Lecture 2 - Need for Analysis, Additional Thermodynamics Functions, State and Path Variables

# Lecture 2 - Need for Analysis, Additional Thermodynamics Functions, State and Path Variables

``` Page 1

Thermodynamics (Classical) for Biological Systems
Prof. G.K. Suraishkumar
Department of Biotechnology

Module No. #02
Lecture No. #02
Need for Analysis
State and Path Variables

Let us begin today by looking at the need for analysis of a biological system. As we all
know, engineers are typically introduced to the information or the knowledge; they
understand the knowledge toward analysis and design of the relevant system. Taking that
view for biological engineering, we can look at getting the information first,
understanding that, and using that to analyse and design systems of biological
importance. To understand this a little better, let us first consider bio process industry;
you know in the bio process industry, products of biological relevance or using
biological systems are made for the use of mankind.
In a biological process, it is easy to imagine or let us imagine that a liquid needs to be
moved from one place a to another place b; typically this movement occurs through
pipes of different sizes. And deciding on what pump to use to move the fluid from say
point a to point b is a very important design aspect in a bioprocess. As you will learn
later or you may have already done fluid flow courses; if you have done fluid flow
courses, you would already know this. One of the important aspects in deciding what
pump size to use is to know the type of flow that happens in the pipe. There are two
major types of flows; one is the laminar flow, in which it is an ordered flow in layers,
and the other is a turbulent flow, where pockets of fluid tumble over each other and flow
through a pipe.
The power requirement depends on what kind of flow we have in the pipe, to move the
fluid from one place to another. Let us say that we do not have any information about
whether the flow is laminar or turbulent; and let us say that we do not really know how
Page 2

Thermodynamics (Classical) for Biological Systems
Prof. G.K. Suraishkumar
Department of Biotechnology

Module No. #02
Lecture No. #02
Need for Analysis
State and Path Variables

Let us begin today by looking at the need for analysis of a biological system. As we all
know, engineers are typically introduced to the information or the knowledge; they
understand the knowledge toward analysis and design of the relevant system. Taking that
view for biological engineering, we can look at getting the information first,
understanding that, and using that to analyse and design systems of biological
importance. To understand this a little better, let us first consider bio process industry;
you know in the bio process industry, products of biological relevance or using
biological systems are made for the use of mankind.
In a biological process, it is easy to imagine or let us imagine that a liquid needs to be
moved from one place a to another place b; typically this movement occurs through
pipes of different sizes. And deciding on what pump to use to move the fluid from say
point a to point b is a very important design aspect in a bioprocess. As you will learn
later or you may have already done fluid flow courses; if you have done fluid flow
courses, you would already know this. One of the important aspects in deciding what
pump size to use is to know the type of flow that happens in the pipe. There are two
major types of flows; one is the laminar flow, in which it is an ordered flow in layers,
and the other is a turbulent flow, where pockets of fluid tumble over each other and flow
through a pipe.
The power requirement depends on what kind of flow we have in the pipe, to move the
fluid from one place to another. Let us say that we do not have any information about
whether the flow is laminar or turbulent; and let us say that we do not really know how
to decide whether the flow is laminar and turbulent. The way to go about or the approach
would be to visualize a flow in some fashion with itself it is quite difficult; you need
transparent pipes and so on and so forth, which may not be suitable for all fluids that are
applicable. We need to look at, what all aspects would change the type of flow involved.
Do experiments one after another to figure out, what kind of flow exists in a particular
piping system. We do not even know, what decides the kind of flow that happens in a
piping system.
Luckily for us, a lot of work has been done earlier starting from the 1900s, 1908
Reynolds did the flow visualization experiment, where he, as a result of which, we know
that there are four parameters that decide whether the flow is going to be laminar or
turbulent. The four parameters are the density of the fluid, the velocity of the fluid, the
diameter of the pipe through which the fluid is flowing, and the viscosity of the fluid.
These four parameters decide on the nature of flow; suppose we did not know this at all,
we did not have to do experiments one after another may be thousands of experiments to
arrive at the same information.
Somebody has done this, somebody has used the intuition to come up with, what you
may already know as a Reynolds number, which is nothing but the density into velocity
into diameter by the viscosity rho V D by mu. In a pipe flow situation, you may know
that if the Reynolds number is less than about 2000 or 2100, the flow is going to be
laminar, otherwise the flow is... Or above 4000 let us say, in a pipe, the flow is going to
be turbulent. What information we could get out of thousands and thousands of
experiments, is all compressed into this one single beautiful relationship, it is called the
Reynolds number. And that is the advantage in analysing something, and coming up with
a useful parameter.
We are in the process of understanding biological systems better, and we are nowhere
near that level of completeness in the case of a biological system. Let me present
something else to you to understand the need for analysis, so that the design can be much
better; and also analysis has its own benefits in terms of better and better understanding
of the system. To do that, I am going to read out parts of a paper, this paper is titled, can
a biologist fix a radio or what I learnt studying apoptosis. This paper is authored by a
person called Yuri Lazebnik; he is from cold spring harbour lab, which is a very
prestigious lab. This was published in cancer cell in 2002. I am going to read out parts of
Page 3

Thermodynamics (Classical) for Biological Systems
Prof. G.K. Suraishkumar
Department of Biotechnology

Module No. #02
Lecture No. #02
Need for Analysis
State and Path Variables

Let us begin today by looking at the need for analysis of a biological system. As we all
know, engineers are typically introduced to the information or the knowledge; they
understand the knowledge toward analysis and design of the relevant system. Taking that
view for biological engineering, we can look at getting the information first,
understanding that, and using that to analyse and design systems of biological
importance. To understand this a little better, let us first consider bio process industry;
you know in the bio process industry, products of biological relevance or using
biological systems are made for the use of mankind.
In a biological process, it is easy to imagine or let us imagine that a liquid needs to be
moved from one place a to another place b; typically this movement occurs through
pipes of different sizes. And deciding on what pump to use to move the fluid from say
point a to point b is a very important design aspect in a bioprocess. As you will learn
later or you may have already done fluid flow courses; if you have done fluid flow
courses, you would already know this. One of the important aspects in deciding what
pump size to use is to know the type of flow that happens in the pipe. There are two
major types of flows; one is the laminar flow, in which it is an ordered flow in layers,
and the other is a turbulent flow, where pockets of fluid tumble over each other and flow
through a pipe.
The power requirement depends on what kind of flow we have in the pipe, to move the
fluid from one place to another. Let us say that we do not have any information about
whether the flow is laminar or turbulent; and let us say that we do not really know how
to decide whether the flow is laminar and turbulent. The way to go about or the approach
would be to visualize a flow in some fashion with itself it is quite difficult; you need
transparent pipes and so on and so forth, which may not be suitable for all fluids that are
applicable. We need to look at, what all aspects would change the type of flow involved.
Do experiments one after another to figure out, what kind of flow exists in a particular
piping system. We do not even know, what decides the kind of flow that happens in a
piping system.
Luckily for us, a lot of work has been done earlier starting from the 1900s, 1908
Reynolds did the flow visualization experiment, where he, as a result of which, we know
that there are four parameters that decide whether the flow is going to be laminar or
turbulent. The four parameters are the density of the fluid, the velocity of the fluid, the
diameter of the pipe through which the fluid is flowing, and the viscosity of the fluid.
These four parameters decide on the nature of flow; suppose we did not know this at all,
we did not have to do experiments one after another may be thousands of experiments to
arrive at the same information.
Somebody has done this, somebody has used the intuition to come up with, what you
may already know as a Reynolds number, which is nothing but the density into velocity
into diameter by the viscosity rho V D by mu. In a pipe flow situation, you may know
that if the Reynolds number is less than about 2000 or 2100, the flow is going to be
laminar, otherwise the flow is... Or above 4000 let us say, in a pipe, the flow is going to
be turbulent. What information we could get out of thousands and thousands of
experiments, is all compressed into this one single beautiful relationship, it is called the
Reynolds number. And that is the advantage in analysing something, and coming up with
a useful parameter.
We are in the process of understanding biological systems better, and we are nowhere
near that level of completeness in the case of a biological system. Let me present
something else to you to understand the need for analysis, so that the design can be much
better; and also analysis has its own benefits in terms of better and better understanding
of the system. To do that, I am going to read out parts of a paper, this paper is titled, can
a biologist fix a radio or what I learnt studying apoptosis. This paper is authored by a
person called Yuri Lazebnik; he is from cold spring harbour lab, which is a very
prestigious lab. This was published in cancer cell in 2002. I am going to read out parts of
a paper.
Yuri Lazebnik considers the transistor radio, something that existed a long time ago, but
I guess, he relates to that a lot better. He considers a transistor radio to be equivalent to
the cell. The particular aspect that he is going to consider is an old broken transistor
radio. And the objective here is to fix the radio or to repair the radio, so that it functions
properly. Therefore, we can consider this radio to be equivalent to a human being or a
cell to begin with; something is wrong, and we need to fix it, so that it functions
properly.
Reading from this paper, some parts of it; conceptually a radio functions similarly to a
signal transaction path way in a cell, in that both convert a signal from one form to into
a 100 various components such as resistors, capacitors and transistors, which is
comparable to the number of molecules in a reasonably complex signal transduction
pathway in a cell. If we take a biological way of looking at things right now, the way a
biologist would look at it; he gives the some of the ways, in which a biologist would
approach this problem.
Biologist as I am talking of a classical experimental biologist, and I am sure a lot of
people work in interdisciplinary areas now, but a classical biologist would will approach
it a certain way. And eventually all the components will be catalogued; connections
between them will be described, and the consequences of removing each component or
their combinations will be documented. Can the information that we accumulated help us
to repair the radio? The information itself is wonderful; it helps, it gives a lot more inside
into what is happening, but is it good enough to repair the radio, is the question. The
answer is, most likely no; unless there is a certain piece of luck that helps you in setting
right the radio or the cell.
Coming back to this paper, yet we know with near certainty that an engineer could fix
the radio; what makes the difference? I think it is the languages that these two groups
use. It is common knowledge that the human brain can keep track of only so many
variables. It is also common experience that once the number of components in a system
reaches a certain threshold understanding the system without formal analytical tools
requires geniuses; who are so rare even outside biology. In engineering, this scarcity of
Page 4

Thermodynamics (Classical) for Biological Systems
Prof. G.K. Suraishkumar
Department of Biotechnology

Module No. #02
Lecture No. #02
Need for Analysis
State and Path Variables

Let us begin today by looking at the need for analysis of a biological system. As we all
know, engineers are typically introduced to the information or the knowledge; they
understand the knowledge toward analysis and design of the relevant system. Taking that
view for biological engineering, we can look at getting the information first,
understanding that, and using that to analyse and design systems of biological
importance. To understand this a little better, let us first consider bio process industry;
you know in the bio process industry, products of biological relevance or using
biological systems are made for the use of mankind.
In a biological process, it is easy to imagine or let us imagine that a liquid needs to be
moved from one place a to another place b; typically this movement occurs through
pipes of different sizes. And deciding on what pump to use to move the fluid from say
point a to point b is a very important design aspect in a bioprocess. As you will learn
later or you may have already done fluid flow courses; if you have done fluid flow
courses, you would already know this. One of the important aspects in deciding what
pump size to use is to know the type of flow that happens in the pipe. There are two
major types of flows; one is the laminar flow, in which it is an ordered flow in layers,
and the other is a turbulent flow, where pockets of fluid tumble over each other and flow
through a pipe.
The power requirement depends on what kind of flow we have in the pipe, to move the
fluid from one place to another. Let us say that we do not have any information about
whether the flow is laminar or turbulent; and let us say that we do not really know how
to decide whether the flow is laminar and turbulent. The way to go about or the approach
would be to visualize a flow in some fashion with itself it is quite difficult; you need
transparent pipes and so on and so forth, which may not be suitable for all fluids that are
applicable. We need to look at, what all aspects would change the type of flow involved.
Do experiments one after another to figure out, what kind of flow exists in a particular
piping system. We do not even know, what decides the kind of flow that happens in a
piping system.
Luckily for us, a lot of work has been done earlier starting from the 1900s, 1908
Reynolds did the flow visualization experiment, where he, as a result of which, we know
that there are four parameters that decide whether the flow is going to be laminar or
turbulent. The four parameters are the density of the fluid, the velocity of the fluid, the
diameter of the pipe through which the fluid is flowing, and the viscosity of the fluid.
These four parameters decide on the nature of flow; suppose we did not know this at all,
we did not have to do experiments one after another may be thousands of experiments to
arrive at the same information.
Somebody has done this, somebody has used the intuition to come up with, what you
may already know as a Reynolds number, which is nothing but the density into velocity
into diameter by the viscosity rho V D by mu. In a pipe flow situation, you may know
that if the Reynolds number is less than about 2000 or 2100, the flow is going to be
laminar, otherwise the flow is... Or above 4000 let us say, in a pipe, the flow is going to
be turbulent. What information we could get out of thousands and thousands of
experiments, is all compressed into this one single beautiful relationship, it is called the
Reynolds number. And that is the advantage in analysing something, and coming up with
a useful parameter.
We are in the process of understanding biological systems better, and we are nowhere
near that level of completeness in the case of a biological system. Let me present
something else to you to understand the need for analysis, so that the design can be much
better; and also analysis has its own benefits in terms of better and better understanding
of the system. To do that, I am going to read out parts of a paper, this paper is titled, can
a biologist fix a radio or what I learnt studying apoptosis. This paper is authored by a
person called Yuri Lazebnik; he is from cold spring harbour lab, which is a very
prestigious lab. This was published in cancer cell in 2002. I am going to read out parts of
a paper.
Yuri Lazebnik considers the transistor radio, something that existed a long time ago, but
I guess, he relates to that a lot better. He considers a transistor radio to be equivalent to
the cell. The particular aspect that he is going to consider is an old broken transistor
radio. And the objective here is to fix the radio or to repair the radio, so that it functions
properly. Therefore, we can consider this radio to be equivalent to a human being or a
cell to begin with; something is wrong, and we need to fix it, so that it functions
properly.
Reading from this paper, some parts of it; conceptually a radio functions similarly to a
signal transaction path way in a cell, in that both convert a signal from one form to into
a 100 various components such as resistors, capacitors and transistors, which is
comparable to the number of molecules in a reasonably complex signal transduction
pathway in a cell. If we take a biological way of looking at things right now, the way a
biologist would look at it; he gives the some of the ways, in which a biologist would
approach this problem.
Biologist as I am talking of a classical experimental biologist, and I am sure a lot of
people work in interdisciplinary areas now, but a classical biologist would will approach
it a certain way. And eventually all the components will be catalogued; connections
between them will be described, and the consequences of removing each component or
their combinations will be documented. Can the information that we accumulated help us
to repair the radio? The information itself is wonderful; it helps, it gives a lot more inside
into what is happening, but is it good enough to repair the radio, is the question. The
answer is, most likely no; unless there is a certain piece of luck that helps you in setting
right the radio or the cell.
Coming back to this paper, yet we know with near certainty that an engineer could fix
the radio; what makes the difference? I think it is the languages that these two groups
use. It is common knowledge that the human brain can keep track of only so many
variables. It is also common experience that once the number of components in a system
reaches a certain threshold understanding the system without formal analytical tools
requires geniuses; who are so rare even outside biology. In engineering, this scarcity of
geniuses is compensated at least in part by a formal language that successfully unites the
efforts of many individuals; that is achieving the desired effect.
Very nicely put here; let me read it again. In engineering, the scarcity of geniuses is
compensated, at least in part by a formal language that successfully unites the efforts of
many individuals, thus achieving a desired effect. The language that is relevant is
mathematics; and the tools that are relevant for understanding the systems, as we are
going to look at are thermo dynamics, may be transport aspects, fluxes and forces and so
on, and other relevant things. In this course, we will off course look at one aspect of
thermodynamics, which can be used to analyse biological systems. When we finished up
in the last class, we had reviewed some of the principles that we already knew some of
the concepts that we already knew in thermodynamics, from your earlier classes may be
in your school or in the first year of engineering.
And we are going to take things further here. And one of the important things that we
considered was classical thermodynamics verses statistical thermodynamics. We said
that classical thermodynamics is very good to apply in the continuum regime, where
individual molecules are not really important; whereas statistical thermodynamics is a lot
more complete, and it gains better relevance, when it is applied to non continuum
systems. With that, let us move forward here. Let us begin module 2; module 2, we will
look at additional useful thermodynamic functions.
(Refer Slide Time: 11:28)

Page 5

Thermodynamics (Classical) for Biological Systems
Prof. G.K. Suraishkumar
Department of Biotechnology

Module No. #02
Lecture No. #02
Need for Analysis
State and Path Variables

Let us begin today by looking at the need for analysis of a biological system. As we all
know, engineers are typically introduced to the information or the knowledge; they
understand the knowledge toward analysis and design of the relevant system. Taking that
view for biological engineering, we can look at getting the information first,
understanding that, and using that to analyse and design systems of biological
importance. To understand this a little better, let us first consider bio process industry;
you know in the bio process industry, products of biological relevance or using
biological systems are made for the use of mankind.
In a biological process, it is easy to imagine or let us imagine that a liquid needs to be
moved from one place a to another place b; typically this movement occurs through
pipes of different sizes. And deciding on what pump to use to move the fluid from say
point a to point b is a very important design aspect in a bioprocess. As you will learn
later or you may have already done fluid flow courses; if you have done fluid flow
courses, you would already know this. One of the important aspects in deciding what
pump size to use is to know the type of flow that happens in the pipe. There are two
major types of flows; one is the laminar flow, in which it is an ordered flow in layers,
and the other is a turbulent flow, where pockets of fluid tumble over each other and flow
through a pipe.
The power requirement depends on what kind of flow we have in the pipe, to move the
fluid from one place to another. Let us say that we do not have any information about
whether the flow is laminar or turbulent; and let us say that we do not really know how
to decide whether the flow is laminar and turbulent. The way to go about or the approach
would be to visualize a flow in some fashion with itself it is quite difficult; you need
transparent pipes and so on and so forth, which may not be suitable for all fluids that are
applicable. We need to look at, what all aspects would change the type of flow involved.
Do experiments one after another to figure out, what kind of flow exists in a particular
piping system. We do not even know, what decides the kind of flow that happens in a
piping system.
Luckily for us, a lot of work has been done earlier starting from the 1900s, 1908
Reynolds did the flow visualization experiment, where he, as a result of which, we know
that there are four parameters that decide whether the flow is going to be laminar or
turbulent. The four parameters are the density of the fluid, the velocity of the fluid, the
diameter of the pipe through which the fluid is flowing, and the viscosity of the fluid.
These four parameters decide on the nature of flow; suppose we did not know this at all,
we did not have to do experiments one after another may be thousands of experiments to
arrive at the same information.
Somebody has done this, somebody has used the intuition to come up with, what you
may already know as a Reynolds number, which is nothing but the density into velocity
into diameter by the viscosity rho V D by mu. In a pipe flow situation, you may know
that if the Reynolds number is less than about 2000 or 2100, the flow is going to be
laminar, otherwise the flow is... Or above 4000 let us say, in a pipe, the flow is going to
be turbulent. What information we could get out of thousands and thousands of
experiments, is all compressed into this one single beautiful relationship, it is called the
Reynolds number. And that is the advantage in analysing something, and coming up with
a useful parameter.
We are in the process of understanding biological systems better, and we are nowhere
near that level of completeness in the case of a biological system. Let me present
something else to you to understand the need for analysis, so that the design can be much
better; and also analysis has its own benefits in terms of better and better understanding
of the system. To do that, I am going to read out parts of a paper, this paper is titled, can
a biologist fix a radio or what I learnt studying apoptosis. This paper is authored by a
person called Yuri Lazebnik; he is from cold spring harbour lab, which is a very
prestigious lab. This was published in cancer cell in 2002. I am going to read out parts of
a paper.
Yuri Lazebnik considers the transistor radio, something that existed a long time ago, but
I guess, he relates to that a lot better. He considers a transistor radio to be equivalent to
the cell. The particular aspect that he is going to consider is an old broken transistor
radio. And the objective here is to fix the radio or to repair the radio, so that it functions
properly. Therefore, we can consider this radio to be equivalent to a human being or a
cell to begin with; something is wrong, and we need to fix it, so that it functions
properly.
Reading from this paper, some parts of it; conceptually a radio functions similarly to a
signal transaction path way in a cell, in that both convert a signal from one form to into
a 100 various components such as resistors, capacitors and transistors, which is
comparable to the number of molecules in a reasonably complex signal transduction
pathway in a cell. If we take a biological way of looking at things right now, the way a
biologist would look at it; he gives the some of the ways, in which a biologist would
approach this problem.
Biologist as I am talking of a classical experimental biologist, and I am sure a lot of
people work in interdisciplinary areas now, but a classical biologist would will approach
it a certain way. And eventually all the components will be catalogued; connections
between them will be described, and the consequences of removing each component or
their combinations will be documented. Can the information that we accumulated help us
to repair the radio? The information itself is wonderful; it helps, it gives a lot more inside
into what is happening, but is it good enough to repair the radio, is the question. The
answer is, most likely no; unless there is a certain piece of luck that helps you in setting
right the radio or the cell.
Coming back to this paper, yet we know with near certainty that an engineer could fix
the radio; what makes the difference? I think it is the languages that these two groups
use. It is common knowledge that the human brain can keep track of only so many
variables. It is also common experience that once the number of components in a system
reaches a certain threshold understanding the system without formal analytical tools
requires geniuses; who are so rare even outside biology. In engineering, this scarcity of
geniuses is compensated at least in part by a formal language that successfully unites the
efforts of many individuals; that is achieving the desired effect.
Very nicely put here; let me read it again. In engineering, the scarcity of geniuses is
compensated, at least in part by a formal language that successfully unites the efforts of
many individuals, thus achieving a desired effect. The language that is relevant is
mathematics; and the tools that are relevant for understanding the systems, as we are
going to look at are thermo dynamics, may be transport aspects, fluxes and forces and so
on, and other relevant things. In this course, we will off course look at one aspect of
thermodynamics, which can be used to analyse biological systems. When we finished up
in the last class, we had reviewed some of the principles that we already knew some of
the concepts that we already knew in thermodynamics, from your earlier classes may be
in your school or in the first year of engineering.
And we are going to take things further here. And one of the important things that we
considered was classical thermodynamics verses statistical thermodynamics. We said
that classical thermodynamics is very good to apply in the continuum regime, where
individual molecules are not really important; whereas statistical thermodynamics is a lot
more complete, and it gains better relevance, when it is applied to non continuum
systems. With that, let us move forward here. Let us begin module 2; module 2, we will
look at additional useful thermodynamic functions.
(Refer Slide Time: 11:28)

We also saw during the review that the consequences of the 0
th
law if you if you recall
what 0
th
law was f x is an thermal equilibrium with z, y another body in thermal
equilibrium with z, then separately they are in thermal equilibrium with z, then they are
in thermal equilibrium with each other. And what came out as a consequence of the 0
th

law, was temperature. What came out of the first law, which essentially related the
energy, that energies, that cross the system boundaries to the energy changes that happen
inside the system; that give rise to the first law. And the consequence of the first law was
the thermodynamic property called internal energy, which is represented by the symbol
U.
The consequence of the second law, which essentially gave us a means for the
directionality of the process is, what we saw in the review was the thermodynamic
quantity entropy, which is represented by the letter S. These three thermodynamics
properties T, U and S along with pressure and volume or specific volume are actually
sufficient to describe the thermodynamics or thermodynamics relationship of any system.
Nevertheless for ease of use in certain applications, say processes at constant temperature
or at constant pressure or at constant specific volume and so on and so forth. We could
derive certain other thermodynamics variables that will turn out be easier to use. And let
us define some other, some such thermodynamic properties next.
(Refer Slide Time: 13:46)

The first thermodynamic property that we are going to additional thermodynamic
```