# Biothermodynamics

## Objectives

**Learning objectives**

• Develop problem solving skillso Learn when and how to use how to solve thermodynamics problems

• Basic concepts of thermodynamicso

Laws of thermodynamics: zero, first, second, third

o Open and closed systems, pure substances and mixtures

o Specific heat, enthalpy, entropy

o The system in equilibrium and not equilibrium

Thermodynamic Potentials

• Relationship between these thermodynamic concepts and biological systems

**Transversal Competencies**

• Development of scientific reasoning; Analysis and resolution of problems; Connection to concepts and instruments of other curricular units such as Mathematics.

## General characterization

##### Code

12573

##### Credits

6.0

##### Responsible teacher

António Alberto Dias

##### Hours

Weekly - 5

Total - 67

##### Teaching language

Português

### Prerequisites

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

### Bibliography

1) Thermodynamics, James H. Luscombe, 2018 CRC Press

2) Modern thermodynamics: from heat engines to dissipative structures, Dilip Kondepudi, Ilya Prigogine, 2015 John Wiley & Sons, Ltd.

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

4) Physical Chemistry for the Life Sciences, Peter Atkins, Julio de Paula, 2006, Oxford University Press.

### 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. Active participation in class requires enrollment in the theoretical shift, T.

2. Theoretical classes have a teaching contact period of 2.5 hours/week, divided into two classes per week.

3. At the beginning of the semester, a provisional schedule of classes and tests is made available in the clip.

4 The assessment of this component is carried out through a knowledge test or exam. Within the scope of continuous assessment, 2 tests will be carried out throughout the semester, whose classification is rounded to the nearest tenth.

5. The T component classification (CT) is the arithmetic mean, rounded to the nearest unit, of the marks obtained in the tests or the final exam classification.

6. The student who obtains a CT classification equal to or greater than 10 values obtain approval in the theoretical component.

**Article 2 - Theoretical-Practical Component - TP**

1. Theoretical-practical classes are mandatory, with attendance records, in order to obtain attendance. Students who have obtained attendance are exempt from this component, but may ask the teacher of the shift to attend classes.

2. The duration of Practical classes is 1.5 hours/week.

3. At the beginning of the semester, a provisional schedule of classes is made available.

4. In these classes, problems on the subject taught in the theoretical classes will be discussed and solved.

5.Students must manage the possibility of not being able to attend 1/3 of the classes in order to be able to use these absences for eventual commitments or imponderable situations, including occasional situations of illness.

**Article 3 - Practical Component - P**

1. Practical classes are mandatory, with attendance registration, in order to obtain attendance. Students who have obtained attendance are exempt from this component.

2. The duration of the practical classes is 2 hours and they will run every two weeks.

3. In the first practical class of each shift, laboratory work groups are formed (no more than 2 students per group); a review is carried out on the analysis of results; and the planning of practical classes is presented.

4. The performance of each laboratory work and respective mini-report is classified from 0 to 20 values. Absence from class or non-delivery of report is classified with zero values.

5.The student who obtains an average grade in the mini-reports, MR, rounded to the nearest unit, greater than or equal to ten values, is approved in the laboratory component.

6. The student approved in the practical component has access to a practical test, Tp, at the end of the semester, individual and without consultation, which may involve questions from all the works planned for their group and the contents related to the analysis of results.

7. The practical component score, CP, is rounded to the nearest unit, and is 70% of the MR score plus 30% of the score obtained in Tp.

**Article 4 - Attendance**

1. The student who participates in at least 2/3 of the TP classes and obtains approval in the P component, obtain frequency in this Curricular Unit (UC).

2. The list of students who attended in previous years will be on CLIP under "Support Documentation > Others, until the end of the first week of classes.

**Article 5 - Approval**

1. The student with frequency and who obtains a CT grade greater than or equal to ten values, obtain approval in this UC.

**Article 6 - Final Classification**

1. The final classification (CF) is the result of the following expression approximated to unity: CF = CT×0.7 + CP×0.3

2. If the final classification is higher than 16, the student is admitted to an additional test (eg oral).

3. In the additional test, the student can raise or lower his classification, with a guarantee of a minimum grade of 16 values.

4. The absence of the additional test translates the acceptance by the student of the final grade of 16 values.

**Article 7 - Grade Improvement**

1. The student who intends to improve his grade must comply, for this purpose, with the legal formalities of registration.

2. The student who obtains a final grade, by improvement, greater than 16 values is subject to the conditions described in points 2, 3 and 4 of Article 6.

**Article 8 - Conduct in Class**

1. In order for everyone to benefit from the learning experience, every student is required to respect the following in class:

The. Punctuality: Must be present in the classroom at the start of class. The teacher may prevent entry for delays greater than 5 minutes;

B. Class preparation and participation in discussions: Active participation requires each student to prepare the material presented and discussed in class, and to contribute positively to the scientific discussions of the topics.

**Article 9 - Tests and Examination**

1. Each test will essentially cover all the subjects taught in Theoretical classes until the class before the test.

2. Although the assessment in the tests is not cumulative, and due to the nature of the subjects covered in this UC, it is not excluded that an assessment element relies on knowledge regarding the subject assessed in a previous element(s).

3. The timetable and rooms for the tests and exams will be published in CLIP, on the day of the test.

4. Each student can only have with him/her during the assessment test:

A. Pen;

B. Identification document with photograph;

C. Scientific calculating machine, non-programmable and non-graphical.

5. During the tests, it is not allowed to consult any personal or other elements, beyond the form distributed with the test.

6. It is not allowed to unstaple the sheets of statements.

7. The race will be canceled if paragraphs 4, 5 or 6 are not satisfied.

8. Fraud situations, at any time of evaluation, will be treated as indicated in the regulation of knowledge evaluation of this Faculty.

**Article 10 - Others**

1. When contacting any teacher by e-mail, they must indicate in the “Subject” the following information: “Biothermodynamics - Name – Student No. – Subject”.

2. Questions whose answers are included in the Assessment Method or on this UC page on CLIP are not answered.

## Subject matter

**1. Basic Concepts of Thermodynamics**

System, boundary, states and their thermodynamic properties. Processes and equation of state. Thermoelastic properties. 3D and 2D diagram of thermodynamic properties. Introduction to the laws of thermodynamics. Thermodynamic potentials. Introduction to the thermodynamics of living organisms (bio); open systems and out-of-equilibrium systems.

**2. First Law of Thermodynamics**

Forms of energy and internal energy. Heat, calorimetry and specific heats of gases. Work. First Law. Enthalpy and Latent Heat. Internal energy equations. Adiabatic versus Isothermal. 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. Second Law of Thermodynamics**

Spontaneous process. Irreversibility measure – Entropy. Reversible process. Entropy calculation. Classical entropy statements. Carnot''s Theorem. Thermodynamic temperature scale. TS diagram. Clausius inequality. Maximum work. Fundamental relationship of thermodynamics. TdS equations and other energy equations. Statistical entropy. Application in biological systems.

**5. Power and Cooling Devices**

Carnot and Sterling machines. Rankine cycle. Heat Pump and Refrigeration Machine

**6. Thermodynamic Potentials**

Internal energy and enthalpy. Helmholtz energy. Gibbs energy HT and GT diagrams. Application in closed system and with electromagnetic fields; and with change in composition. Maxwell Relations.

**7. Processes and Third Law of Thermodynamics**

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**

Gas, liquid, solid and phase transition analysis. 1st order phase transition and others. Gibbs phase equilibrium rule. Clausius-Clapeyron equation. Gibbs-Duhem equation Pure substances and mixtures. Gibbs energy and heat capacity at constant pressure.

**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. Non-Equilibrium Thermodynamics**

Non-equilibrium thermodynamics – Onsager relations. Bio organism – non-equilibrium thermodynamic system. Bio applications.