Search Results for author:
Found 21 papers, 7 papers with code
A probabilistic model of relapse in drug addiction
More than 60% of individuals recovering from substance use disorder relapse within one year.
Kinetic theories of state- and generation-dependent cell populations
We formulate a general, high-dimensional kinetic theory describing the internal state (such as gene expression or protein levels) of cells in a stochastically evolving population.
Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies
We find that loss of fidelity for longer proofreading steps relies on the specific strategy of information extraction and show that in the first-passage time (FPT) discrimination strategy, longer proofreading steps can exponentially improve the accuracy of KPR at the cost of speed.
Squared Wasserstein-2 Distance for Efficient Reconstruction of Stochastic Differential Equations
We provide an analysis of the squared Wasserstein-2 ($W_2$) distance between two probability distributions associated with two stochastic differential equations (SDEs).
A Spectral Approach for Learning Spatiotemporal Neural Differential Equations
Rapidly developing machine learning methods has stimulated research interest in computationally reconstructing differential equations (DEs) from observational data which may provide additional insight into underlying causative mechanisms.
Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation
The dissociation process can be facilitated by DNA binding proteins or processing molecular motors that compete with histones for histone-DNA contact sites.
Order-of-mutation effects on cancer progression: models for myeloproliferative neoplasm
In some patients with myeloproliferative neoplasms, two genetic mutations can be found, JAK2 V617F and TET2.
The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus
Recent studies show that newly sampled monkeypox virus (MPXV) genomes exhibit mutations consistent with Apolipoprotein B mRNA Editing Catalytic Polypeptide-like3 (APOBEC3)-mediated editing, compared to MPXV genomes collected earlier.
Overcompensation of transient and permanent death rate increases in age-structured models with cannibalistic interactions
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 predation or harvesting.
Stochastic dynamics and ribosome-RNAP interactions in Transcription-Translation Coupling
Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection during the transcription, and/or regulates the timing of transcript and protein formation.
A mathematical model of reward-mediated learning in drug addiction
Substances of abuse are known to activate and disrupt neuronal circuits in the brain reward system.
Mathematical Characterization of Private and Public Immune Repertoire Sequences
Complementing the results on simulated repertoires, we derive explicit expressions for the richness and its uncertainty for specific, single-parameter truncated power-law probability distributions.
Spectrally Adapted Physics-Informed Neural Networks for Solving Unbounded Domain Problems
We propose a solution to such problems by combining two classes of numerical methods: (i) adaptive spectral methods and (ii) physics-informed neural networks (PINNs).
Controlling epidemics through optimal allocation of test kits and vaccine doses across networks
Efficient testing and vaccination protocols are critical aspects of epidemic management.
Density- and elongation speed-dependent error correction in RNA polymerization
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity.
Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities
We find that the average excess death across the entire US is 13$\%$ higher than the number of reported COVID-19 deaths.
Modeling the impact of birth control policies on China's population and age: effects of delayed births and minimum birth age constraints
We consider age-structured models with an imposed refractory period between births.
A machine learning approach to using Quality-of-Life patient scores in guiding prostate radiation therapy dosing
A convolutional neural network then analyzed the relationship between patient-reported quality-of-life and radiation.
PDE models of adder mechanisms in cellular proliferation
Existence and uniqueness of weak solutions to our 2+1-dimensional PDE model are proved, leading to the convergence of the discretized numerical solutions and allowing us to numerically compute the dynamics of cell population densities.
How heterogeneous thymic output and homeostatic proliferation shape naive T cell receptor clone abundance distributions
Using a mean-field approximation to the solution of a regulated birth-death-immigration model and a modification arising from sampling, we systematically quantify how TCR-dependent heterogeneities in immigration and proliferation rates affect the shape of clone abundance distributions (the number of different clones that are represented by a specific number of cells, or "clone counts").
Quantifying the Sensitivity of HIV-1 Viral Entry to Receptor and Coreceptor Expression
The early steps of membrane fusion and viral capsid entry are mediated by adsorption to the cell surface, and receptor and coreceptor binding.
