Applied Photophysics Chirascan LD User manual

User Manual
Chirascan Couette Cell LD Accessory
Applied Photophysics Limited
21 Mole Business Park
Leatherhead
Surrey
KT22 7BA
United Kingdom
Tel: [phone]
Fax: [phone]
Email: [e-mail]
Applied Photophysics, Inc.
100 Cummings Center
Suite 440-C
Beverly
MA 01915
United States
Tel: [phone]
Email: [e-mail]
www.photophysics.com

Document 4207Q258 V3.00 January 2018 Page 2 of 30
Chirascan Couette Cell LD Accessory User Manual
This document contains important safety information. Read this document and the
Chirascan V100 Spectrometer User Manual before attempting to install or use the
Couette Cell LD Accessory. Failure to do so could result in death or serious injury.

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Chirascan Couette Cell LD Accessory User Manual
CONTENTS
CONTENTS........................................................................................................................................................3
USE OF THIS DOCUMENT ...............................................................................................................................4
HAZARD AND OTHER INDICATORS ...............................................................................................................5
ESSENTIAL SAFETY INFORMATION...............................................................................................................6
CHIRASCAN COUETTE CELL LD ACCESSORY INSTALLATION AND OPERATIONAL REQUIREMENTS 7
GLOSSARY........................................................................................................................................................8
1 INTRODUCTION.............................................................................................................................................9
2 PREPARATION.............................................................................................................................................12
2.1 Removing the installed accessories ...................................................................................................12
2.2 LD calibration......................................................................................................................................12
2.3 References..........................................................................................................................................16
3 THE COUETTE CELL LD ACCESSORY......................................................................................................17
3.1 Components of the Couette Cell LD Accessory .................................................................................17
3.2 Installing the Couette Cell LD Accessory............................................................................................18
3.2.1 Installing the accessory body ............................................................................................................ 18
3.2.2 Temperature control connections .................................................................................................... 19
3.3 The Couette cell..................................................................................................................................20
3.3.1 Components of the Couette cell ....................................................................................................... 20
3.3.2 Mounting the rotor assembly ........................................................................................................... 21
3.3.3 Loading the sample and mounting the stator ................................................................................... 22
3.3.4 Checking the sample ......................................................................................................................... 23
3.4 Making Linear Dichroism measurements using the accessory ..........................................................23
3.4.1 The Chirascan Pro-Data control software ......................................................................................... 23
3.4.2 The SmartMotor control software .................................................................................................... 23
3.4.3 The Command Pane .......................................................................................................................... 24
3.4.4 Taking a baseline. .............................................................................................................................. 25
3.5 Making circular dichroism measurements using the accessory .........................................................26
3.5.1 Making a CD measurement using the Couette cell ........................................................................... 26
3.5.2 Making a CD measurement using a rectangular cell ......................................................................... 26
3.6 Other experimental considerations.....................................................................................................27
3.7 Example: Calf thymus DNA ................................................................................................................28
3.8 Dismantling and cleaning....................................................................................................................29
3.9 References..........................................................................................................................................29
4 MAINTENANCE AND STORAGE .................................................................................................................30

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Chirascan Couette Cell LD Accessory User Manual
USE OF THIS DOCUMENT
This document is intended to inform the operator of Applied Photophysics Couette Cell LD Accessory on its
design, installation and operation with a Chirascan V100 Spectrometer, and this document should be used in
conjunction with the User Manual applicable to the spectrometer. It is assumed that the user of this document
is familiar with the operation of the Chirascan spectrometer, and with Applied Photophysics Pro-Data software.
In particular it is assumed that the user is familiar with the hazards associated with the operation of the
spectrometer, and has read the hazard and other safety information contained in its User Manuals.
The information in this document is subject to change without notice and should not be construed as a
commitment by Applied Photophysics, who accept no responsibility for errors that may appear herein. This
document is believed to be complete and accurate at the time of publication, and in no event shall Applied
Photophysics be held responsible for incidental or consequential damages with or arising from the use of this
document.
COPYRIGHT 2018 APPLIED PHOTOPHYSICS LIMITED. ALL RIGHTS RESERVED. THIS DOCUMENT
OR PARTS THEREOF SHALL NOT BE REPRODUCED IN ANY FORM WITHOUT THE WRITTEN
PERMISSION OF THE PUBLISHER.
THE SOFTWARE PROVIDED WITH THE CHIRASCAN AND ITS ACCESSORIES (PRO-DATA CHIRASCAN,
PRO-DATA VIEWER, ETC.) IS THE PROPERTY OF APPLIED PHOTOPHYSICS LIMITED AND IS
SUPPLIED UNDER LICENSE. APPLIED PHOTOPHYSICS IS WILLING TO LICENSE THE SOFTWARE
ONLY UPON THE CONDITION THAT THE LICENSEE ACCEPTS ALL THE TERMS CONTAINED IN THE
LICENSE AGREEMENT. THESE INCLUDE THAT THE LICENSEE MAY NOT SELL, RENT, LOAN OR
OTHERWISE ENCUMBER OR TRANSFER LICENSED SOFTWARE IN WHOLE OR IN PART TO ANY
THIRD PARTY. FOR A FULL COPY OF THE LICENSE PLEASE CONTACT APPLIED PHOTOPHYSICS OR
SEE THE SOFTWARE INSTALLATION DISK.
Chirascan is a trademark of Applied Photophysics Limited.
All other trademarks or registered trademarks are the sole property of their respective owners

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Chirascan Couette Cell LD Accessory User Manual
HAZARD AND OTHER INDICATORS
HAZARD INDICATORS USED IN THIS DOCUMENT
The sign to the left is used to indicate a hazardous situation, which, if not avoided, could result
in death or serious injury.
The sign to the left is used to indicate a hazardous situation, which, if not avoided, could result
in minor or moderate injury.
OTHER INFORMATORY INDICATORS USED IN THIS DOCUMENT
The sign to the left is used to indicate a situation which, if not avoided, could result in damage
to the instrument.
HAZARD INDICATORS USED ON THE SPECTROMETER OR ITS ACCESSORIES
Note that these hazard indicators may be either colored as below or as black and white.
The sign to the left is a general hazard indicator, indicating the presence of a hazard that is either
described by text accompanying the sign or in this User Manual.
The sign to the left is a high voltage hazard indicator.
The sign to the left is a flammable hazard indicator

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Chirascan Couette Cell LD Accessory User Manual
ESSENTIAL SAFETY INFORMATION
MAKE SURE THAT YOU HAVE READ AND UNDERSTOOD ALL THE SAFETY INFORMATION CONTAINED
IN THIS DOCUMENT BEFORE ATTEMPTING TO INSTALL OR OPERATE COUETTE CELL LD
ACCESSORY. IF YOU HAVE ANY QUESTIONS REGARDING THE OPERATION OF THE ACCESSORY,
PLEASE CONTACT APPLIED PHOTOPHYSICS TECHNICAL SUPPORT AT THE ADDRESS SHOWN ON
THE FIRST PAGE OF THIS USER MANUAL.
OBSERVE ALL SAFETY LABELS AND NEVER ERASE OR REMOVE SAFETY LABELS.
PERFORMANCE OF INSTALLATION, OPERATION OR MAINTENANCE PROCEDURES OTHER THAN
THOSE DESCRIBED IN THIS USER MANUAL MAY RESULT IN A HAZARDOUS SITUATION AND WILL
VOID THE MANUFACTURERS WARRANTY.
The Chirascan spectrometer is powered by the mains electricity supply which can produce a
shock leading to serious injury or death. Do not connect or disconnect the instrument from the
mains supply unless the supply is powered off at source. Ensure all communications and
electrical connections are made before powering on the spectrometer. Exercise care during
operation and do not operate units with their covers removed. Operate the spectrometer using
only the cables provided. Never operate a spectrometer with damaged cables.
The Photomultiplier Tube (PMT) and Large Area Photodiode (LAAPD) detectors used with the
Chirascan spectrometers operate at high voltages and can produce a shock leading to serious
injury or death. Do not connect or disconnect the detector from the spectrometer unless the
spectrometer is powered off.
Do not allow any item, including any component of the alignment jig or the a to come into
contact with the front end of the detector while the detector is connected and powered up, as
this may cause an electrical short leading to serious injury to the user and damage to the
detector.
Although the main components of the accessory are temperature rated from 5°C to 95°C,
some of the standard fittings for the circulating water are only rated to 60°C, and could fail at
higher temperatures, causing injury to the user and damage to the accessory. The standard
operating range should be taken as 5°C to 60°C. Do not use the accessory at temperatures
outside this range unless the standard fittings have been replaced with high temperature
alternatives by Applied Photophysics.
If the water pressure of the circulator used for controlling the temperature is too high, the tubing
can be forced from the connectors within the spectrometer sample housing unit. Do not exceed
an input water pressure of 1.7 bar (24 p.s.i.).
Corrosive chemical and organic solvents can cause damage to the accessory body. Do not
allow corrosive fluids to come into contact with any part of the accessory body. Do not clean
the body with organic solvents. Use only a soft cloth and water or a mild detergent solution.

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Chirascan Couette Cell LD Accessory User Manual
CHIRASCAN COUETTE CELL LD ACCESSORY INSTALLATION AND OPERATIONAL
REQUIREMENTS
Environmental and electrical requirements
The Couette Cell LD Accessory has no environmental requirements additional to those of the Chirascan
spectrometer. The accessory has a power unit that requires a separate mains electricity supply.
Bench space
The Couette Cell LD Accessory power supply has a footprint of about 260 x 260 mm and should stand to the
right of the spectrometer sample chamber.
Nitrogen purge gas
The Couette Cell LD Accessory has no purge gas requirements additional to those of the Chirascan
spectrometer.
Circulating water
For temperature control, the Couette Cell LD Accessory requires a circulating water flow rate of about 200 –
300 ml per minute. To achieve this, a pressure of approximately 0.2 –0.3 bar (3 to 4.5 p.s.i.) is needed. For
further information on suitable circulators, please contact the Applied Photophysics Technical Support
Department at the address given on the front of this User Manual.
Servicing
Servicing of the Couette Cell LD Accessory should only be undertaken by qualified personnel. If you are in any
doubt at all please contact the Applied Photophysics Technical Support Department at the address given on
the first page of this User Manual.

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Chirascan Couette Cell LD Accessory User Manual
GLOSSARY
The following abbreviations may be found in this User Manual
CD Circular dichroism
LAAPD Large area avalanche photodiode
LD Linear dichroism
PMT Photomultiplier tube
rad s-1 radians per second, a measure of angular velocity.
rps revolutions per second, a measure of rotational speed
HYPERLINKS
This document contains hyperlinks between references (for example the Contents tables, or references to
Sections or Figures in the text), and sources. To follow a link, place the cursor over the reference and use
CTRL+click. Hyperlinks in the text are indicated by underlined blue font.
.

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Chirascan Couette Cell LD Accessory User Manual
1 INTRODUCTION
The Chirascan High Shear Couette Cell LD Accessory is designed to be used with the Chirascan V100
Spectrometer. The accessory is shown in Figure 1.1.
Figure 1.1: The Applied Photophysics Couette Cell LD accessory
The accessory is usually used for linear dichroism (LD) measurements. Linear dichroism is the difference in
the absorbance of light polarized parallel and perpendicular to an orientation axis (Equation 1.1)
A = A|| - A1.1
where A is the absorbance of the linearly polarized light, and the subscripts || and indicate parallel and
perpendicular respectively. For a sample to have non-zero linear dichroism it must be anisotropic; the
anisotropy may be intrinsic, as in liquid crystals for example, or it may be induced, for example by stretching a
polymer film, by the application of an electrical field or by alignment of deformation in a shear field.
The accessory uses a Couette cell to generate a shear field. The sample is contained in the annular gap
between two concentric quartz cylinders, the outer of which, the rotor, is rotated about its cylindrical axis, while
the inner, the stator, is stationary. This arrangement is named after its originator, Maurice Couette.
A shearing motion is shown in two dimensions in Figure 1.2, where the blue rectangle, of height y, deforms to
the yellow parallelogram, with the top edge of the rectangle moving by a distance x in the direction of the
arrow. The shear strain, , is then defined as x/y, and the shear rate, γ󰇗, as d/dt, in the limit as y goes to zero
(the overdot is Isaac Newton’s original symbol for the time derivative, and is still universally used by
rheologists). The strain is therefore dimensionless, and the shear rate has dimensions of reciprocal time (s-1
in the S.I. system)

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Chirascan Couette Cell LD Accessory User Manual
Figure 1.2: Two-dimensional representation of a shearing motion
Shearing can cause large particles in the liquid to align or deform. For example rigid, rod-like, particles such
as carbon nanotubes and glass fibers, will align, whereas vesicles, micelles and flexible polymers will deform
from their equilibrium conformations, extending in the direction of shear. Linear dichroism is then used to
determine the direction of net electron transfer in an absorbed chromophore relative to the shear direction, and
thereby to the alignment direction of the absorbing species or membrane.
A schematic of the Couette cell used in the accessory is shown in Figure 1.3. In the figure, the sample is shown
in blue, the light path in violet. The black arrows indicate the standard direction of rotation of the outer cylinder,
which is anticlockwise (counterclockwise) when viewed from above.
Figure 1.3: Schematic of the Couette cell; top view is shown on the right with the light path in violet
The sample is therefore sheared between the two cylinders in the cell, at a rate proportional to the angular
velocity of the rotor, . The angular velocity is measured in radians per second (rad s-1), and is equal to 2x
the rotational speed in revolutions per second (rps). The shear rate is measured in reciprocal seconds (s-1 
1/s).
The diameter of the rotor in the cell is 9.55 mm, and of the stator is 9.05 mm; the annular gap is thus 0.25 mm,
but note that since the light passes though the sample twice, the pathlength is 0.5 mm (these dimensions may
vary slightly, but will always be known precisely).
Outer cylinder
(rotor)
Inner cylinder
(stator)
Sample
Outer cylinder
(rotor)
Inner cylinder
(stator)
Sample
Light path