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Complex envelope and reduced phase simulation models describing the dynamical behavior of an optoelectronic oscillator (OEO) under injection by an external source are described. The models are built on the foundations of a previously…
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…
A comprehensive understanding of the electrode-electrolyte interface in energy conversion systems remains challenging due to the complex and multifaceted nature of interfacial processes. This complexity hinders the development of more…
In the context of high penetration of renewables, the need to build dynamic models of power system components based on accessible measurement data has become urgent. To address this challenge, firstly, a neural ordinary differential…
This article is an attempt to provide a self consistent picture, including existence analysis and numerical solution algorithms, of the mathematical problems arising from modeling photocurrent transients in Organic-polymer Solar Cells…
Optical Mie resonators based on silicon nanostructures allow tuning of light-matter-interaction with advanced design concepts based on CMOS compatible nanofabrication. Optically active materials such as transition-metal dichalcogenide (TMD)…
Motivation: Modeling biological signaling networks using ordinary differential equations (ODEs) has proven to be a powerful technique for generating insight into cellular dynamics, but it typically requires estimating rate parameters based…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Electrochemical Biosensors are uniquely positioned to offer real-time in vivo molecular sensing due to their robustness to both biofluids and contaminants found in biofluids, and their adaptability for the detection of different analytes by…
Organic electrochemical transistors offer powerful functionalities for biosensors and neuroinspired electronics, with still much to understand on the time dependent behavior of this electrochemical device. Here, we report on distributed…
Up to now, the methods available for measuring the rate constants of reactions taking place on heterogeneous catalysts require that the catalyst be stable over long measurement times. But catalyst are often non-stationary, they may become…
By interpreting the forward dynamics of the latent representation of neural networks as an ordinary differential equation, Neural Ordinary Differential Equation (Neural ODE) emerged as an effective framework for modeling a system dynamics…
Single-chip CMOS-based biosensors that feature microcantilevers as transducer elements are presented. The cantilevers are functionalized for the capturing of specific analytes, e.g., proteins or DNA. The binding of the analyte changes the…
Optical beam deflection is a popular method to measure the deformation of micromechanical devices. As it measures mostly a local slope, its sensitivity depends on the location and size of the optical spot. We present a method to evaluate…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
We introduce, analyze, and implement a new method for parameter identification for system of ordinary differential equations that are used to model sets of biochemical reactions. Our method relies on the integral formulation of the ODE…
Stochastic differential equations (SDEs) are established tools to model physical phenomena whose dynamics are affected by random noise. By estimating parameters of an SDE intrinsic randomness of a system around its drift can be identified…
In this article we propose and investigate a hierarchy of mathematical models based on partial differential equations (PDE) and ordinary differential equations (ODE) for the simulation of the biophysical phenomena occurring in the…
Multistationarity in molecular systems underlies switch-like responses in cellular decision making. Determining whether and when a system displays multistationarity is in general a difficult problem. In this work we completely determine the…
Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…