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Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
We present a holographic quantum simulation algorithm to variationally prepare thermal states of $d$-dimensional interacting quantum many-body systems, using only enough hardware qubits to represent a ($d$-1)-dimensional cross-section. This…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…
Quantum Recurrent Neural Networks (QRNNs) are robust candidates for modelling and predicting future values in multivariate time series. However, the effective implementation of some QRNN models is limited by the need for mid-circuit…
Principles of feedback control have been shown to naturally arise in biological systems and successfully applied to build synthetic circuits. In this work we consider Biochemical Reaction Networks (CRNs) as a paradigm for modelling…
Accurate, label-free quantification of multiple analytes in complex biological media remains a major challenge due to limited multiplexing, signal cross-correlations, and inconsistency across sensor samples and measurement runs. We…
We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class…
In this paper the kinetic corrected Schr\"{o}dinger-Poisson model is used to obtain the pseudoforce system in order to study variety of streaming electron beam-plasmon interaction effects. The noninteracting stream model is used to…
Quasisymmetry (QS) provides a novel route to understand and control near-degeneracies, Berry curvature, optical selection rules, and symmetry-protected phenomena in quantum materials. Here we give physical interpretations of the emergence…
We propose a novel protocol for the creation of macroscopic quantum superposition (MQS) states based on a measurement of a non-monotonous function of a quantum collective variable. The main advantage of this protocol is that it does not…
Quantum computers have the potential to simulate chemical systems beyond the capability of classical computers. Recent developments in hybrid quantum-classical approaches enable the determinations of the ground or low energy states of…
Optical chemical structure recognition (OCSR) systems aim to extract the molecular structure information, usually in the form of molecular graph or SMILES, from images of chemical molecules. While many tools have been developed for this…
We present a method for estimating parameters in stochastic models of biochemical reaction networks by fitting steady-state distributions using Wasserstein distances. We simulate a reaction network at different parameter settings and train…
Quasi-steady state (QSS) reduction is a commonly used method to lower the dimension of a differential equation model of a chemical reaction network. From a mathematical perspective, QSS reduction is generally interpreted as a special type…
This thesis deals with the generation, estimation and preservation of novel quantum states of two and three qubits, on an NMR quantum information processor. Using the maximum likelihood ansatz, we have developed a method for state…
Magombedze and Mulder (2013) studied the gene regulatory system of \textit{Mycobacterium Tuberculosis} (\textit{Mtb}) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each…
Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of…
We construct the quasi-stationary (QS) distribution for two models of heterogeneous catalysis having two absorbing states: the ZGB model for the oxidation of CO, and a version with noninstantaneous reactions. Using a mean-field-like…