Quantitative Biology
There has been renewed interest in understanding the mathematical structure of ecological population models that lead to overcompensation, the process by which a population recovers to a higher level after suffering a permanent increase in…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Substances of abuse are known to activate and disrupt neuronal circuits in the brain reward system. We propose a simple and easily interpretable dynamical systems model to describe the neurobiology of drug addiction that incorporates the…
Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs…
Efficient testing and vaccination protocols are critical aspects of epidemic management. To study the optimal allocation of limited testing and vaccination resources in a heterogeneous contact network of interacting susceptible, recovered,…
We derive the full kinetic equations describing the evolution of the probability density distribution for a structured population such as cells distributed according to their ages and sizes. The kinetic equations for such a "sizer-timer"…
We consider age-structured models with an imposed refractory period between births. These models can be used to formulate alternative population control strategies to China's one-child policy. By allowing any number of births, but with an…
Thanks to advancements in diagnosis and treatment, prostate cancer patients have high long-term survival rates. Currently, an important goal is to preserve quality-of-life during and after treatment. The relationship between the radiation a…
Stochastic models that incorporate birth, death and immigration (also called birth-death and innovation models) are ubiquitous and applicable to many research topics such as quantifying species sizes in ecological populations, describing…
Chemotaxis is typically modeled in the context of cellular motion towards a static, exogenous source of chemoattractant. Here, we propose a time-dependent mechanism of chemotaxis in which a self-propelled particle ({\it e.g.}, a cell)…
Oscillatory activity in auditory cortex is thought to play a central role in auditory and speech processing by synchronizing neural rhythms to external acoustic features of the speech stream. To support this function, cortical oscillators…
Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…
RNA inverse sequence design has broad biological and engineering applications, but computational methods for practical design queries remain limited. Such queries may impose several constraints at once, including target folds or motifs,…
The emergence of a hantavirus variant aboard a commercial cruise ship presents a significant public health concern. This study develops a discrete-time stochastic Susceptible-Exposed-Infectious-Recovered-Dead model to estimate transmission…
The success of machine learning in drug discovery hinges on learning the relationship between a chemical structure and its biological activity. While DNA-Encoded Library (DEL) technology can generate the massive datasets required for this…
A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…
The study of cultural evolution seeks to understand the processes by which behavioral variants are chosen in cultures over time, often as the result of large numbers of individual human choices. The selection of new popes, each of whom…
Functional connectivity (FC) derived from resting-state fMRI is widely used to characterize large-scale brain network alterations in neurological and psychiatric disorders. However, FC construction critically depends on the choice of brain…
Our understanding of cell division control in bacteria still relies largely on interpreting correlations between phenomenological variables, with limited connection to the underlying molecular mechanisms. Here, we analytically solve a…
Trial-to-trial variability of neural responses has been linked to important aspects of neural computation and is essential for understanding how neuronal populations respond. While current overdispersion models treat each neuron's gain as…