Related papers: Modeling and Modifying Response of Biochemical Pro…
In biomanufacturing, developing an accurate model to simulate the complex dynamics of bioprocesses is an important yet challenging task. This is partially due to the uncertainty associated with bioprocesses, high data acquisition cost, and…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Interconvertible enzyme cascades, exemplified by the mitogen activated protein kinase (MAPK) cascade, are a frequent mechanism in signal transduction pathways. There has been much speculation as to the role of these pathways, and how their…
The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
The field of computer-aided synthesis planning (CASP) has seen rapid advancements in recent years, achieving significant progress across various algorithmic benchmarks. However, chemists often encounter numerous infeasible reactions when…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
In this paper, a set of Python methods is described that can be used to compute the frequency response of an arbitrary biochemical network given any input and output. Models can be provided in standard SBML or Antimony format. The code…
Signal processing is a fundamental component of almost any sensor-enabled system, with a wide range of applications across different scientific disciplines. Time series data, images, and video sequences comprise representative forms of…
A flexible treatment for gas- and aerosol-phase chemical processes has been developed for models of diverse scale, from box models up to global models. At the core of this novel framework is an "abstracted aerosol representation" that…
Contour integrals in the complex plane are the basis of effective numerical methods for computing matrix functions, such as the matrix exponential and the Mittag-Leffler function. These methods provide successful ways to solve partial…
Building on the phenomenological and microscopic models reviewed in Part I, this second part focuses on network-level mechanisms that generate emergent temperature response curves. We review deterministic models in which temperature…
Modellers of complex biological or social systems are often faced with an invidious choice: to use simple models with few mechanisms that can be fully analysed, or to construct complicated models that include all the features which are…
Multi-stage screening pipelines are ubiquitous throughout experimental and computational science. Much of the effort in developing screening pipelines focuses on improving generative methods or surrogate models in an attempt to make each…
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…