Research
Research
Research
Research
365+ open-access research outputs.
Genome-Scale Metabolic Models (GEMs) describe the interactions between genes, proteins, and the biochemical reactions that underpin an organism's metabolism aiming to computationally simulate function…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological cir…
Alzheimer's disease is the most common neurodegenerative disorder. Its pathological development is connected with the misfolding and accumulation of two toxic proteins: amyloid-beta and tau proteins. …
Recently, the statistical properties of empirical Entropic Optimal Transport (EOT) have attracted great interest, as this quantity has been shown to be useful for complex data analysis, among other re…
We study community detection in stochastic block models under pure node-level differential privacy, a stringent notion that protects the participation of an individual together with all of their incid…
This tutorial contrasts probabilistic modeling and robust optimization to determine decisions in humanitarian logistics, specifically supply chains subject to adversarial (natural and human) disruptio…
Robust oscillations play crucial roles in a wide variety of biological processes and are often generated by deterministic mechanisms. However, stochastic fluctuations often generate complex perturbati…
We study population dynamics through a general growth/degrowth-fragmentation process, with resource consumption and unbounded growth/degrowth, birth and death rates. Our model is structured in a posit…
We present a systematic classification of uncolored bonded knots with singularity number at most seven. Bonded knots provide a topological model for closed protein chains with intramolecular bridges, …
Mathematical modeling offers a valuable approach to understanding Alzheimers disease (AD) given its complexity, unknown causes, and lack of effective treatments. Models, once validated, offer a powerf…
Ion transport through narrow channels is described by the coupled Poisson--Nernst--Planck--Stokes equations (PNPS) on a continuum scale. However, direct numerical simulations in two or three dimension…
We present a complete classification of spherical knotoids with up to six crossings and conjecture that our classification up to seven crossings is complete. Our work extends the tradition of knot tab…
Extreme weather events, like flooding, disrupt urban transportation networks by reducing speeds and capacities, and by closing roadways. These hazards create regime-dependent uncertainty in link perfo…
The global optimization of atomic clusters represents a fundamental challenge in computational chemistry and materials science due to the exponential growth of local minima with system size (i.e., the…
Genetic mutations frequently disrupt protein structure, stability, and solubility, acting as primary drivers for a wide spectrum of diseases. Despite the critical importance of these molecular alterat…
Accumulation of amyloid beta proteins is a defining feature of Alzheimer's disease, and is usually accompanied by cerebrovascular pathology. Evidence suggests that amyloid beta and cerebrovascular pat…
Rare events in molecular dynamics are often related to noise-induced transitions between different macroscopic states (e.g., in protein folding). A common feature of these rare transitions is that the…
Motivated by the use of Taylor-Couette flow in extracorporeal circulation devices [K$\ddot{\rm o}$rfer et al., 2003, 26(4): 331-338], where it leads to an accumulation of platelets and plasma proteins…
The Low Order-Value Optimization (LOVO) problem involves minimizing the minimum among a finite number of function values within a feasible set. LOVO has several practical applications such as robust p…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under…
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