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Instantaneous arithmetic computation via ratio-encoding in chemical reaction networks
David F. Anderson, Badal Joshi
We develop a general framework for instantaneous arithmetic computation using chemical reaction networks. Numerical values are encoded by ratios of species concentrations: an exten…
Bistability, Absolute Concentration Robustness, and Hysteresis in Dual-Site Futile Cycles with Bifunctional Enzymes
Badal Joshi, Tung D. Nguyen, Matthew D. Johnston
Bifunctional enzymes, which catalyze both the forward and reverse steps of a substrate modification reaction, arise naturally in bacterial two-component signaling systems and metab…
Computing with reaction networks at input-independent speed: exponential and logarithmic functions
David F. Anderson, Badal Joshi, Tung D. Nguyen
The concept of \textit{input-independent computational speed} for chemistry-based analog computers was introduced in Anderson-Joshi (2025), where it was shown that arithmetic opera…
Chemical mass-action systems as analog computers: implementing arithmetic computations at specified speed
David F. Anderson, Badal Joshi
Recent technological advances allow us to view chemical mass-action systems as analog computers. In this context, the inputs to a computation are encoded as initial values of certa…
Power-engine-load form for dynamic absolute concentration robustness
Badal Joshi, Gheorghe Craciun
In a reaction network, the concentration of a species with the property of dynamic absolute concentration robustness (dynamic ACR) converges to the same value independent of the ov…
Reaction Network Motifs for Static and Dynamic Absolute Concentration Robustness
Badal Joshi, Gheorghe Craciun
Networks with absolute concentration robustness (ACR) have the property that a translation of a coordinate hyperplane either contains all steady states (static ACR) or attracts all…
Multistationarity in cyclic sequestration-transmutation networks
Gheorghe Craciun, Badal Joshi, Casian Pantea +1
We consider a natural class of reaction networks which consist of reactions where either two species can inactivate each other (i.e., sequestration), or some species can be transfo…
Foundations of Static and Dynamic Absolute Concentration Robustness
Badal Joshi, Gheorghe Craciun
Absolute Concentration Robustness (ACR) was introduced by Shinar and Feinberg as robustness of equilibrium species concentration in a mass action dynamical system. Their aim was to…
Autocatalytic systems and recombination: a reaction network perspective
Gheorghe Craciun, Abhishek Deshpande, Badal Joshi +1
Autocatalytic systems are very often incorporated in the "origin of life" models, a connection that has been analyzed in the context of the classical hypercycles introduced by Manf…
Autocatalytic Networks: An Intimate Relation between Network Topology and Dynamics
Badal Joshi, Gheorghe Craciun
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system call…
Detailed balance = complex balance + cycle balance. A graph-theoretic proof for reaction networks and Markov chains
Stefan Müller, Badal Joshi
We further clarify the relation between detailed-balanced and complex-balanced equilibria of reversible chemical reaction networks. Our results hold for arbitrary kinetics and also…
Which small reaction networks are multistationary?
Badal Joshi, Anne Shiu
Reaction networks taken with mass-action kinetics arise in many settings, from epidemiology to population biology to systems of chemical reactions. Bistable reaction networks are p…
A survey of methods for deciding whether a reaction network is multistationary
Badal Joshi, Anne Shiu
Which reaction networks, when taken with mass-action kinetics, have the capacity for multiple steady states? There is no complete answer to this question, but over the last 40 year…
Complete characterization by multistationarity of fully open networks with one non-flow reaction
Badal Joshi
This article characterizes certain small multistationary chemical reaction networks. We consider the set of fully open networks, those for which all chemical species participate in…
Atoms of multistationarity in chemical reaction networks
Badal Joshi, Anne Shiu
Chemical reaction systems are dynamical systems that arise in chemical engineering and systems biology. In this work, we consider the question of whether the minimal (in a precise…
Simplifying the Jacobian Criterion for precluding multistationarity in chemical reaction networks
Badal Joshi, Anne Shiu
Chemical reaction networks taken with mass-action kinetics are dynamical systems that arise in chemical engineering and systems biology. In general, determining whether a chemical…