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Evolutionary accessibility of random and structured fitness landscapes
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype.
Exclusion model of mRNA translation with collision-induced ribosome drop-off
The translation of messenger RNA transcripts to proteins is commonly modeled as a one-dimensional totally asymmetric exclusion process with extended particles.
Unpredictable repeatability in molecular evolution
At the same time, the probability of parallel evolution is non-self-averaging, that is, it does not converge to its mean value even when a large number of mutations are involved.
Nonlinear dynamics of an epidemic compartment model with asymptomatic infections and mitigation
A significant proportion of the infections driving the current {SARS-CoV-2} pandemic are transmitted asymptomatically.
A Driven Disordered Systems Approach to Biological Evolution in Changing Environments
With evolutionary dynamics that follow fitness gradients, the evolution of the system under slowly changing antibiotic concentration resembles the athermal dynamics of disordered physical systems under external drives.
Geometry of fitness landscapes: Peaks, shapes and universal positive epistasis
Because of constraints on the shapes for $L=3$ imposed by peaks, there are in total 25 possible combinations of peak patterns and shapes.
Non-equilibrium Roughness Evolution of Small Molecule Mixed Films Reflecting Equilibrium Phase Behavior
Understanding non-equilibrium phenomena, such as growth, and connecting them to equilibrium phase behavior is a major challenge, in particular for complex multicomponent materials.
Applied Physics Computational Physics
The fitness landscapes of translation
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation.
From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution.
Accessibility Percolation on Cartesian Power Graphs
A path in a fitness landscape is a sequence of genotypes connected by single mutational steps.
Accessibility percolation in random fitness landscapes
Studies of accessibility percolation use probabilistic fitness landscape models to explore the emergence of such paths as a function of the initial fitness, the parameters of the landscape or the structure of the genotype graph.
