Related papers: Computing the Frequency Response of Biochemical Ne…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…
We present a numerical code to simulate maps of Galactic emission in intensity and polarization at microwave frequencies, aiding in the design of Cosmic Microwave Background experiments. This Python code builds on existing efforts to…
Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models…
Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
The finite amplitude method is a feasible and efficient method for the linear response calculation based on the time-dependent density functional theory. It was originally proposed as a method to calculate the strength functions. Recently,…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
We introduce a mixed-integer linear programming (MILP) framework capable of determining whether a chemical reaction network possesses the property of being endotactic or strongly endotactic. The network property of being strongly endotactic…
The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable…
This paired article aims to develop an automated and programmable biochemical fully connected neural network (BFCNN) with solid theoretical support. In Part I, a concrete design for BFCNN is presented, along with the validation of the…
This thesis details a Python-based software designed to calculate the Jones polynomial, a vital mathematical tool from Knot Theory used for characterizing the topological and geometrical complexity of curves in \( \mathbb{R}^3 \), which is…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
Random linear network coding is a feasible encoding tool for network coding, specially for the non-coherent network, and its performance is important in theory and application. In this letter, we study the performance of random linear…
Computed tomography perfusion (CTP) and magnetic resonance perfusion (MRP) are widely used in acute ischemic stroke assessment and other cerebrovascular conditions to generate quantitative maps of cerebral hemodynamics. While commercial…
We review models and approaches for error-control in order to prevent the buildup of noise when gates for digital chemical and biomolecular computing based on (bio)chemical reaction processes are utilized to realize stable, scalable…
Model-based prediction of stochastic noise in biomolecular reactions often resorts to approximation with unknown precision. As a result, unexpected stochastic fluctuation causes a headache for the designers of biomolecular circuits. This…
Reconstruction of biochemical reaction networks is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and…
Spectroscopic Amplitudes (SA) in the Interacting Boson Fermion Fermion Model (IBFFM) are necessary for the computation of $0\nu\beta\beta$ decays but also for cross sections of heavy-ion reactions, in particular, Double Charge Exchange…
Computer-assisted methods have emerged as valuable tools for retrosynthesis analysis. However, quantifying the plausibility of generated retrosynthesis routes remains a challenging task. We introduce Retro-BLEU, a statistical metric adapted…