Stochastic dynamical systems in biology: numerical methods and applications

Programme theme

In the past decades, quantitative biology has been driven by new modelling-based stochastic dynamical systems and partial differential equations. Examples from gene regulation, molecular signalling, cell division and molecular transport, as recently revealed by live cell images, have shown that many processes in cells and in molecular biology are inherently driven by stochastic events. One of the biggest challenges we propose to address in this programme is to develop methods and analysis, as well as efficient algorithms for simulations, to bridge the range of different biological scales. In support of this goal, the programme will focus on

Analysis of stochastic dynamical systems and applications in molecular and cellular biology.
Development of efficient computational methods for simulating stochastic equations over various scales.
Identifying new research areas.

In particular, three interlinked focus areas will run throughout the programme:

Analysis, computation and development of non-spatial (well mixed) models.
Analysis, computation and development of spatio-temporal reaction-diffusion models, including Brownian dynamics and compartment-based simulations (reaction-diffusion master equation).
Multiscale methods.

The programme will feature an opening, midterm and closing workshop at the Isaac Newton Institute, as well as a Satellite Meeting.

Fellowships are available to partially cover travel costs for some junior US participants thanks to a grant from the NSF. Graduate students and postdocs should send:

1. A current CV.

2. A short letter of recommendation from a professor at your home institution. This letter must attest to the relevance of the workshop/programme to the applicant’s career and research interests, and briefly summarise any previous research by the applicant.

3. Information on which workshop you are applying to attend and what type of support you are requesting. If you are an invited speaker or invited programme participant please note this in your email.

Please send all information by email to sdb_nsf_funding@math.bu.edu.

Priority for funding will be given to applicants, particularly those from underrepresented groups, who are actively working in areas directly related to the programme and workshop themes.

Review of applications will begin on 11 October 2015.

The Institute kindly requests that any papers published as a result of this programme’s activities are credited as such. Please acknowledge the support of the Institute in your paper using the following text:

The author(s) would like to thank the Isaac Newton Institute for Mathematical Sciences, Cambridge, for support and hospitality during the programme Stochastic dynamical systems in biology: numerical methods and applications, where work on this paper was undertaken. This work was supported by EPSRC grant EP/K032208/1.

Click here to download the programme's final scientific report

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Preprints

Title	Year	Programme	Publication Date
Multilevel Monte Carlo for scalable Bayesian computations Authors: T Nagapetyan, Lukasz Szpruch, Sebastian Vollmer, Konstantinos Zygalakis Download PDF	2015	SDB	21 October 2016
Constrained approximation of effective generators for multiscale stochastic reaction networks and application to conditioned path sampling Authors: Simon Cotter Download PDF	2015	SDB	21 October 2016

Title

Year

Programme

Publication Date

Multilevel Monte Carlo for scalable Bayesian computations

Authors: T Nagapetyan, Lukasz Szpruch, Sebastian Vollmer, Konstantinos Zygalakis

Download PDF

2015

SDB

21 October 2016

Constrained approximation of effective generators for multiscale stochastic reaction networks and application to conditioned path sampling

Authors: Simon Cotter

Download PDF

2015

SDB

21 October 2016

Workshops

SDBW01

Opening workshop

18 January 2016 to 22 January 2016

Satellite

SDBW02

Multiscale methods for stochastic dynamical systems in biology

29 February 2016 to 4 March 2016

SDBW03

Advances in numerical and analytic approaches for the study of non-spatial stochastic dynamical systems in molecular biology

4 April 2016 to 8 April 2016

SDBW04

Spatially distributed stochastic dynamical systems in biology

20 June 2016 to 24 June 2016

The Organisers would like to thank the following sponsors for their generous support of the event:

Seminars

Tuesday 12th January 2016
15:00 to 16:00	Ulrich Dobramysl University of Cambridge; University of Oxford Role and dynamics of cytoskeletal actin bundles	Room 2

Wednesday 13th January 2016
15:00 to 16:00	Karen Lipkow Cellular Systems Biology of Chromosome Dynamics	Room 2

Tuesday 26th January 2016
15:00 to 16:00	Grant Lythe University of Leeds Stochastic modelling and immunology	Room 2

Wednesday 27th January 2016
15:00 to 16:00	Steve Andrews Open problems in stochastic cell biology: information transfer, macromolecular crowding, and filament simulation	Room 2

Friday 29th January 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 1: Stochastic modeling, asymptotics, simulations and data analysis of super-resolution trajectories: application to cellular biology	Room 2

Tuesday 2nd February 2016
15:00 to 16:00	Pietro Cicuta University of Cambridge Subdiffusive fluctuations in bacterial chromosomes	Room 2

Wednesday 3rd February 2016
15:00 to 16:00	Konstantinos Zygalakis Hybrid modelling of stochastic chemical kinetics	Room 1

Friday 5th February 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 2: Introduction to the stochastic integral and Ito calculus,	Room 1

Tuesday 9th February 2016
15:00 to 16:00	Yongzheng Sun Influence of noise and time delay on the collective behavior of self-propelled particles system	Room 1

Wednesday 10th February 2016
15:00 to 16:00	Bence Mélykúti Albert-Ludwigs-Universität Freiburg Equilibrium distributions of simple biochemical reaction systems for time-scale separation in stochastic reaction networks	Room 2

Friday 12th February 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Stochastic modeling, asymptotics, simulations and data analysis of super-resolution trajectories: application to cellular biology	Room 1

Tuesday 16th February 2016
15:00 to 16:00	Framework for Construction of Caricature Chemical Reaction Systems	Room 2

Wednesday 17th February 2016
15:00 to 16:00	Omer Dushek A novel biophysical method for the study of tethered signalling reactions	Room 2

Tuesday 23rd February 2016
15:00 to 16:00	Grant Lythe University of Leeds Stochastic modelling and immunology	Room 2

Wednesday 24th February 2016
15:00 to 16:00	Krasimira Tsaneva University of Exeter Modelling gonadotrophin-releasing hormone signalling: dynamics, noise and reliability	Room 2

Friday 26th February 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 4	Room 2

Friday 4th March 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 5: (U. of Cambridge): Activation escape through a potential well.	Room 2

Tuesday 8th March 2016
15:00 to 16:00	Mark Flegg Monash University Stochastic simulation of high order molecular interactions with spatial resolution and individual molecule detail: A generalised Smoluchowski theory	Room 2

Wednesday 9th March 2016
15:00 to 16:00	Andreas Hellander Uppsala Universitet PyURDME, MOLNs and StochSS — from new algorithms for spatial stochastic simulation to large-scale distributed computational experiments in “the cloud"	Room 2

Friday 11th March 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris No lecture	Room 2

Tuesday 15th March 2016
15:00 to 16:00	Shuohao Liao University of Oxford Tensor Methods for Parameter Estimation and Bifurcation Analysis of Stochastic Reaction Networks	Room 2

Wednesday 16th March 2016
15:00 to 16:00	Romain Yvinec Université François-Rabelais Tours; INRA - Institut National de la Recherche Agronomique Stochastic coagulation-fragmentation models for the study of protein aggregation phenomena	Room 2

Friday 18th March 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 7: (U. of Cambridge): Additive property of the MFPT, Fokker-Planck with a killing term, Non-Poissonnian escape	Room 2

Monday 21st March 2016
14:00 to 15:00	Stefan Hellander Reaction rates for nearest-neighbor reactions in the reaction-diffusion master equation	Room 2

Tuesday 22nd March 2016
15:00 to 16:00	Julius Kirkegaard University of Cambridge Stochastic Aspects of Choanoflagellates	Room 2

Tuesday 29th March 2016
15:00 to 16:00	Peter Roland Kramer Rensselaer Polytechnic Institute Stochastic Fluctuations in Suspensions of Swimming Microorganisms	Room 2

Wednesday 30th March 2016
15:00 to 16:00	Sandro Azaele Stochastic Modeling of Species-Rich Ecosystems	Room 2

Tuesday 12th April 2016
15:00 to 16:00	Yiannis Kaznessis Multiscale Models for New Antibiotic Technologies	Room 2

Wednesday 13th April 2016
15:00 to 16:00	James Rothman Yale University On the Structural Biochemical Mechanism of Synaptic Neurotransmission in the Brain	Room 1

Friday 15th April 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 8: (U. of Cambridge): Oscillatory escape: a Non-Poissonnian escape process	Room 2

Tuesday 19th April 2016
15:00 to 16:00	Bob Eisenberg Rush University Mathematics and physiology	Room 2

Friday 22nd April 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 9: (U. of Cambridge): Oscillatory escape: a Non-Poissonnian escape process	Room 2

Tuesday 26th April 2016
15:00 to 16:00	André Leier The use of delays in modelling and simulation of biochemical reaction systems and exact model reduction	Room 2

Wednesday 27th April 2016
15:00 to 16:00	Jay Newby Metastable dynamics: rare events in cell biology	Room 2

Thursday 28th April 2016
11:00 to 12:00	Colin Gillespie Efficient construction of optimal designs for stochastic kinetic models	Room 2

Friday 29th April 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 10: (U. of Cambridge): Escape through a cusp. Applications to diffusion in a crowded membrane	Room 2

Wednesday 4th May 2016
15:00 to 16:00	Chuan Xue Ohio State University Multiscale Modeling of Axonal Cytoskeleton Dynamics in Disease	Room 2

Thursday 5th May 2016
16:00 to 17:00	Tatiana T Marquez Lago Spatial stochastic models of cell polarity and personalized medicine	Room 2

Friday 6th May 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 11: (U. of Cambridge): statistics and analysis of super-resolution Single Particle trajectories.	Room 2

Tuesday 10th May 2016
15:00 to 16:00	German A. Enciso Absolute robustness in deterministic and stochastic chemical reaction networks	Room 2

Wednesday 11th May 2016
10:00 to 13:00	Steve Andrews Fred Hutchinson Cancer Research Centre Smoldyn Tutorial	Discussion Room
15:00 to 16:00	Ralf Metzler Universität Potsdam Anomalous diffusion in biological membranes and their mathematical description	Room 2

Friday 13th May 2016
11:00 to 12:00	John Fricks Pennsylvania State University Time Series Analysis of Diffusion with Transient Binding	Room 2
14:30 to 15:30	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 12: (U. of Cambridge): Stochastic chemical reactions: modelling and analysis	Room 2

Tuesday 17th May 2016
15:00 to 16:00	Jürgen Reingruber CNRS - Ecole Normale Superieure Paris Modeling and stochastic analysis of autoregulation of the Krox20 transcription factor driving cellular diversification and hindbrain patterning	Room 2

Wednesday 18th May 2016
15:00 to 16:00	Kevin Burrage Queensland University of Technology What we have been doing while at INI for the last 5 weeks: a mathematical study on anomalous diffusion	Room 2

Thursday 19th May 2016
16:00 to 17:00	Dan Coombs Particle tracking to elucidate cell surface receptor motion and signalling	Room 2

Friday 20th May 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 13: (U. of Cambridge): Stochastic biology: stochastic telomere model and Rouse polymer model.	Room 2

Wednesday 25th May 2016
15:00 to 16:00	John Tyson Getting Things Right in a Noisy Milieu: Stochastic Models of Cell Cycle Dynamics in Budding Yeast and Bacteria	Room 2

Friday 27th May 2016
14:30 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 14: (U. of Cambridge): Anomalous diffusion for a monomer, mean time for a polymer to loop.	Room 1

Tuesday 31st May 2016
15:00 to 16:00	Stephen Smith University of Edinburgh Four arguments against the reaction-diffusion master equation (and one in its favour).	Room 2

Wednesday 1st June 2016
15:00 to 16:00	Garyk Papoian Stochastic Mechanochemistry of the Eukaryotic Cytoskeleton	Room 2

Monday 6th June 2016
15:00 to 16:00	Vahid Shahrezaei Multi-scale modelling of stochastic gene expression	Room 2

Tuesday 7th June 2016
15:00 to 16:00	André Leier Stochastic membrane processes in biomedicine	Room 2

Wednesday 8th June 2016
15:00 to 16:00	David Schnoerr University of Edinburgh Cox process representation and inference for stochastic reaction-diffusion processes	Room 2

Thursday 9th June 2016
16:00 to 17:00	Tuomas Knowles University of Cambridge Kinetics of filamentous protein self-assembly	Room 2

Friday 10th June 2016
11:00 to 12:00	Jonathan Mattingly Scaling limits of a model for selection at two scales Joint with Shishi Luo	Room 2

Monday 13th June 2016
15:00 to 16:00	Justine Dattani Imperial College London Stochastic models of gene transcription with upstream drives: Exact solution and sample path characterisation	Room 2

Tuesday 14th June 2016
11:00 to 12:00	Ben o'shaughnessy Columbia University Mechanics of cell division by the actomyosin contractile ring	Room 2
15:00 to 16:00	Markos A. Katsoulakis Path-space information metrics for uncertainty quantification and coarse-graining of molecular systems	Room 2

Wednesday 15th June 2016
15:00 to 16:00	Kevin Lin An analysis of implicit samplers in the small-noise limit	Room 2

Thursday 16th June 2016
11:00 to 12:00	Bence Mélykúti Albert-Ludwigs-Universität Freiburg Cross-contamination rate estimation for digital PCR in lab-on-a-chip microfluidic devices	Room 2

Friday 17th June 2016
14:15 to 17:00	David Holcman CNRS - Ecole Normale Superieure Paris Lecture 15 (University of Cambrdige). Polymer model, mean looping time and interpretation of Hi-C data (Enounter frequencies data)	Room 2

Stochastic dynamical systems in biology: numerical methods and applications

Organisers

Radek Erban
David Holcman CNRS - Ecole Normale Superieure Paris
Samuel Isaacson
Konstantinos Zygalakis

Speakers

Steve Andrews Fred Hutchinson Cancer Research Centre
Sandro Azaele
Kevin Burrage Queensland University of Technology
Pietro Cicuta University of Cambridge
Daniel Coombs University of British Columbia
Justine Dattani Imperial College London
Ulrich Dobramysl University of Cambridge
Omer Dushek
Bob Eisenberg Rush University
German A. Enciso
Mark Flegg Monash University
John Fricks Pennsylvania State University
Colin Gillespie
Andreas Hellander
Stefan Hellander
David Holcman CNRS - Ecole Normale Superieure Paris
Markos A. Katsoulakis
Yiannis Kaznessis
Julius Kirkegaard University of Cambridge
Tuomas Knowles University of Cambridge
Peter Roland Kramer Rensselaer Polytechnic Institute
André Leier
Shuohao Liao University of Oxford
Kevin Lin
Karen Lipkow University of Cambridge
Grant Lythe University of Leeds
Tatiana T Marquez Lago
Jonathan Mattingly
Ralf Metzler Universität Potsdam
Bence Mélykúti Albert-Ludwigs-Universität Freiburg
Jay Newby
Ben o'shaughnessy Columbia University
Garyk Papoian
Jürgen Reingruber CNRS - Ecole Normale Superieure Paris
James Rothman Yale University
David Schnoerr University of Edinburgh
Vahid Shahrezaei
Stephen Smith University of Edinburgh
Yongzheng Sun Fudan University
Krasimira Tsaneva University of Exeter
John Tyson Virginia Polytechnic Institute and State University
Chuan Xue Ohio State University
Romain Yvinec INRA - Institut National de la Recherche Agronomique
Konstantinos Zygalakis University of Southampton

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Participants

Assyr Abdulle
Jun Allard University of California, Irvine
Assaf Amitai Massachusetts Institute of Technology
David Anderson University of Wisconsin-Madison
Steve Andrews Fred Hutchinson Cancer Research Centre
Daniele Avitabile University of Nottingham
Sandro Azaele
Ruth Baker University of Oxford
Casper Beentjes University of Oxford
Erik Bollt CNRS - Université de Caen Basse-Normandie; Capital Normal University
Maria Bruna
Pamela Burrage Queensland University of Technology
Kevin Burrage Queensland University of Technology
Jérôme Cartailler École Normale Supérieure
Edward Codling
Daniel Coombs University of British Columbia
Simon Cotter University of Manchester
Justine Dattani Imperial College London
Luis de la Higuera
Ulrich Dobramysl University of Cambridge
Andrew Duncan
Omer Dushek
German A. Enciso
Stefan Engblom Uppsala Universitet
Radek Erban University of Oxford
Marco Ferrarini
John Fricks Pennsylvania State University
Mike Giles University of Oxford
Colin Gillespie
Raymond Goldstein University of Cambridge
Andy Golightly
Ramon Grima University of Edinburgh
Claire Guerrier CNRS - Ecole Normale Superieure Paris; CREST and Université Paris 6
Jan Haskovec
Andreas Hellander
Stefan Hellander
Des Higham
David Holcman CNRS - Ecole Normale Superieure Paris
Rebecca Hoyle University of Southampton
Nick Jones Imperial College London
Hye-Won Kang University of Maryland, Baltimore County
Markos A. Katsoulakis
Nikos Kavallaris None / Other
Yiannis Kaznessis
Yannis Kevrekidis Princeton University
Peter Roland Kramer Rensselaer Polytechnic Institute
Rachel Kuske University of British Columbia
André Leier
Ben Leimkuhler University of Edinburgh
Shuohao Liao University of Oxford
Kevin Lin
Karen Lipkow University of Cambridge
Grant Lythe University of Leeds
Martin López-García
Per Lötstedt
Tatiana T Marquez Lago
Jonathan Mattingly
Scott McKinley Tulane University
Ralf Metzler Universität Potsdam
Bence Mélykúti Albert-Ludwigs-Universität Freiburg
Jay Newby
James Norris University of Cambridge
Ben o'shaughnessy Columbia University
Garyk Papoian
Pierre Parutto CNRS - Ecole Normale Superieure Paris
Tomislav Plesa University of Oxford
Jürgen Reingruber CNRS - Ecole Normale Superieure Paris
Martin Robinson University of Oxford
Tim Rogers
Edward Rolls University of Oxford
Sten Rüdiger
Francesco Salvarani Université Paris-Dauphine; Università degli Studi di Pavia
Ruben Sanchez-Garcia University of Southampton
David Schnoerr University of Edinburgh
Vahid Shahrezaei
Ofir Shukron CNRS - Ecole Normale Superieure Paris
Stephen Smith University of Edinburgh
Konstantinos Spiliopoulos
Yongzheng Sun Fudan University
Peter Swain
Lukasz Szpruch
Pieter Rein ten Wolde
Krasimira Tsaneva University of Exeter
John Tyson Virginia Polytechnic Institute and State University
Sebastian Vollmer
Jonathan Wattis University of Nottingham
Darren Wilkinson Newcastle University
Kit Yates University of Bath
Romain Yvinec INRA - Institut National de la Recherche Agronomique
Konstantinos Zygalakis University of Southampton