65 citations · 149 across the 11 of their papers we have counts for
13 papers
CRNDiff: Count-Native Diffusion Framework via Chemical Reaction Networks
Yuxuan Qiu, Praful Gagrani, Tetsuya J Kobayashi
Scientific measurements such as single-cell RNA (scRNA) sequencing often take the form of nonnegative integer counts, whereas continuous-state diffusion models approximate this dis…
Large-deviations theory for growing chemical reaction networks
Praful Gagrani, Ignacio Madrid, Tetsuya J Kobayashi
Growing biochemical systems are intrinsically noisy, with one important source of stochasticity arising from the discrete reaction events of the underlying biochemical network. Bec…
Topological bounds on the dynamical growth rate of chemical reaction networks
Praful Gagrani, Jiwei Wang, Yannick De Decker +1
Growth and decay are system-level properties of chemical reaction networks (CRNs) relevant from prebiotic chemistry to cellular metabolism. Their properties are typically analyzed…
Mathematical Analysis for a Class of Stochastic Copolymerization Processes
David F. Anderson, Jingyi Ma, Praful Gagrani
We study a stochastic model of a copolymerization process that has been extensively investigated in the physics literature. The main questions of interest include: (i) what are the…
Thermodynamic ranking of pathways in reaction networks
Praful Gagrani, Nino Lauber, Eric Smith +1
One of the puzzles left open by energetic analyses of irreversible stochastic processes is that boundary conditions that prevent the performance of work or the dissipation of heat…
Identifying Self-Amplifying Hypergraph Structures through Mathematical Optimization
Víctor Blanco, Gabriel González, Praful Gagrani
In this paper, we introduce the concept of self-amplifying structures for hypergraphs, positioning it as a key element for understanding propagation and internal reinforcement in c…
An Open-Ended Approach to Understanding Local, Emergent Conservation Laws in Biological Evolution
Alyssa M Adams, Eliott Jacopin, Praful Gagrani +1
While fields like Artificial Life have made huge strides in quantifying the mechanisms that distinguish living systems from non-living ones, particular mechanisms remain difficult…
The evolution of complexity and the transition to biochemical life
Praful Gagrani, David Baum
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins o…
Polyhedral geometry and combinatorics of an autocatalytic ecosystem
Praful Gagrani, Victor Blanco, Eric Smith +1
Developing a mathematical understanding of autocatalysis in reaction networks has both theoretical and practical implications. We review definitions of autocatalytic networks and p…
Action Functional Gradient Descent algorithm for estimating escape paths in Stochastic Chemical Reaction Networks
Praful Gagrani, Eric Smith
We first derive the Hamilton-Jacobi theory underlying continuous-time Markov processes, and then use the construction to develop a variational algorithm for estimating escape (leas…
An ecological framework for the analysis of prebiotic chemical reaction networks and their dynamical behavior
Zhen Peng, Alex Plum, Praful Gagrani +1
It is becoming widely accepted that very early in the origin of life, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifes…
Information Content of the Angular Multipoles of Redshift-Space Galaxy Bispectrum
Praful Gagrani, Lado Samushia
The redshift-space bispectrum (three point statistics) of galaxies depends on the expansion rate, the growth rate, and geometry of the Universe, and hence can be used to measure ke…
Optimal Weights For Measuring Redshift Space Distortions in Multi-tracer Galaxy Catalogues
David W. Pearson, Lado Samushia, Praful Gagrani
Since the volume accessible to galaxy surveys is fundamentally limited, it is extremely important to analyse available data in the most optimal fashion. One way of enhancing the co…