| 1. |
- Chigansky, Pavel, et al.
(author)
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Populations with interaction and environmental dependence: From few, (almost) independent, members into deterministic evolution of high densities
- 2019
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In: Stochastic Models. - : Informa UK Limited. - 1532-6349 .- 1532-4214. ; 35:2, s. 108-118
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Journal article (peer-reviewed)abstract
- Many populations, e.g. not only of cells, bacteria, viruses, or replicating DNA molecules, but also of species invading a habitat, or physical systems of elements generating new elements, start small, from a few lndividuals, and grow large into a noticeable fraction of the environmental carrying capacity K or some corresponding regulating or system scale unit. Typically, the elements of the initiating, sparse set will not be hampering each other and their number will grow from Z0 = z0 in a branching process or Malthusian like, roughly exponential fashion, Zt ~atW, where Z t is the size at discrete time t → ∞, a > 1 is the offspring mean per individual (at the low starting density of elements, and large K), and W a sum of z0 i.i.d. random variables. It will, thus, become detectable (i.e. of the same order as K) only after around K generations, when its density Xt := Z t /K will tend to be strictly positive. Typically, this entity will be random, even if the very beginning was not at all stochastic, as indicated by lower case z0 , due to variations during the early development. However, from that time onwards, law of large numbers effects will render the process deterministic, though inititiated by the random density at time log K, expressed through the variable W. Thus, W acts both as a random veil concealing the start and a stochastic initial value for later, deterministic population density development. We make such arguments precise, studying general density and also system-size dependent, processes, as K → ∞. As an intrinsic size parameter, K may also be chosen to be the time unit. The fundamental ideas are to couple the initial system to a branching process and to show that late densities develop very much like iterates of a conditional expectation operator. The “random veil”, hiding the start, was first observed in the very concrete special case of finding the initial copy number in quantitative PCR under Michaelis-Menten enzyme kinetics, where the initial individual replication variance is nil if and only if the efficiency is one, i.e. all molecules replicate.
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| 2. |
- Chigansky, P., et al.
(author)
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What can be observed in real time PCR and when does it show?
- 2018
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In: Journal of Mathematical Biology. - : Springer Science and Business Media LLC. - 0303-6812 .- 1432-1416. ; 76:3, s. 679-695
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Journal article (peer-reviewed)abstract
- Real time, or quantitative, PCR typically starts from a very low concentration of initial DNA strands. During iterations the numbers increase, first essentially by doubling, later predominantly in a linear way. Observation of the number of DNA molecules in the experiment becomes possible only when it is substantially larger than initial numbers, and then possibly affected by the randomness in individual replication. Can the initial copy number still be determined? This is a classical problem and, indeed, a concrete special case of the general problem of determining the number of ancestors, mutants or invaders, of a population observed only later. We approach it through a generalised version of the branching process model introduced in Jagers and Klebaner (J Theor Biol 224(3):299-304, 2003. doi: 10.1016/S0022-5193(03) 001668), and based on Michaelis-Menten type enzyme kinetical considerations from Schnell and Mendoza (J Theor Biol 184(4):433-440, 1997). A crucial role is played by the Michaelis-Menten constant being large, as compared to initial copy numbers. In a strange way, determination of the initial number turns out to be completely possible if the initial rate v is one, i.e all DNA strands replicate, but only partly so when v < 1, and thus the initial rate or probability of succesful replication is lower than one. Then, the starting molecule number becomes hidden behind a "veil of uncertainty". This is a special case, of a hitherto unobserved general phenomenon in population growth processes, which will be adressed elsewhere.
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| 3. |
- Hamza, K., et al.
(author)
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On the establishment, persistence, and inevitable extinction of populations
- 2016
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In: Journal of Mathematical Biology. - : Springer Science and Business Media LLC. - 0303-6812 .- 1432-1416. ; 72:4, s. 797-820
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Journal article (peer-reviewed)abstract
- Comprehensive models of stochastic, clonally reproducing populations are defined in terms of general branching processes, allowing birth during maternal life, as for higher organisms, or by splitting, as in cell division. The populations are assumed to start small, by mutation or immigration, reproduce supercritically while smaller than the habitat carrying capacity but subcritically above it. Such populations establish themselves with a probability wellknown from branching process theory. Once established, they grow up to a band around the carrying capacity in a time that is logarithmic in the latter, assumed large. There they prevail during a time period whose duration is exponential in the carrying capacity. Even populations whose life style is sustainble in the sense that the habitat carrying capacity is not eroded but remains the same, ultimately enter an extinction phase, which again lasts for a time logarithmic in the carrying capacity. However, if the habitat can carry a population which is large, say millions of individuals, and it manages to avoid early extinction, time in generations to extinction will be exorbitantly long, and during it, population composition over ages, types, lineage etc. will have time to stabilise. This paper aims at an exhaustive description of the life cycle of such populations, from inception to extinction, extending and overviewing earlier results. We shall also say some words on persistence times of populations with smaller carrying capacities and short life cycles, where the population may indeed be in danger in spite of not eroding its environment.
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| 4. |
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| 5. |
- Jagers, Peter, 1941
(author)
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On the Complete Life Career of Populations in Environments with a Finite Carrying Capacity
- 2015
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In: Pliska Studia Mathematica. - 0204-9805. ; 24, s. 55-60
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Journal article (peer-reviewed)abstract
- If a general branching process evolves in a habitat with a finite carrying capacity, i. e. a number such that reproduction turns subcritical as soon as population size exceeds that number, then the population may either die out quickly, or else grow up to arround the carrying capacity, where it will linger for a long time, until it starts decaying exponentially to extinction.
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