of the crisis was April 15, 2020. In this new version, we discuss what changed in the two weeks which passed since then. The trend changed drastically on March 17, 2020, when the Italian health system reached its capacity limit. Without this limit, probably 3500 more people would have died. Instead, due to the limitations, 17.000 people are expected to die now, which is a five-fold increase. The predicted end of the crisis now shifted to May 8, 2020.

    Comment: 2 pages
    Keywords Quantitative Biology - Populations and Evolution ; Physics - Physics and Society ; covid19
    Publishing date 2020-03-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Book ; Online: Forecasting the outcome and estimating the epidemic model parameters from the fatality time series in COVID-19 outbreaks

    Vattay, Gabor

    2020  

    Abstract: In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. ... ...

    Abstract In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. Detailed epidemic models may contain a large number of empirical parameters, which cannot be determined with sufficient accuracy. In this paper, we show that the cumulative number of deaths can be regarded as a master variable, and the parameters of the epidemic such as the basic reproduction number, the size of the susceptible population, and the infection rate can be determined. In the SIR model, we derive an explicit single variable differential equation for the evolution of the cumulative number of fatalities. We show that the epidemic in Spain, Italy, and Hubei Province, China follows this master equation closely. We discuss the relationship with the logistic growth model, and we show that it is a good approximation when the basic reproduction number is less than $2.3$. This condition is valid for the outbreak in Hubei, but not for the outbreaks in Spain, Italy, and New York. The difference is in the shorter infectious period in China, probably due to the separation policy of the infected. For more complex models, with more internal variables, such as the SEIR model, the equations derived from the SIR model remain valid approximately, due to the separation of timescales.
    Keywords Quantitative Biology - Populations and Evolution ; Physics - Physics and Society ; covid19
    Subject code 612
    Publishing date 2020-04-19
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Experimental Data Confirm Carrier-Cascade Model for Solid-State Conductance across Proteins.

    Papp, Eszter / Vattay, Gábor / Romero-Muñiz, Carlos / Zotti, Linda A / Fereiro, Jerry A / Sheves, Mordechai / Cahen, David

    The journal of physical chemistry. B

    2023  Volume 127, Issue 8, Page(s) 1728–1734

    Abstract: The finding that electronic conductance across ultrathin protein films between metallic electrodes remains nearly constant from room temperature to just a few degrees Kelvin has posed a challenge. We show that a model based on a generalized Landauer ... ...

    Abstract The finding that electronic conductance across ultrathin protein films between metallic electrodes remains nearly constant from room temperature to just a few degrees Kelvin has posed a challenge. We show that a model based on a generalized Landauer formula explains the nearly constant conductance and predicts an Arrhenius-like dependence for low temperatures. A critical aspect of the model is that the relevant activation energy for conductance is either the difference between the HOMO and HOMO-1 or the LUMO+1 and LUMO energies instead of the HOMO-LUMO gap of the proteins. Analysis of experimental data confirms the Arrhenius-like law and allows us to extract the activation energies. We then calculate the energy differences with advanced DFT methods for proteins used in the experiments. Our main result is that the experimental and theoretical activation energies for these three different proteins and three differently prepared solid-state junctions match nearly perfectly, implying the mechanism's validity.
    Language English
    Publishing date 2023-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.2c07946
    Database MEDical Literature Analysis and Retrieval System OnLINE

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