An in-depth introduction to the methodologies and key definitions essential for studying the evolution of pathogens using genomic data. Students will learn the foundational concepts that underpin molecular epidemiology.

DNA Structure: 

A comprehensive exploration of cell structure, the intricacies of DNA and RNA molecules, and a deep dive into the Central Dogma of biology. This lecture lays the groundwork for understanding genetic information.

Causes and consequences of mutations:

A detailed examination of mutations, including their definition, classification into types, an exploration of their consequences on genetic material, and an analysis of the diverse factors contributing to mutagenesis.

Principles of Classification of Micro-organisms:

A nuanced discussion on the principles governing the classification of microorganisms, emphasising both phenetic and phylogenetic relationships. Students will gain insights into the taxonomic frameworks that categorise these entities.

Microbes and Disease:

An exploration of infectious diseases, covering the spectrum from foodborne and waterborne to airborne diseases. Students will gain a broad understanding of the diverse microbial agents responsible for various health challenges.

An introduction to the diverse sequencing techniques employed in bacterial genomics. The lecture will guide students through the process of transforming raw sequencing data into a comprehensible genome, providing essential insights into genomic analyses.

Phylogenetics:

A deep dive into phylogenetic principles, including real-world examples of phylogenies, discussions on phylogenetic tree rooting and topology, applications in diverse contexts, and a critical examination of potential pitfalls in phylogenetic analyses.

Phylogenetic Inference:

Building upon the previous lecture, students will learn the practical aspects of phylogenetic inference. This includes creating alignments, understanding distance matrices, selecting appropriate substitution models, and exploring various approaches to construct phylogenetic trees, such as Neighbour-Joining, Likelihood-based methods, and Bayesian phylogenetic inference.

SARS-CoV-2 Pandemic Response:

A special guest lecture by Dr. Christopher Ruis, offering unique insights into his work during the SARS-CoV-2 pandemic response. Students will gain a first-hand understanding of applying mutational spectra and phylogenetics to decipher pathogen transmission patterns.

Final Presentations:
The culmination of the course, where students present their comprehensive understanding of molecular epidemiology and pathogen evolution. Each presentation will showcase the application of acquired knowledge and skills, providing a tangible demonstration of the course's impact on the students' analytical capabilities and scientific acumen.

We highlight the successes and difficulties of the pre-relativistic physics. The latter was very effective in predicting, for instance, the motion of the planets, but Einstein noticed what appeared to be an inconsistency between Newton’s dynamics and Maxwell’s electromagnetism. This led him to propose a new physical theory and a new transformation law for the coordinates of the same event in two different reference frames. Different observers may assign different times to the same event, a curious feature of what became known as the Lorentz transformation.

Relativistic Kinematics:

The fact that time flows at different rates in different systems of reference has interesting consequences. We shall follow a fast-moving interstellar spaceship and compare the magnitudes of time intervals, distances and velocities measured by those in the ship with the corresponding measurements made by observers at rest. In this context, we shall examine in detail the well-known Twin Paradox.

Relativistic Dynamics:

We introduce the notions of relativistic momentum and energy and study some examples of the conversion of mass into energy and vice-versa. We derive the famous formula E=mc2 and explore its implications in some physical systems.

Relativistic Optics:

The Doppler effect and the aberration of light were known phenomena in non-relativistic physics. We shall assess how Relativity modifies the classic formulas and explore some of the consequences of these changes.
Appearance of rapidly moving objects:

When taking a photograph of a moving object, all rays generated at its boundaries arrive simultaneously at the camera. If the object has a non-negligible size, light rays must then leave its surface at different times. In most instances this causes a significant distortion on the appearance of objects that move at speeds close to the speed of light. However, perhaps surprisingly, some objects keep their shape in the photographs.

The first quarter of the twentieth century is often regarded as one of the most productive periods in the history of science. We shall study the ideas of Planck, de Broglie, Heisenberg, Schrodinger, and others which culminated in 1925-1926 with the formulation of the Quantum Theory.

The postulates of Quantum Mechanics and simple applications:

We introduce the notion of wave function, quantised energy levels and solve Schrodinger’s equation for simple systems. We discuss how the equation can be applied to more complicated systems such as the hydrogen atom.

The EPR paradox and the Bohr-Einstein debate:

The new ideas were not accepted without reluctance by some, among them Einstein. In 1935, together with Podolsky and Rosen, he wrote an article in which an apparent paradox suggested that the formulation of Quantum Mechanics was incomplete. We shall discuss their reasoning and the more modern version of the paradox due to Bohm.

Bell’s Inequality:

Almost 30 years after the EPR argument was formulated, Bell wrote what has been described as one of the most important scientific works of the 20th century, in which it was shown that Quantum Mechanics could not be completed with the so-called hidden variables. We shall have a good discussion of Bell’s theorem and some of its variants, namely due to d’Espagnat.

Final Presentation

We introduce differentiation, give some simple example; we introduce sketching simple functions.

Integration 1 and differential equations 1:

We introduce integration of simple functions and the construction of differential equations using simple physical examples where possible.

Exponential and Logarithms

We introduce, learn to sketch, and learn to differentiate exponentials and logarithmic functions.

Trigonometry and Hyperbolics:

We introduce, learn to sketch, and learn to differentiate several useful trigonometric functions (including inverses and hyperbolics).

Differentiation 2:

We introduce product, quotient, and chain rule for differentiation; we introduce implicit differentiation.

We introduce integration by substitution and by parts; we introduce the integration of differential equations.

Differential equations 3:

We proceed in learning how to work with differential equations, strongly tying it back to physics wherever possible.

Complex Numbers:

We need the formalism of complex numbers to solve harder physics problems; we introduce and use the cartesian and polar forms.

Differential equations 4:

Simple harmonic oscillator physics requires a different style of solution that will use Complex Numbers.

Final Presentations

Introduction to the fundamentals of Psychology.

Methods:

The scientific method and how it applies to Psychology and Neuroscience.

Nuclear Safety and Waste disposal:

Regulatory systems, probabilistic risk assessment, waste immobilisation and disposal.

Cognitive Psychology:

Theoretical frameworks of how humans think and process information.

Cognitive Neuroscience:

Studying the brain with neuro-imaging methods and computational approaches, and what it reveals about how the mind works.

How visual information is perceived and processed in the brain: organisation of the visual systems in humans and animals, visual illusions, effects of lesions on visual experience.

Memory:

Mechanisms underlying the formation and retrieval of memories: short- versus long-term memory, memory formation, remembering, patient studies.

Attention:

Attention guides how we perceive the world: theories of attention, selective attention, active perception.

Psychopathology:

What happens when the brain and behaviour work atypically: the diagnostic process and treatments for mental disorders.

Final Presentations

a. Duration: 3 hours (2 hours of lecture; 1 hour of problems/discussion)
b. Syllabus: ideal engineering system, S-shaped curve, transition to the super-system, micro-scale interactions, systematic innovation, nature-inspired innovation, examples.
c. In-class problems: finding bio-inspired solutions for the improvement of the performance of a car.
d. Assignment: definition of ideal car and identification of barriers to innovation.

Operating Systems 1:

virtual memory for protection between processes. Address translation. Hardware acceleration.

Sustainability and Life cycle assessment:

a. Duration: 3 hours (2 hours of lecture; 1 hour of problems/discussion)
b. Syllabus: the lifecycle of a component/system, climate crisis, the concept of sustainability, multi-criteria decision analysis, the various phases of the life cycle assessment, example.
c. In-class problems: life cycle assessment of a car.
d. Assignment: multi-criteria decision analysis.

Vehicle Dynamics:

a. Duration: 3 hours (2 hours of lecture; 1 hour of problems/discussion)
b. Syllabus: forces on vehicles, wheels and forces exchanged on the ground, power requirements.
c. In-class problems: identification of engine power requirements for a given performance.
d. Assignment: computation of power required for different slope angles.

Aerodynamic forces:

a. Duration: 3 hours (2 hours of lecture; 1 hour of problems/discussion)
b. Syllabus: fundamentals of friction and drag, flow separation, streamlining, wing profiles, lift and downforce.
c. In-class problems: computations of reduction of drag (case study).
d. Assignment: sketch of an aerodynamic vehicle.

Internal Combustion Engines:

a. Duration: 3 hours (2 hours of lecture; 1 hour of problems/discussion)
b. Syllabus: overview of internal engines, fundamentals of thermodynamics, torque, power, efficiency.
c. In-class problems: coupling between an engine and a car; introduction to gear box.

a. Duration: 3 hours (2 hours of lecture; 1 hours of problems/discussion)
b. Syllabus: classification of fuels, emissions from engines, biofuels, hydrogen
c .In-class problems: quantification of carbon dioxide emitted by hydrocarbon combustion.

Electrification of cars:

a. Duration: 3 hours (2.5 hours of lecture; 0.5 hours of problems/discussion)
b. Syllabus: hybrid cars, fully electric cars, fundamentals of fuel cells and batteries, energy, and power density.
c. In-class problems: coupling between a car and an electrical powertrain.

Future vehicle concepts:

a. Duration: 3 hours (1.5 hours of lecture; 1.5 hour of problems/discussion)
b. Syllabus: autonomous vehicles, urban air mobility, electric aircraft.
c. In-class problems: conceptual design of a sustainable vehicle.

Ethics and Intellectual property:

a. Duration: 3 hours (2 hours of lecture; 1 hour of problems/discussion)
b. Syllabus: patents, copyright, registered design, trademark, confidentiality, professional ethics, engineering ethics.
c. In-class problems: patent search, patent reading.

Final presentation