6 research outputs found
Coarse-graining the Dynamics of Ideal Branched Polymers
AbstractWe define a class of local stochastic rewrite rules on directed site trees. We give a compact presentation of (often countably infinite) coarse-grained differential systems describing the dynamics of these rules in the deterministic limit, and study in a simple case finite approximations based on truncations to a certain size. We show an application to the modelling of the dynamics of sugar polymers
On a thermodynamic approach to biomolecular interaction networks
We explore the direct and inverse problem of thermodynamics in the context of
rule-based modelling. The direct problem can be concisely stated as obtaining
a set of rewriting rules and their rates from the description of the energy
landscape such that their asymptotic behaviour when t → ∞ coincide. To
tackle this problem, we describe an energy function as a finite set of connected
patterns P and an energy cost function e which associates real values to each of
these energy patterns.We use a finite set of reversible graph rewriting rules G to
define the qualitative dynamics by showing which transformations are possible.
Given G and P, we construct a finite set of rules Gp which i) has the same
qualitative transition system as G and ii) when equipped with rates according
to e, defines a continuous-time Markov chain that has detailed balance with
respect to the invariant probability distribution determined by the energy
function. The construction relies on a technique for rule refinement described
in earlier work and allows us to represent thermodynamically consistent
models of biochemical interaction networks in a concise manner.
The inverse problem, on the other hand, is to i) check whether a rule-based
model has an energy function that describes its asymptotic behaviour and
if so ii) obtain the energy function from the graph rewriting rules and their
rates. Although this problem is known to be undecidable in the general case,
we find two suitable subsets of Kappa, our rule-based modelling framework
of choice, were this question can be answer positively and the form of their
energy functions described analytically
Defining complex rule-based models in space and over time
Computational biology seeks to understand complex spatio-temporal phenomena across multiple
levels of structural and functional organisation. However, questions raised in this context
are difficult to answer without modelling methodologies that are intuitive and approachable for
non-expert users. Stochastic rule-based modelling languages such as Kappa have been the focus
of recent attention in developing complex biological models that are nevertheless concise,
comprehensible, and easily extensible. We look at further developing Kappa, in terms of how
we might define complex models in both the spatial and the temporal axes.
In defining complex models in space, we address the assumption that the reaction mixture
of a Kappa model is homogeneous and well-mixed. We propose evolutions of the current iteration
of Spatial Kappa to streamline the process of defining spatial structures for different
modelling purposes. We also verify the existing implementation against established results in
diffusion and narrow escape, thus laying the foundations for querying a wider range of spatial
systems with greater confidence in the accuracy of the results.
In defining complex models over time, we draw attention to how non-modelling specialists
might define, verify, and analyse rules throughout a rigorous model development process. We
propose structured visual methodologies for developing and maintaining knowledge base data
structures, incorporating the information needed to construct a Kappa rule-based model. We
further extend these methodologies to deal with biological systems defined by the activity of
synthetic genetic parts, with the hope of providing tractable operations that allow multiple users
to contribute to their development over time according to their area of expertise.
Throughout the thesis we pursue the aim of bridging the divide between information sources
such as literature and bioinformatics databases and the abstracting decisions inherent in a
model. We consider methodologies for automating the construction of spatial models, providing
traceable links from source to model element, and updating a model via an iterative
and collaborative development process. By providing frameworks for modellers from multiple
domains of expertise to work with the language, we reduce the entry barrier and open the field
to further questions and new research
Developing a framework for semi-automated rule-based modelling for neuroscience research
Dynamic modelling has significantly improved our understanding of the complex
molecular mechanisms underpinning neurobiological processes. The detailed
mechanistic insights these models offer depend on the availability of
a diverse range of experimental observations. Despite the huge increase in
biomolecular data generation from novel high-throughput technologies and
extensive research in bioinformatics and dynamical modelling, efficient creation
of accurate dynamical models remains highly challenging. To study this
problem, three perspectives are considered: comparison of modelling methods,
prioritisation of results and analysis of primary data sets. Firstly, I compare two
models of the DARPP-32 signalling network: a classically defined model with
ordinary differential equations (ODE) and its equivalent, defined using a novel
rule-based (RB) paradigm. The RB model recapitulates the results of the ODE
model, but offers a more expressive and flexible syntax that can efficiently handle
the “combinatorial complexity” commonly found in signalling networks,
and allows ready access to fine-grain details of the emerging system. RB modelling
is particularly well suited to encoding protein-centred features such as
domain information and post-translational modification sites. Secondly, I propose
a new pipeline for prioritisation of molecular species that arise during
model simulation using a recently developed algorithm based on multivariate
mutual information (CorEx) coupled with global sensitivity analysis (GSA) using
the RKappa package. To efficiently evaluate the importance of parameters,
Hilber-Schmidt Independence Criterion (HSIC)-based indices are aggregated
into a weighted network that allows compact analysis of the model across conditions.
Finally, I describe an approach for the development of disease-specific
dynamical models using genes known to be associated with Attention Deficit
Hyperactivity Disorder (ADHD) as an exemplar. Candidate disease genes are
mapped to a selection of datasets that are potentially relevant to the modelling
process (e.g. interactions between proteins and domains, protein-domain and
kinase-substrates mappings) and these are jointly analysed using network clustering
and pathway enrichment analyses to evaluate their coverage and utility
in developing rule-based models
Cooperative assembly systems
Several molecular systems form large-scale objects. One would like to understand their assembly and how this assembly is regulated. As a first step, we investigate the phase transition structure of a class of sim- ple cooperative assembly systems.We characterize which of these systems have a (probabilistic) equilibrium and find an explicit form for their lo- cal energy (§2).We obtain, under additional limitations on cooperativity, the average dynamics of some partial observables (§4). Combining both steps, we obtain conditions for the appearance of a large cluster (§5)