Biothermodynamics

General characterization

Prerequisites

Prior approval in Mathematical Analysis II C and Biophysics is recommended.

Bibliography

A   Termodinâmica Aplicada, E.G. Azevedo, 4ª Ed., 2018, Escolar Editora.

B  Modern thermodynamics: from heat engines to dissipative structures, D. Kondepudi, I. Prigogine, 2015 John Wiley & Sons, Ltd.

C  Biothermodynamics: The Role of Thermodynamics in Biochemical Engineering, Edited by Urs von Stockar, 2013 EPFL Press.

D  Non-Equilibrium Thermodynamics For Engineers, S.Kjelstrup, J. Gross e E. Johannessen, 2ª Ed., 2017, World Scientific Publishing Ltd.

Teaching method

The BioThermodynamics curricular unit is divided into the following components: Theoretical (T); Theoretical-Practical (TP) ; and a practical component (P). Theoretical classes, T, have a duration of 2.5 hours per week (1 hour + 1:30 hours) and TP classes last 1.5 h per week. The P classes have a workload of two hours every two weeks.

The T classes serve to introduce students to the structural content of the Thermodynamics as a fundamental area. In TP classes, a discussion and resolution of exercises apply the concepts exposed in the Ts. In P laboratory classes, experimental work is carried out with the aim of verifying physical phenomena or processes described in the theoretical-practical classes and to develop laboratorial skills as well as handling relevant equipment.

General information about this discipline, such as rules, important dates, evaluation notes and other complementary information are available on the course''''''''''''''''s page in the CLIP. Documentation necessary for the realization of practical classes should be consulted in the CLIP in the folder “Protocols”. Contents and Bibliography, are also available on CLIP.

Evaluation method

Article 1 - Theoretical Component – T
1. At the beginning of the semester, a provisional schedule of theoretical classes and test dates will be provided.
2. Assessment of this component is carried out through knowledge tests or exams. As part of continuous assessment, 2 tests will be conducted throughout the semester, and the grades will be rounded to the nearest tenth.
3. The grade for the T component (CT) is the arithmetic mean, rounded to the nearest whole number, of the grades obtained in the tests or the final exam grade.
4. A student who achieves a CT grade equal to or greater than 10 points will pass the theoretical component.

Article 2 - Theoretical-Practical Component – TP
1. Theoretical-practical classes are mandatory, with attendance being recorded, for all students without prior attendance.
2. Justifications for occasional absences are not accepted. Each student must manage the possibility of missing up to 1/3 of the classes to accommodate potential commitments or unforeseen circumstances, including occasional illness.
3. Students with prior attendance are exempt from TP classes.
4. In these classes, problems related to the material taught in theoretical classes will be discussed and solved.
5. The assessment of the theoretical-practical component (CTP) is the arithmetic mean, rounded to the nearest whole number, of the two best grades obtained in the mini-tests that will be administered randomly during the theoretical-practical classes. Absences from mini tests will result in a grade of zero.

Article 3 - Practical Component – P
1. Practical classes are mandatory for all students without prior attendance.
2. Practical classes will be held on alternating weeks, except for the first day, which will be held simultaneously for both groups. If a group member does not attend the class, they will receive a zero grade.
3. In the first practical class, the laboratory groups (2 students per group) will be formed, a review of result analysis will be conducted, and the class schedule will be presented.
4. Preparation for each practical class is graded from 0 to 5 points. The execution of each laboratory task and the corresponding mini report is graded from 0 to 15 points. Absence from class or failure to submit a report result in a zero grade. Each task will be given a MR grade, from 0 to 20 points (preparation and mini-report grades).
5. A student who achieves an average grade of the practical tasks, CP, rounded to the nearest whole number, of 10 points or more, will pass the practical component.

Article 4 - Attendance
1. A student who attends at least 2/3 of the theoretical-practical classes and passes the practical component, CP ≥ 10, will be granted attendance.
2. The list of students with prior attendance in previous years will be available on CLIP in "Supporting Documents > Others" until the end of the first week of classes.

Article 5 - Final Grade
1. The final grade (CF) is calculated using the following formula, rounded to the nearest whole number:
o CF = CT × 0.6 + CTP × 0.1 + CP × 0.3   (attendance in the current academic year)
o CF = CT × 0.7 + CP × 0.3                        (attendance in the previous school year)
2. Any student with attendance and a final grade equal to or greater than 10 points will pass this Course Unit.
3. If the final grade is greater than 16 points, the student may be required to take an additional exam (e.g., oral).
4. Failure to attend the additional exam implies the student''s acceptance of the final grade of 16 points.

Article 6 - Grade Improvement
1. A student wishing to improve their grade must complete the necessary legal registration procedures.
2. If the final grade after improvement is greater than 16 points, the student will be subject to the conditions described in points 3 and 4 of Article 5.

Article 7 - Classroom Conduct
1. To ensure that everyone benefits from the learning experience, each student is expected to adhere to the following during classes: a. Punctuality: You must be present in the classroom at the start of the lesson. The lecturer may prevent entry for delays exceeding 5 minutes. The classroom is not a café, where one can enter or leave at any time. b. Unless requested by the professor, mobile phone use during class is not permitted. Photography using any device is not allowed.

Article 8 - Assessment Period
1. Each assessment test will primarily focus on the material covered up to the last theoretical class, which has not yet been assessed.
2. Although the tests are not cumulative, due to the nature of the topics covered in this course (UC), it is not excluded that an assessment may rely on knowledge of material previously evaluated.
3. The schedule and room assignments for the tests or exam will be published on CLIP on the day of the assessment.
4. Registration for tests is mandatory and must be done exclusively through the CLIP platform. The registration period begins two weeks before the test and ends one week prior. If a registered student does not arrive in the exam room within the first fifteen minutes, they will be considered as not registered.
5. Unregistered students may only take the test if, fifteen minutes after the start of the exam, there are available seats and test booklets for all interested students.
6. The test will end at the same time for all students (both registered and unregistered).
7. During the test, each student is prohibited from having with them a mobile phone, watch, or any electronic communication device. Failure to comply with this point will always be treated as fraud.
8. Upon entering the exam room, students must have the following items, which they may take to their exam desk: identification card, scientific calculator (non-programmable and non-graphical), and writing materials (only answers written in pen, with no traces of pencil, will be graded). All other student belongings must be placed in the area of the room indicated by the invigilating lecturer.
9. During the test, consulting any personal materials or those of others is not permitted. Failure to comply with this point will always be treated as fraud.
10 Test sheets are not required for the assessment. Each student will be provided with a test booklet, which must not be unbound, and a formula sheet.
11. Any instances of fraud at any point during the assessment will be handled in accordance with the regulations for knowledge assessment of this Faculty.

Article 9 - Miscellaneous
1. When contacting any professor via email, you must include the following in the "Subject": "BioT - Name - Student Number - Subject."
2. Questions whose answers are found in the Assessment Method or on the CLIP page of this Course Unit will not be answered

Subject matter

1. Concepts of Thermodynamics
System, boundary, states and their thermodynamic properties. Processes and equation of state. Thermoelastic properties. State of balance. Equation of State. Phase equilibrium diagram and thermodynamic components. Zeroth Law of Thermodynamics. Introduction to the 1st Law; 2nd Law and 3rd Law. Thermodynamic potentials. Introduction to thermodynamics of living organisms (bio); open systems and systems out of equilibrium.

2. First Law
Forms of energy and internal energy. Heat, calorimetry and specific heats of gases. Configuration work. Other forms of work: magnetic work; electrical work; surface work. First Law. Enthalpy and Latent Heat. Influence of pressure and temperature on enthalpy. Kirchhoff''''s Law. Enthalpy change of a reaction. Internal energy equations. Poisson equation and Mayer relation. Adiabatic versus isothermal process. Application in bio system.

3. Heat Transfer Processes
Conduction – Fourier''''''''s Law. Convection – Newton''''''''s Law of Cooling. Radiation – Stefan-Boltzmann Law. Metabolism and thermoregulation of bio systems. 

4. Irreversibility and Second Law
Spontaneous process. Measure of irreversibility – Entropy. Reversible process. entropy calculation. Classic entropy statements. Properties of heat engines: Carnot engine. Carnot''''s theorem. Thermodynamic temperature scale. Ts diagram. Clausius inequality. Maximum work. Fundamental relationship of thermodynamics. Tds equations and other energy equations. Influence of pressure and temperature on entropy Maximum work. Entropy and equilibrium criterion. Statistical interpretation of entropy. Microstates and entropy configurations. Boltzmann distribution. Application in bio systems.

5. Power and Cooling Devices
Carnot and Sterling machines. Rankine cycle. Heat Pump and Refrigeration Machine

6. Thermodynamic Potentials
Internal energy, enthalpy, Helmholtz energy and Gibbs energy in a non-cyclic reversible process. hT and gT diagrams. Application in closed system with alteration of composition. Maxwell relations. Gibbs-Duhem equation. Gibbs-Helmholtz equation.

7. Thermodynamics Processes and Third Law
Dulong-Petit Law. Einstein Model. Debye''''''''s Law. Enthalpy variation with temperature – Kirchhoff''''''''s Law. Pressure effect on enthalpy. Gibbs energy and entropy of the process. Third Law.

8. Equilibrium Thermodynamics - Simple and compound system
Gas, liquid, solid and phase transition analysis; graphic representation. 1st order phase transition and others. Gibbs phase equilibrium rule. Clausius-Clapeyron equation. Simple system thermodynamics and mixtures. Gibbs energy and heat capacity at constant pressure. Simple ideal gas properties and mixtures. Dalton''''s Law. Non-ideal gases - equations of state. Van der Walls fluid. Formation of liquid mixture: Raoult''''s Law and Henry''''s Law. Variation in thermodynamic properties in the liquid mixture. Intersection method. Regular mixture.

9. Kinetic Theory of Gases and Diffusion
Bernoulli Equation – Pressure. Average kinetic energy – Temperature. Energy Equipartition Theorem. Maxwell-Boltzmann velocity distribution. Free average route. Fluid. Archimedes and Pascal''''''''s Principles. Stationary flow. Continuity equation. Flow Bernoulli equation. Flow measurement. Diffusion and osmosis phenomena. Application to bio systems.

10. Biothermodynamics - Non-Equilibrium Thermodynamics
Flow equations. Flow-force coupling in an out-of-equilibrium system. Onsager Relations. Lost work and entropy production. Local equilibrium in simple systems. Balance equations. Total heat flow and measurable heat flow. Prigogine''''s theorem. Model for Bio system description and its parameterization.

Programs

Programs where the course is taught: