Related papers: A Low Dimensional Approximation For Competence In …

We focus on an efficient approach for quantification of uncertainty in complex chemical reaction networks with a large number of uncertain parameters. Parameter dimension reduction is accomplished by computing an active subspace that…

Biomolecular condensates play essential roles in cellular processes, and recent efforts have focused on understanding their assembly and rational design principles. In this study, we have employed an explicit-solvent minimal statistical…

The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences)…

The bacterium {\em Bacilus subtilis} frequently forms biofilms at the interface between the culture medium and the air. We develop a mathematical model that couples a description of bacteria as individual discrete objects to the standard…

Reaction-diffusion models are widely used to study spatially-extended chemical reaction systems. In order to understand how the dynamics of a reaction-diffusion model are affected by changes in its input parameters, efficient methods for…

This note provides an introduction to molecular dynamics, the computational implementation of the theory of statistical physics. The discussion is focused on the properties of Langevin dynamics, a degenerate stochastic differential equation…

A probabilistic model describes a system in its observational state. In many situations, however, we are interested in the system's response under interventions. The class of structural causal models provides a language that allows us to…

We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…

Single molecular motor kinesin harnesses thermal and non-thermal fluctuations to transport various cargoes along microtubules, converting chemical energy to directed movements. To describe the non-thermal fluctuations generated by the…

We study an excitable active rotator with slowly adapting nonlinear feedback and noise. Depending on the adaptation and the noise level, this system may display noise-induced spiking, noise-perturbed oscillations, or stochastic busting. We…

In this work, we consider the problem of identifying an unknown linear dynamical system given a finite hypothesis class. In particular, we analyze the effect of the excitation input on the sample complexity of identifying the true system…

Many systems in physics, engineering, and biology exhibit multiscale stochastic dynamics, where low-dimensional slow variables evolve under the influence of high-dimensional fast processes. In practice, observations are often limited to a…

Biological systems, with many interacting components, face high-dimensional environmental fluctuations, ranging from diverse nutrient deprivations to toxins, drugs, and physical stresses. Yet, many biological control mechanisms are `simple'…

A central concern of molecular dynamics simulations are the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system, and have generally been calculated using either predefined…

The run and tumble process is well established in order to describe the movement of bacteria in response to a chemical stimulus. However the relation between the tumbling rate and the internal state of bacteria is poorly understood. The…

Advances in nanotechnology have allowed scientists to study biological processes on an unprecedented nanoscale molecule-by-molecule basis, opening the door to addressing many important biological problems. A phenomenon observed in recent…

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…

Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs),…

For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…

Uncertainty quantification plays an important role in biomedical engineering as measurement data is often unavailable and literature data shows a wide variability. Using state-of-the-art methods one encounters difficulties when the number…