Chris Gordon-Smith 24th September 2014

On Wednesday 24th September, Chris Gordon-Smith, from the SimSoup project, will give the talk

“Molecules Designed for Chemical Network Memory and Non-Genetic Inheritance”

Please note the temporary change of venue.

Nuffield Theatre (Building 6) Room 1081 (Nuffield Room B), Highfield Campus, 4pm. All welcome. Refreshments served after the talk.


In this talk I will present a memory system based on an artificial chemistry. This is relevant as a ‘proof of concept’ for metabolism based Origin of Life theories, and in the field of biological and chemical computing. Each memory unit can be switched between three alternative active states. A unit maintains itself in a particular state using an autocatalytic reaction process. Switching between states occurs when an external stimulus triggers the autocatalytic process for the new state, along with an associated process that inhibits autocatalytic activity for the old state. I will show artificial molecular species with structures that support the autocatalytic and inhibiting processes. I will also present results from the SimSoup artificial chemistry simulator showing the operation of a 5-unit memory system with 243 alternative states (equivalent to just under 8 bits of memory). The design supports systems with more units, but computational requirements to run the simulator increase substantially. I will conclude the talk with a short review of some alternative network architectures for chemical memory and inheritance.

Remi Louf 14th May 2014


On Wednesday 14th May, Remi LoufInstitut de Physique Théorique, will give the talk

“How congestion shapes cities: a physicist’s perspective.”

Building 53 Room 4025, Highfield Campus, 4pm. All welcome. Refreshments served after the talk.


In a rapidly urbanising world, understanding the behaviour of cities has broad implications. Indeed, while cities are known to foster creativity and economic growth, they also engender higher crime rates and pollution levels. It is therefore crucial to quantify these effects and understand the underlying processes if we want to design effective policies and make the urban transition as smooth as possible.
Although the recent availability of data has brought fresh insights, most of the observed regularities remain unexplained. For instance, we find that quantities such as the total surface area, the total length of roads, the total daily driven distance scale non-linearly with population size. In this presentation, I will show how simple physical arguments and a bottom-up modelling approach allow us to understand these behaviours. I will discuss how, with simple approaches of this kind, we are able to identify some of the driving forces behind the evolution of urban systems. In particular, I will highlight the role of congestion, and its consequences on life in cities.

Guillaume Achaz 12th March 2014

On Wednesday 12th March, Dr Guillaume Achaz, Atelier de BioInformatique, will give the talk “Epistatic constraints in evolution, theory and practice.”

Building 53 Room 4025, Highfield Campus, 4pm. All welcome. Refreshments served after the talk.


How constrained is life’s evolution? Can mutations occur in any order? What fundamental processes dictate how evolution can proceed? I will discuss some work on experimental and model fitness landscapes that aims at understanding what is the minimum set of rules that are needed to characterize constraints in evolving genetic systems. The work tries to maximize the fit between real biological data and theroretical models. In particular, I will illustrate how both data analysis and model building can feed each other and may utlimately converge. This project aims at taking a step further in our comprehension of the life as it was, is and will be.

James Dyke 26th Feb 2014

jdyke-29nov-ne-s1On Wednesday 26th February, Dr James Dyke, Institute for Complex Systems Simulation, University of Southampton, will give the talk “Is the Earth alive? A planetary odyssey”

Building 53 Room 4025, Highfield Campus, 4pm. All welcome. Refreshments served after the talk.

“It seems somewhat eccentric if not a little absurd to suggest that a planet is a living thing. Earth has life on it, but it’s not a biological organism. Any theory or argument which concludes that the Earth is alive could be safely filed under “not even wrong”. So when James Lovelock and Lynn Margulis first proposed the Gaia Hypothesis in the early 1970s, some seized on the possible implication that the Earth is a form of biological organism. The Earth is alive? Nonsense! In the decades since, the Gaia Hypothesis has significantly developed and been instrumental in the creation of the new discipline of Earth Systems Science which seeks to understand both the living and non-living components of the Earth in a holistic manner.

In this talk I will give an overview of some of the developments of the mathematical and conceptual theories that underpin Gaia Theory and argue why such approaches are important in a global change context. Humans are currently affecting the Earth via a spectrum of effects. While there is no danger of us destroying the Earth’s biosphere, we are at risk of nudging it into states that would be deleterious to us.”

Ondrej Hovorka 5th Feb 2014

OH_fotoOn Wednesday 5th February, Dr Ondrej Hovorka, Computational Modelling Group, University of Southampton, will give the talk “Spin models of critical phenomena in systems with multi-scale dynamics”

Building 53 Room 4025, Highfield Campus, 4pm. All welcome. Refreshments served after the talk.


This talk will give a general summary of computational models for studying the emergent non-equilibrium phenomena in interacting spin systems spanning a broad range of length- and time-scales. This will include the Langevin dynamics of a set of coupled stochastic ODEs to model thermal fluctuations in spin systems, the master-equation formalism of long timescale memory effects and hysteresis, and the cellular automaton approach to describe multiscale dynamics of avalanche systems, such as earthquakes for example. The individual approaches will be demonstrated using applications in biomedicine, optimisation of modern hard disk drive technologies, and to analysing the out-of-equilibrium phase transition behaviour in avalanching systems.

Mike Harfoot 29th Jan 2014

Mike HarfootOn Wednesday 29th January, Dr Mike Harfoot, United Nations Environment Program and Microsoft Research Cambridge will give the talk “Attempting to model all life on earth –  a proof of concept General Ecosystem Model”

Building 53 Room 4025, Highfield Campus, 4pm. All welcome. Refreshments served after the talk.


Over the past few years, Microsoft Research and the United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), both in Cambridge, UK, have built a global ecosystem model for terrestrial and marine ecosystems. Called the Madingley model, it captures the broad-scale structure and function of ecosystems around the world by simulating processes — including feeding, reproduction and death — that drive the distribution and abundance of organisms. From the relationship between the mass of individual organisms and how long they live, or the effects of  human perturbations such as hunting, to the distribution of biomass across Earth, the model’s outputs are broadly consistent with current understanding of ecosystems. Global ecosystem models such as the Madingley model could radically improve understanding of the biosphere and help inform policy decisions about biodiversity and conservation.

Martyn Amos 15th Jan 2014

On Wednesday 15th January, Prof Martyn Amos, Manchester Metropolitan University, will give the talk “Population-based microbial computing”

Building 53 Room 4025, Highfield Campus, 3:15-4:15pm (this is an hour earlier than usual). All welcome. Refreshments served after the talk.

Synthetic biology is an emerging research field, in which engineering principles are applied to natural, living systems. A major goal of synthetic biology is to harness the inherent “biological nanotechnology” of living cells for the purposes of computation, production, or diagnosis. As the field evolves, it is gradually moving away from a single-cell approach (akin to using standalone computers) to a distributed, population-based approach (rather like using networks of connected machines). In this talk we present several recent results from our group, describing various aspects of this new form of biological engineering. Specifically, we show, using computational studies aligned with laboratory work, how reconfigurable logic devices may be constructed using bacteria, how these may be used as the basis for a “client-server” model of microbial computing, and how bacterial conjugation may provide a new (and, potentially, very rich) communication scheme.