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We construct a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species posses genetic information, which is inherited according to the rules of the Penna model of genetic evolution.…
RNA viruses exist in large intra-host populations which display great genotypic and phenotypic diversity. We analyze a model of viral competition between two different viral strains infecting a constantly replenished cell pool, in which we…
Mathematical models are formal and simplified representations of the knowledge related to a phenomenon. In classical epidemic models, a neglected aspect is the heterogeneity of disease transmission and progression linked to the viral load…
Single-stranded RNA viruses efficiently encapsulate their genome into a protein shell called the capsid. Electrostatic interactions between the positive charges in the capsid protein's N-terminal tail and the negatively charged genome have…
Following transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible…
Empirical studies suggest that contact patterns follow heterogeneous inter-event times, meaning that intervals of high activity are followed by periods of inactivity. Combined with birth and death of individuals, these temporal constraints…
In this article, we investigate the evolution of sexual diploid populations which are hosts for active TE families. Our purpose is to explore the relationship between the environmental change, that influences such population and activity of…
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic…
Pathogen transmission and virulence are main evolutionary variables broadly assumed to be linked through trade-offs. In well-mixed populations, these trade-offs are often ascribed to physiological restrictions, while populations with…
Transcription factor combinations determine gene locus activity and thereby cell identity. However, the precise link between concentrations of such activating transcription factors and target-gene activity is ambiguous. Here we investigate…
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection which precedes structural rearrangements by…
Detection of gravitational-wave (GW) sources enables the characterisation of binary compact objects and of their in-spiral. However, other dissipative processes can affect the in-spiral. Here we show that the in-spiral of compact objects…
Forecasting the change in the distribution of viral variants is crucial for therapeutic design and disease surveillance. This task poses significant modeling challenges due to the sharp differences in virus distributions across…
Viral quasispecies can be regarded as a swarm of genetically related mutants or a quasispecies (QS). A common formalism to approach QS is the replicator-mutator equation (RME). However, a problem with the RME is how to quantify the…
We present a generative neural network which enables us to generate plausible 3D indoor scenes in large quantities and varieties, easily and highly efficiently. Our key observation is that indoor scene structures are inherently…
This paper explores a number of questions regarding optimal strategies evolved by viruses upon entry into a vertebrate host. The infected cell life cycle consists of a non-productively infected stage in which it is producing virions but not…
Arboviruses represent a significant threat to human, animal, and plant health worldwide. To elucidate transmission, anticipate their spread and efficiently control them, mechanistic modelling has proven its usefulness. However, most models…
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection that precedes structural rearrangements by…
Is it possible to break the host-vector chain of transmission when there is an influx of infectious hosts into a na\"{i}ve population and competent vector? To address this question, a class of vector-borne disease models with an arbitrary…
Several pathogens use evolvability as a survival strategy against acquired immunity of the host. Despite their high variability in time, some of them exhibit quite low variability within the population at any given time, a somehow…