Related papers: Implicit dose-response curves
For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
It is shown in "SIAM J. Sci. Comput. 39 (2017):B424-B441" that free-form curves used in computer aided geometric design can usually be represented as the solutions of linear differential systems and points and derivatives on the curves can…
Cataloging the complex behaviors of dynamical systems can be challenging, even when they are well-described by a simple mechanistic model. If such a system is of limited analytical tractability, brute force simulation is often the only…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
A new class of implicit-explicit (IMEX) methods combined with a p-adaptive mixed finite element formulation is proposed to simulate the diffusion of reacting species. Hierarchical polynomial functions are used to construct an…
A computation-oriented representation of uncertain kinetic systems is introduced and analysed in this paper. It is assumed that the monomial coefficients of the ODEs belong to a polytopic set, which defines a set of dynamical systems for an…
We consider linear elimination of variables in steady state equations of a chemical reaction network. Particular subsets of variables corresponding to sets of so-called reactant-noninteracting species, are introduced. The steady state…
We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address…
Calibrating chemical kinetics in a reaction-diffusion system is challenging because of complex dynamics governed by tightly coupled chemistry and transport, while experimental observations are often sparse and noisy. We propose a physics…
In this paper, we present a semi-implicit numerical solver for a first order hyperbolic formulation of two-phase flow with surface tension and viscosity. The numerical method addresses several complexities presented by the PDE system in…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
The concept of limiting step gives the limit simplification: the whole network behaves as a single step. However, in its simplest form this idea is applicable only to the simplest linear cycles in steady states. For such the simplest cycles…
We propose graph-dependent implicit regularisation strategies for distributed stochastic subgradient descent (Distributed SGD) for convex problems in multi-agent learning. Under the standard assumptions of convexity, Lipschitz continuity,…
We study nonparametric distance-based (isotropic) local polynomial methods for estimating the boundary average treatment effect curve, a causal functional that captures treatment effect heterogeneity in boundary discontinuity designs. We…
The induced kinetic differential equation of a reaction network endowed with mass action type kinetics is a system of polynomial differential equations. The problem studied here is: Given a polynomial differential equation, is it possible…
In this article we present a computational framework for isolating spatial patterns arising in the steady states of reaction-diffusion systems. Such systems have been used to model many different phenomena in areas such as developmental and…