LF30515 Dynamics of Biological Systems
Introductory description
This module will introduce students to the "systems dynamical" nature of cells. We will introduce the student to this system level view of the cell and explain the experimental and mathematical approaches used to achieve a system levels understanding of cellular function. The module will also outline how a detailed understanding of system dynamics enables researchers to engineer novel biological systems for the first time, in a synthetic biology approach.
Module aims
 Acquiring a more quantitative/physical view of cells
 Understanding ‘design principles’ of cellular systems involved in gene regulation, signalling and metabolism
 Understanding (system) dynamics of cellular systems (e.g. bistability, oscillations)
 Understanding physical properties and limits of cellular systems (thermodynamics, mechanical forces, electrical properties)
Outline syllabus
This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.
Quantitative skills in cell biology (4 lectures)
 Cell (physical and dynamical) properties. Cellular properties: Composition, size, speed, energy, time scales, forces (MA)
 Cell scales. Functions and scales: Numbers, exponentials, time scales (BM)
 Mechanistic vs. phenomological models (system dynamics models). Rigorous rules for sloppy calculations and the power of (quantitative) models (OS, BM)
 Model choice (Occam’s razor level), model fitting (very basic), optimisation, modelexpw cycle. Dynamics and stability (BM, OS)
Cell metabolism (5 lectures)
5. Free energy of binding and the mass action rule (OSS)
6. Enzyme kinetics and writing differential equations to model a biochemical system (ODE models) (OSS)
7. Modeling metabolism (ODE and FBA models) (OSS)
8. Metabolic control: carbon source hierarchy, diauxic shifts and overflow metabolism (biologically relevant case) (OSS)
9. Metabolic oscillations (biologically relevant case) (OSS)
Cellular signalling (4 lectures)
10. Ligand binding, allostery, Hill function (basic numbers/processes) (BM)
11. Signal amplification and ultrasensitivity (MAPK type cascade) (BM)
12. Two component cascades (BM)
13. Chemotaxis (biologically relevant case) (OSS, BM)
Gene regulation 1 (3 lectures)
14. Ribosome binding and principles of gene regulation, Simple gene regulation models and network motifs, e.g. selfregulating TF (feedback loop) (MA)
15. Excitatory dynamics in the context of competency / differentiation (biologically relevant case) (MA)
16. Limit cycle oscillation (MA)
Gene regulation 2 (3 lectures)
17. Low numbers in gene regulation and intro to stochastic modelling (DH)
18. Chemical master equation and how to construct stochastic models (DH)
19. 1 and 2state models of gene expression and how it experimentally tested (DH)
 Advanced topics of interest: Maximum likelihood, model choice (link back to beginning), parameter sampling, experimentmodel cycle.
Learning outcomes
By the end of the module, students should be able to:
 Learn about dynamic responses/behavior of cells in terms of metabolism, gene regulation, and signalling.
 Learn about experimental approaches for acquiring quantitative and singlecell data of cellular systems;
 Learn about building computational/mathematical models that can allow hypotheses to be devised from acquired quantitative data and guide new data collection experiments
 Writing biochemical reactions from pathway diagrams or ODEs
 Acquiring quantitative thinking skills for cellular biology
Indicative reading list
Essential Reading
 Online book on building a quantitative sense for cells: "Biology by the Numbers" by Ron Milo and Rob Phillips
 Select chapters from online book on biological modeling: "Mathematical Modeling in Systems Biology: An Introduction" by Brian Ingalls
 Physical Biology of the Cell (https://www.amazon.co.uk/PhysicalBiologyCellRobPhillips/dp/0815344503)
 Physiology of bacterial cell (https://www.amazon.co.uk/PhysiologyBacterialCellMolecularApproach/dp/0878936084)
 Klipp, E, Liebermeister, E et al "Systems Biology: A Textbook", Wiley VCH Blackwell (2009), ISBN: 97835273187742
 Alon, Uri "An Introduction to Systems Biology: Design Principles of Biological Circuits", Taylor and Francis (2006), ISBN: 9781584886426
Recommended Reading  Berg, Howard C "Random Walks in Biology", University Press of California (1993), ISBN: 9780091000640
 Strogatz, Steven H "Nonlinear Dynamics and Chaos", The Perseus Books Group (2000), ISBN: 9780738204536
 Ptashne, Mark "A Genetic Switch", Cold Spring Harbour Laboratory Press (2004), ISBN: 9780879697167
 Murray, James D "Mathematical Biology: An Introduction: Part 1" 3rd , SpringerVerlag (2002), ISBN: 9780387952239
 Britton, Nicholas F "Essential Mathematical Biology", Springer (2005), ISBN: 9781852335366
 Kaneko, Kunihiko "Life: An introduction to complex systems Biology" , Springerverlag (2006), ISBN: 978364206
 Additional reading material will be assigned for specific lecture and lab sections
Subject specific skills
 Quantitative thinking skills in the context of cellular systems
 Gather an appreciation of the systems view of cellular biology and the complexity of biological systems at the cellular level;
 Gain an appreciation for the role of quantitative data and mathematical modelling in understanding cellular systems;
 Apply a range of computational and mathematical methods to analyze biological data and model diverse cellular phenomena;
 Combine experimental and theoretical concepts, literature and ideas.
Transferable skills
 Work in small groups to tackle complex problems;
 Communicate with scientists with experimental and/or theoretical backgrounds;
 Think creatively and beyond traditional discipline boundaries.
Study time
Type  Required 

Lectures  20 sessions of 1 hour (13%) 
Private study  130 hours (87%) 
Total  150 hours 
Private study description
130 hrs of selfstudy and directed reading to prepare for the open book assessment
Costs
No further costs have been identified for this module.
You do not need to pass all assessment components to pass the module.
Students can register for this module without taking any assessment.
Assessment group A
Weighting  Study time  Eligible for selfcertification  

InModule Test (1)  20%  No  
Inmodule MCQ Test 

InModule Test (2)  20%  No  
Inmodule MCQ Test 

Open Book Assessment  60%  20 hours  No 
Final assessment for the module will be on open book assessment. This is an essay based assessment consisting of 4 questions students need to answer 2. The essays cannot be answered using lecture notes alone students will need to perform background research and essays will need to be fully referenced. 
Assessment group R
Weighting  Study time  Eligible for selfcertification  

Open Book Assessment  100%  No  
Final assessment for the module will be on open book assessment. This is an essay based assessment consisting of 4 questions students need to answer 2. The essays cannot be answered using lecture notes alone students will need to perform background research and essays will need to be fully referenced. 
Feedback on assessment
Pastoral meeting with academic tutor
Courses
This module is Core for:
 Year 3 of UMDACF10 Undergraduate Integrated Natural Sciences (MSci)
This module is Optional for:
 Year 3 of UBSAC700 Undergraduate Biochemistry

ULFAC1A2 Undergraduate Biochemistry (MBio)
 Year 3 of C1A2 Biochemistry
 Year 3 of C700 Biochemistry
 Year 4 of ULFAC702 Undergraduate Biochemistry (with Placement Year)
 Year 3 of ULFAC1A6 Undergraduate Biochemistry with Industrial Placement (MBio)
 Year 3 of UBSA3 Undergraduate Biological Sciences
 Year 3 of ULFAC1A1 Undergraduate Biological Sciences (MBio)
 Year 4 of ULFAC113 Undergraduate Biological Sciences (with Placement Year)
 Year 3 of ULFAC1A5 Undergraduate Biological Sciences with Industrial Placement (MBio)
 Year 3 of UBSAC1B9 Undergraduate Biomedical Science

ULFAC1A3 Undergraduate Biomedical Science (MBio)
 Year 3 of C1A3 Biomedical Science
 Year 3 of C1B9 Biomedical Science
 Year 3 of ULFAC1A7 Undergraduate Biomedical Science with Industrial Placement (MBio)
 Year 4 of ULFACB18 Undergraduate Biomedical Science with Placement Year
 Year 3 of ULFAB140 Undergraduate Neuroscience (BSc)
 Year 3 of ULFAB142 Undergraduate Neuroscience (MBio)
 Year 3 of ULFAB143 Undergraduate Neuroscience (with Industrial Placement) (MBio)
 Year 4 of ULFAB141 Undergraduate Neuroscience (with Placement Year) (BSc)