40 research outputs found
Graph-theoretic analysis of multistationarity using degree theory
Biochemical mechanisms with mass action kinetics are often modeled by systems
of polynomial differential equations (DE). Determining directly if the DE
system has multiple equilibria (multistationarity) is difficult for realistic
systems, since they are large, nonlinear and contain many unknown parameters.
Mass action biochemical mechanisms can be represented by a directed bipartite
graph with species and reaction nodes. Graph-theoretic methods can then be used
to assess the potential of a given biochemical mechanism for multistationarity
by identifying structures in the bipartite graph referred to as critical
fragments. In this article we present a graph-theoretic method for conservative
biochemical mechanisms characterized by bounded species concentrations, which
makes the use of degree theory arguments possible. We illustrate the results
with an example of a MAPK network
Switching in mass action networks based on linear inequalities
Many biochemical processes can successfully be described by dynamical systems
allowing some form of switching when, depending on their initial conditions,
solutions of the dynamical system end up in different regions of state space
(associated with different biochemical functions). Switching is often realized
by a bistable system (i.e. a dynamical system allowing two stable steady state
solutions) and, in the majority of cases, bistability is established
numerically. In our point of view this approach is too restrictive, as, one the
one hand, due to predominant parameter uncertainty numerical methods are
generally difficult to apply to realistic models originating in Systems
Biology. And on the other hand switching already arises with the occurrence of
a saddle type steady state (characterized by a Jacobian where exactly one
Eigenvalue is positive and the remaining eigenvalues have negative real part).
Consequently we derive conditions based on linear inequalities that allow the
analytic computation of states and parameters where the Jacobian derived from a
mass action network has a defective zero eigenvalue so that -- under certain
genericity conditions -- a saddle-node bifurcation occurs. Our conditions are
applicable to general mass action networks involving at least one conservation
relation, however, they are only sufficient (as infeasibility of linear
inequalities does not exclude defective zero eigenvalues).Comment: in revision SIAM Journal on Applied Dynamical System
A global convergence result for processive multisite phosphorylation systems
Multisite phosphorylation plays an important role in intracellular signaling.
There has been much recent work aimed at understanding the dynamics of such
systems when the phosphorylation/dephosphorylation mechanism is distributive,
that is, when the binding of a substrate and an enzyme molecule results in
addition or removal of a single phosphate group and repeated binding therefore
is required for multisite phosphorylation. In particular, such systems admit
bistability. Here we analyze a different class of multisite systems, in which
the binding of a substrate and an enzyme molecule results in addition or
removal of phosphate groups at all phosphorylation sites. That is, we consider
systems in which the mechanism is processive, rather than distributive. We show
that in contrast with distributive systems, processive systems modeled with
mass-action kinetics do not admit bistability and, moreover, exhibit rigid
dynamics: each invariant set contains a unique equilibrium, which is a global
attractor. Additionally, we obtain a monomial parametrization of the steady
states. Our proofs rely on a technique of Johnston for using "translated"
networks to study systems with "toric steady states", recently given sign
conditions for injectivity of polynomial maps, and a result from monotone
systems theory due to Angeli and Sontag.Comment: 23 pages; substantial revisio
Identifying parameter regions for multistationarity
Mathematical modelling has become an established tool for studying the
dynamics of biological systems. Current applications range from building models
that reproduce quantitative data to identifying systems with predefined
qualitative features, such as switching behaviour, bistability or oscillations.
Mathematically, the latter question amounts to identifying parameter values
associated with a given qualitative feature.
We introduce a procedure to partition the parameter space of a parameterized
system of ordinary differential equations into regions for which the system has
a unique or multiple equilibria. The procedure is based on the computation of
the Brouwer degree, and it creates a multivariate polynomial with parameter
depending coefficients. The signs of the coefficients determine parameter
regions with and without multistationarity. A particular strength of the
procedure is the avoidance of numerical analysis and parameter sampling.
The procedure consists of a number of steps. Each of these steps might be
addressed algorithmically using various computer programs and available
software, or manually. We demonstrate our procedure on several models of gene
transcription and cell signalling, and show that in many cases we obtain a
complete partitioning of the parameter space with respect to multistationarity.Comment: In this version the paper has been substantially rewritten and
reorganised. Theorem 1 has been reformulated and Corollary 1 adde
On the existence of Hopf bifurcations in the sequential and distributive double phosphorylation cycle
Protein phosphorylation cycles are important mechanisms of the post
translational modification of a protein and as such an integral part of
intracellular signaling and control. We consider the sequential phosphorylation
and dephosphorylation of a protein at two binding sites. While it is known that
proteins where phosphorylation is processive and dephosphorylation is
distributive admit oscillations (for some value of the rate constants and total
concentrations) it is not known whether or not this is the case if both
phosphorylation and dephosphorylation are distributive. We study four
simplified mass action models of sequential and distributive phosphorylation
and show that for each of those there do not exist rate constants and total
concentrations where a Hopf bifurcation occurs. To arrive at this result we use
convex parameters to parameterize the steady state and Hurwitz matrices
N-site phosphorylation systems with 2N-1 steady states
Multisite protein phosphorylation plays a prominent role in intracellular
processes like signal transduction, cell-cycle control and nuclear signal
integration. Many proteins are phosphorylated in a sequential and distributive
way at more than one phosphorylation site. Mathematical models of -site
sequential distributive phosphorylation are therefore studied frequently. In
particular, in {\em Wang and Sontag, 2008,} it is shown that models of -site
sequential distributive phosphorylation admit at most steady states.
Wang and Sontag furthermore conjecture that for odd , there are at most
and that, for even , there are at most steady states. This, however,
is not true: building on earlier work in {\em Holstein et.al., 2013}, we
present a scalar determining equation for multistationarity which will lead to
parameter values where a -site system has steady states and parameter
values where a -site system has steady states. Our results therefore are
counterexamples to the conjecture of Wang and Sontag. We furthermore study the
inherent geometric properties of multistationarity in -site sequential
distributive phosphorylation: the complete vector of steady state ratios is
determined by the steady state ratios of free enzymes and unphosphorylated
protein and there exists a linear relationship between steady state ratios of
phosphorylated protein