Entrance hall of the ICMS

Multiscale methods for stochastic dynamical systems in biology

Feb 29, 2016 - Mar 04, 2016

ICMS, 15 South College Street

Organisers

Name Institution
Chaplain, Mark University of St Andrews
Erban, Radek University of Oxford
Kevrekidis, Yannis University of Princeton
Leimkuhler, Ben University of Edinburgh
Painter, Kevin Heriot-Watt University

 

The workshop will begin with registration on Monday morning 29 February and close around midday on Friday 4 March 2016.   Please take these timings into account when booking your travel. 

 

This workshop is part of the Stochastic Dynamical Systems in Biology: Numerical Methods and Applications programme  being held from January - June 2016 at the Isaac Newton Institute in Cambridge

Three main objectives of the Satellite Meeting are:

    i.    to increase participation of researchers from the north of the UK in the INI programme;
    ii.    to introduce both main themes of the INI programme (spatial and non-spatial models);
    iii.    to discuss the most recent advances in multiscale modelling.


The speakers of this Satellite Workshop will deal with issues relating to multiple temporal and spatial scales. In particular, this workshop will cover the two main themes of the INI programme and will be both a dedicated research workshop, and an introduction to the INI programme. The participants of the workshop will be encouraged to contribute to the programme by working on research topics investigated by Cambridge-based research participants, and by attending the third and fourth workshops organized in Cambridge in April and June, 2016. These two follow up workshops will be dedicated to each of the two main themes of the INI programme (spatial and non-spatial modelling).


This  Satellite Workshop at ICMS is organized as the second workshop of four in the programme. It is jointly funded by the INI programme and the ICMS.

Arrangements

The event will begin with registration at 08:30 on Monday 29 February and close on Friday 4 March  at 12:45.

 

Participation

INVITED SPEAKERS

  • Invitees/Speakers should have already received and replied to their invitation online. Anyone who has not yet done so please can you do so as soon as possible. The invitation contains a link to your individual registration form.    

PUBLIC APPLICATIONS

  • The deadline for public applicants has now closed.  The organisers have now made their decisions and all successful applicants should now have been informed.

Registration Fee:
A 70.00 GBP registration fee is payable for some participants.

  • Payment can be made on arrival at ICMS - at Registration we will accept cash, credit/debit card payments and sterling cheques (payable to “Heriot-Watt University”).  Unfortunately, we do not yet have an on-line payment system at ICMS.   If you wish to pay by credit/debit card, please complete the form (available in the link below) and bring the completed form to Registration.  

Venue and Talks
The workshop will be held at 15 South College Street, Edinburgh.  You may also find this map useful for the workshop.  All lectures will be held in the Newhaven Lecture Theatre.  The Lecture Theatre is equipped with a data projector, computer, visualiser (the new generation of overhead projectors) and two blackboards.  The projector and one board may be used simultaneously.  It is best to bring your presentation on a memory stick to use in our ICMS computer.  Alternatively, it is possible for you to use your own laptop with our dataprojector, but please be aware that you may have to alter your laptop resolutions/settings.   

Travel
Information about travel to the UK and Edinburgh is available here.

Please note that it is your responsibility to have adequate travel insurance to cover medical and other emergencies (volcanic ash disruptions) that may occur on your trip.

A taxi directly from the airport will cost approximately 16.00 to 20.00 GBP to the city centre for a one-way journey.  There is also a bus service direct from the airport to the city centre which will cost 4.00 single or 7.00 GBP return - the Airlink 100.  This is a frequent service (every 10 minutes during peak times) and will bring you close to Waverley Railway Station, only a short walk to the accommodation and the workshop venue (see map in 'Venue' section above). 

Lothian buses charge £1.50 for a single, £3.50 for a day ticket.  Please note that the exact fare is required and no change is given.

If travelling by train, please note that Edinburgh has several railway stations - Waverley Railway Station being the main station and closest to the workshop venue at 15 South College Street. If you alight at Edinburgh Waverley, the workshop venue is an easy 10 minute walk over North and South Bridge.  The other railway stations are Haymarket and Edinburgh Park at the West End of the city centre.

UK Visas
If you are travelling from overseas you may require an entry visa.  A European visa does not guarantee entry to the UK. Please use this link to the UK Visas site to find out if you need a visa and if so how to apply for one.

Accommodation
You should have now all received details of your accommodation.

Catering
The workshop grant will cover refreshments throughout the event, lunch on three days, an informal wine reception and a workshop dinner.

Dinner
There will be a workshop dinner on Thursday 3 March at Blonde Restaurant, 75  St. Leonard's Street, Edinburgh

Public Lecture

On Tuesday 1 March , Sarah Harris (University of Leeds), will give a Public Lecture (title and abstract below).  Doors will open to the Public at 17.30, with the Lecture beginning at 18.00.  The Public Lecture will be followed by an informal wine reception in the Chapterhouse at ICMS from 19.00-20.00.  Seats have been reserved in the Lecture Theatre for all the workshop participants so there is no need for you to book a seat.

Physics meets Biology in the Garden of Earthly Delights

"Theoretical physics can quantitatively describe a diverse range of inert materials, from high energy plasmas in fusion reactors to ultra-cold atoms at temperatures close to absolute zero. However, even with the most power supercomputers we are not currently able to predict how biological molecules, such as proteins and DNA, will interact with each other or how they will respond to an environmental change. I will discuss what makes the molecules that constitute living systems so difficult to understand, using computer simulations to visualise how the interplay between order and chaos at the molecular level gives rise to their complex behaviours. While modern supercomputers are used to perform the computations, an equivalent portrait of life on Earth as a balance between the tranquillity of Heaven and the tumults of Hell is expressed by the Garden of Earthly Delights, painted 500 years ago by Hleronymus Bosch".

POSTERS
If you are presenting a poster at this workshop please note your poster should be A1 size (594x841mm), preferably in portrait format.  These will be displayed all week in the Chapterhouse during the Workshop, helping discussion during breaks as well as during the designated poster session. These will be dispalyed all week in the Chapterhouse PLEASE hand this to a member of ICMS staff at registration. You will be expected to give a 'poster pitch' in the afternoon session prior to the poster session that evening. (Please see the programme below). You have only been allocated 5 minutes for this so please stick to this schedule. You have been asked to bring your 5 minute 'pitch' with you on  a memory stick and hand this to Moira Spencer or another member of the ICMS staff at registration. All these talks will be uploaded on to our PC during the lunch break on Monday.

PROGRAMME FOR POSTER PITCHES

14:45 Diana Danciu
Mathematical modelling of stem cell dynamics in fish branchia
14:50 Romain Yvinec
Time scales in a coagulation-fragmentation model
14:55 Edward Rolls
Multiscale modelling of DNA dynamics
15:00 Duong Pham
Variance based dynamic sensitivity analysis for detecting non-identifiable parameter
15:05 Mohammed Cherkaoui
Mechanistic Model to Predict DDIs in the Liver
15:10 Christopher Lester
Parameter sensitivity estimation for spatially-extended reaction networks
15:15 Sandesh Athni Hiremath
A stochastic model featuring acid induced gaps during tumour progression
15:20 Bence Melykuti
Equilibrium distributions of simple biochemical reaction systems for time-scale separation in stochastic reaction networks
15:25 Casper Beentjes
How can cells determine locations using chemical sensing?

BREAK 15:30 – 16:00

16:00 Núria Folguera Blasco
Robustness of bistable gene regulatory circuits under epigenetic regulation: noise-enabled bifurcations in optimal transition path theory
16:05 Stephen Smith
Approximate analytical solution of the chemical master equation with abundant species
16:10 Tomislav Plesa
Framework for Construction of Caricature Chemical Reaction Systems for Stochastic Analysis
16:15 Yen Ting Lin
Effects of bursting noise in gene regulation networks
16:20 Justine Dattani
Linking single-cell sample paths and population-level dynamics: insights from a coarse model of gene transcription
16:25 David Holcman
Modelling and data analysis of electro-diffusion in dendritic spines
16:30 Shuohao Liao
Tensor Methods for Parameter Estimation and Bifurcation Analysis of Stochastic Reaction Networks
16:35 Claudia Cianci
Molecular finite-size effects in stochastic models of equilibrium chemical systems
16:40 Karen Lipkow
Cellular Systems Biology of Chromosome Dynamics
16:45 Yongzheng Sun
Noise can accelerate the emergence of flocking in Cucker-Smale system

 

Programme

 


Monday29 February

08:45-09:30

Registration & Tea/Coffee in the Chapterhouse, Level 1

09:30-09:40

Welcome and Introduction to the INI programme (Radek Erban)

09:40-10:25

Gerhard Hummer (Max Planck Institute of Biophysics)
Molecular simulation and stochastic dynamical modeling of protein function

10:25-11:10

Mark Chaplain (University of St Andrews)
Spatial stochastic modelling of gene regulatory networks

11:10-11:40

Tea/Coffee in the Chapterhouse, Level 1

11:40-12:25

Tim Elston (University of North Carolina at Chapel Hill)
Multiscale modeling of gradient sensing

12:25-14:00

Lunch provided in the Chapterhouse, Level 1

14:00-14:45

Alexandra Jilkine (University of Notre Dame)
The role of cell location and spatial gradients in the evolutionary dynamics of the intestinal crypt

14:45-15:30

Poster pitches (9x5 min)

15:30-16:00

Tea/Coffee in the Chapterhouse, Level 1

16:00-16:45

Poster pitches (9x5 min)

17:00-18:30

Poster session/informal wine reception in the Chapterhouse, Level 1

 

Tuesday 1 March

09:30-10:15

Andreas Deutsch (Technische Universität Dresden)
Cellular automaton modelling of cancer growth and invasion

10:15-11:00

Thomas Hillen (University of Alberta)
Stochastic modelling of the normal tissue complication probability (NTCP) in radiation treatment of cancer
pdf of presentation

11:00-11:30

Tea/Coffee in the Chapterhouse, Level 1  

11:30-12:15

Daan Frenkel (University of Cambridge)
Towards addressable self-assembly

12:20-14:00

Lunch provided in the Chapterhouse, Level 1 (poster setup)

14:00-14:45

Per Lotstedt (Uppsala University)
Diffusion, subdiffusion, reactions, and internal states in mesoscopic models

14:45-15:15

Tea/Coffee in the Chapterhouse, Level 1 (poster setup)

15:15-16:00

Mariya Ptashnyk (University of Dundee)
Stochastic homogenization of a model of plant biomechanics and the Keller-Segel chemotaxis system

16:00-16:45

Garegin Papoian (University of Maryland)
Molecular simulations of acto-myosin network dynamics

17:30

Doors open to the public

18:00-19:00

Public Lecture by Sarah Harris

19:00-20.00

Informal wine reception in the Chapterhouse, Level 1

Wednesday 2 March

09:00-09:45

Assyr Abdulle (École Polytechnique Fédérale de Lausanne)
Numerical techniques for stiff and ergodic stochastic differential equations

09:45-10:30

Hye-Won Kang (University of Maryland)
Multiscale stochastic reaction-diffusion algorithms combining Markov chain models with SPDEs
pdf of presentation                              

10:30-11:15

Coffee/Tea in the Chapterhouse, Level 1

11:15-12:00

Jonathan Chapman (University of Oxford)
Model reduction for slow-fast stochastic systems with metastable behaviour
pdf of presentation

12:00-12:45

Anastasios Matzavinos (Brown University)
Mesoscopic modeling of DNA transport in an array of entropic barriers  

12:45

Free afternoon

Thursday 3 March

09:30-10:15

Franziska Matthaeus(BIOMS/IWR, Heidelberg University)
Stochastic modeling of collective cancer cell migration

10:15-11:00

Radek Erban (University of Oxford)
Mathematical methods for multiscale modelling of intracellular processes
pdf of presentation

11:00-11:30

Coffee/Tea in the Chapterhouse, Level 1

11:30-12:15

Wilhelm Huisinga (Potsdam)
Hybrid stochastic-deterministic solution of the chemical master equation
pdf of presentation

12:15-12:20

Group photo to be taken

12:20-14:00

Lunch provided in the Chapterhouse, Level 1

14:00-14:45

Sarah Harris (University of Leeds)
Fluctuating finite element analysis: modelling biomacromolecules at the mesoscale with continuum mechanics
pdf of presentation

14:45-15:30

Giovanni Samaey (KU Leuven)
Variance-reduced simulation of stochastic agent-based models in biological applications

15:30-16:00

Coffee/Tea in the Chapterhouse, Level 1                                          

16:00-16:45

Ben Leimkuhler (University of Edinburgh)
Enhanced sampling of biomolecular systems using extended dynamics

19.00

Workshop Dinner at Blonde Restaurant, 75 St. Leonard's Street, Edinburgh

Friday 4 March

09:00-09:45

Pep Espanol (Universidad Nacional de Educación a Distancia)
Thermal blobs: non-isothermal coarse-graining of complex moleculesv               

09:45-10:30

Kevin Painter (Heriot-Watt University)
Navigating the flow: Animal orientation under flows

10:30-11:15

Coffee/Tea in the Chapterhouse, Level 1

11:15-12:00

John Chodera (Memorial Sloan-Kettering Cancer Center)
Stochastic modeling of biomolecular conformational dynamics with Markov state models

12:00-12:45

Konstantinos Zygalakis (University of Edinburgh)
Hybrid modelling of stochastic chemical kinetics
pdf of presentation

12:45

Close of workshop (please note that no lunch will be provided)

 

 


Presentations:

Presentation Details
Abdulle, Assyr
Numerical techniques for stiff and ergodic stochastic differential equations
View Abstract Down
Chaplain, Mark
Spatial stochastic modelling of gene regulatory networks
View Abstract Down
Chapman, Jon
Model reduction for slow-fast stochastic systems with metastable behaviour
View Abstract Down
Chodera, John
Stochastic modeling of biomolecular conformational dynamics with Markov state models
View Abstract Down
Deutsch, Andreas
Cellular automaton modelling of cancer growth and invasion
View Abstract Down
Elston, Tim
Multiscale modeling of gradient sensing
View Abstract Down
Erban, Radek
Mathematical methods for multiscale modelling of intracellular processes
View Abstract Down
Espanol, Pep
Thermal blobs: non-isothermal coarse-graining of complex molecules
View Abstract Down
Frenkel, Daan
Towards addressable self-assembly
View Abstract Down
Harris, Sarah
Fluctuating finite element analysis: modelling biomacromolecules at the mesoscale with continuum mechanics
View Abstract Down
Hillen, Thomas
Stochastic modelling of the normal tissue complication probability (NTCP) in radiation treatment of cancer
View Abstract Down
Huisinga, Wilhelm
Hybrid stochastic-deterministic solution of the chemical master equation
View Abstract Down
Hummer, Gerhard
Molecular simulation and stochastic dynamical modeling of protein function
View Abstract Down
Jilkine, Alexandra
The role of cell location and spatial gradients in the evolutionary dynamics of the intestinal crypt
View Abstract Down
Kang, Hye-Won
Multiscale stochastic reaction-diffusion algorithms combining Markov chain models with SPDEs
View Abstract Down
Leimkuhler, Ben
Enhanced sampling of biomolecular systems using extended dynamics
View Abstract Down
Lotstedt, Per
Diffusion, subdiffusion, reactions, and internal states in mesoscopic models
View Abstract Down
Matthaeus, Franziska
Stochastic modeling of collective cancer cell migration
View Abstract Down
Matzavinos, Anastasios
Mesoscopic modeling of DNA transport in an array of entropic barriers
View Abstract Down
Papoian, Garegin
Molecular Simulations of Acto-Myosin Network Dynamics
View Abstract Down
Ptashnyk, Mariya
Stochastic homogenization of a model of plant biomechanics and the Keller-Segel chemotaxis system
View Abstract Down
Samaey, Giovanni
Variance-reduced simulation of stochastic agent-based models in biological applications
View Abstract Down
Yvinec, Romain
Time scales in a coagulation-fragmentation model
View Abstract Down
Zygalakis, Konstantinos
Hybrid modelling of stochastic chemical kinetics
View Abstract Down

Participants

Name Institution
Abdulle, Assyr École Polytechnique Fédérale de Lausanne
Anderson, David University of Wisconsin - Madison
Athni Hiremath, Sandesh TU Kaiserslautern
Beentjes, Casper University of Oxford
Bennett, Jamie Heriot-Watt University
Chaplain, Mark University of St Andrews
Chapman, Jon University of Oxford
Cherkaoui, Mohammed University of Nottingham
Chodera, John Memorial Sloan-Kettering Cancer Center
Cianci, Claudia University of Florence
Danciu, Diana-Patricia University of Heidelberg - Institute of Applied Mathematics and BioQuant
Dattani, Justine Imperial College London
Deutsch, Andreas Technische Universität Dresden
Duncan, Andrew Imperial College London
Elston, Tim University of North Carolina at Chapel Hill
Erban, Radek University of Oxford
Espanol, Pep Universidad Nacional de Educación a Distancia
Folguera-Blasco, Núria Centre de Recerca Matemàtica (CRM)
Frenkel, Daan University of Cambridge
Harris, Sarah University of Leeds
Haskovec, Jan King Abdullah University of Science and Technology
Hillen, Thomas University of Alberta
Holcman, David ENS
Huisinga, Wilhelm Potsdam
Hummer, Gerhard Max Planck Institute of Biophysics
Isaacson, Samuel Boston University
Jilkine, Alexandra University of Notre Dame
Kang, Hye-Won University of Maryland,
Leimkuhler, Ben University of Edinburgh
Lester, Christopher Oxford University
Liao, Shuohao University of Oxford
Lin, Yen Ting The University of Manchester
Lipkow, Karen Babraham Institute, Cambridge
Lord, Gabriel Heriot-Watt University
Lotstedt, Per Uppsala University
Matthaeus, Franziska BIOMS/IWR, Heidelberg University
Matzavinos, Anastasios Brown University
Mélykúti, Bence University of Freiburg
Moraki, Eleni Heriot-Watt University
Painter, Kevin Heriot-Watt University
Papoian, Garegin University of Maryland
Peruzzo, Fabio University of Leeds
Pham, Duong Luxembourg Centre for Systems Biomedicine
Plesa, Tomislav University of Oxford
Ptashnyk, Mariya University of Dundee
Rolls, Edward University of Oxford
Samaey, Giovanni KU Leuven
Schmuck, Markus HWU
Shang, Xiaocheng University of Edinburgh
Smith, Stephen University of Edinburgh
Sun, Yongzheng China University of Mining and Technology
Tanner, Eleanor MIGSAA (Heriot-Watt University and University of Edinburgh)
Trucu, Dumitru University of Dundee
Yvinec, Romain INRA
Zygalakis, Konstantinos University of Edinburgh