相关论文: Nonclassical phase diagram for virus bacterial co-…
Bacteria frequently colonize natural microcavities such as gut crypts, plant apoplasts, and soil pores. Recent studies have shown that the physical structure of these spaces plays a crucial role in shaping the stability and resilience of…
We study the population dynamics of lytic viruses which replicate slowly in dividing host cells within an organism or cell culture, and find a range of viral replication rates that allows viruses to persist, avoiding extinction of host…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
The rise of antimicrobial drug resistance is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of drug-resistant…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in…
In natural environments, solid surfaces present both opportunities and challenges for bacteria. On one hand, they serve as platforms for biofilm formation, crucial for bacterial colonization and resilience in harsh conditions. On the other…
Symmetry principles play an important role in geometry, and physics, allowing for the reduction of complicated systems to simpler, more comprehensible models that preserve the system's features of interest. Biological systems are often…
We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. We compare the number of operations along the evolutionary trajectory to the DCJ distance of the genome from its ancestor…
A stochastic model for the growth of a virus in a cell population is introduced. The virus has two ways of spreading: either by allowing its host cell to live on and duplicate, or else by multiplying in large numbers within the host cell…
Malware detection and classification into families are critical tasks in cybersecurity, complicated by the continual evolution of malware to evade detection. This evolution introduces concept drift, in which the statistical properties of…
A one dimensional stochastic exclusion process with two species of particles, $+$ and $-$, is studied where density of each species can fluctuate but the total particle density is conserved. From the exact stationary state weights we show…
We study evolutionary processes induced by spatio-temporal dynamics in prebiotic evolution. Using numerical simulations we demonstrate that hypercycles emerge from complex interaction structures in multispecies systems. In this work we also…
We study the phase transition from the persistence phase to the extinction phase for the SIRS (susceptible/ infected/ refractory/ susceptible) model of diseases spreading on small world network. We show the effects of all the parameters…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
In active matter, the lack of momentum conservation makes non-reciprocal interactions the rule rather than the exception. They lead to a rich set of emerging behaviors that are hard to account for and to predict starting from the…
Chronic viral infections can persist in an infected person for decades. From the perspective of the virus, a single infection can span thousands of generations, leading to a highly diverse population of viruses with its own complex…
The SIR model is the cornerstone model for mathematical epidemiology, explaining key epidemic features such as the second-order transition between disease-free and epidemic states, the initial exponential growth of outbreaks or the…
Liquid-liquid phase separation plays a major role in the formation and maintenance of various membrane-less subcellular structures in the cytoplasm and nucleus of cells. Biological condensates contain enhanced concentrations of proteins and…
Compartmentalization of self-replicating molecules (templates) in protocells is a necessary step towards the evolution of modern cells. However, coexistence between distinct template types inside a protocell can be achieved only if there is…