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The antibiotics time machine is an optimization question posed by Mira \latin{et al.} on the design of antibiotic treatment plans to minimize antibiotic resistance. The problem is a variation of the Markov decision process. These authors…
We introduce a model called Host-Pathogen game for studying biological competitions. Notably, we focus on the invasive dynamics of external agents, like bacteria, within a host organism. The former are mapped to a population of defectors…
Understanding flow and transport of bacteria in porous media is crucial to technologies such as bioremediation, biomineralization or enhanced oil recovery. While physicochemical bacteria filtration is well-documented, recent studies showed…
We study the continuous absorbing-state phase transition in the one-dimensional diffusive epidemic process via mean-field theory and Monte Carlo simulation. In this model, particles of two species (A and B) hop on a lattice and undergo…
In microbial communities, each species often has multiple, distinct phenotypes, but studies of ecological stability have largely ignored this subpopulation structure. Here, we show that such implicit averaging over phenotypes leads to…
A randomized clinical trial comparing an experimental new treatment to a standard therapy for a life-threatening medical condition should be stopped early on ethical grounds, in either of the following scenarios: (1) it has become…
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…
A branching random walk in presence of an absorbing wall moving at a constant velocity $v$ undergoes a phase transition as the velocity $v$ of the wall varies. Below the critical velocity $v_c$, the population has a non-zero survival…
How is the progression of a virus influenced by properties intrinsic to individual cells? We address this question by studying the susceptibility of cells infected with two strains of the human respiratory syncytial virus (RSV-A and RSV-B)…
The persistence properties of a set of random walkers obeying the A+B -> 0 reaction, with equal initial density of particles and homogeneous initial conditions, is studied using two definitions of persistence. The probability, P(t), that an…
Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we…
Comparing the survival times among two groups is a common problem in time-to-event analysis, for example if one would like to understand whether one medical treatment is superior to another. In the standard survival analysis setting, there…
Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we…
A simulation model of a population having internal (genetic) structure is presented. The population is subject to selection pressure coming from the environment which is the same in the whole system but changes in time. Reproduction has a…
As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of…
Antimicrobial Resistance (RAM) poses a significant threat to global public health, making important medicines less useful. While the medical and biological reasons behind RAM are well studied, we still don't know enough about how false…
Traditional biomedical approaches treat diseases in isolation, but the importance of synergistic disease interactions is now recognized. As a first step we present and analyze a simple coinfection model for two diseases affecting…
We consider a predator-prey population model with prey gathering together for defense purposes. A transmissible unrecoverable disease affects the prey. We characterize the system behavior, establishing that ultimately either only the…
In Part 1, we introduced a stochastic model of an infectious disease, based on the BDI (birth and death with immigration) process. We showed that random processes defined by this model can capture the essence of the stochastic, often…
New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening…