TPS-2 Portable Photosynthesis System
Operator’s Manual
Version 2.02
© 2011 PP Systems. All Rights Reserved
27th May 2011
PP Systems, Inc. 110 Haverhill Road, Suite 301 Amesbury, MA 01913 U.S.A. Tel: +1 978 834-0505 Fax: +1 978 834-0545
Email: [email protected] Web Site: http://www.ppsystems.com
This page is left intentionally blank.
Table of Contents
Table of Contents
Table of Contents ...... 3 Preface ...... 5 Notice ...... 5 Documentation Conventions ...... 5 User Registration ...... 5 Service & Warranty ...... 6 Contact Information ...... 6 Unpacking Your Equipment ...... 6 System Calibration ...... 7 System Notes ...... 7 Technical Specifications ...... 8 Measurement Background and Theory ...... 10 TPS-2 Main Console ...... 12 Power Switch ...... 12 Battery Charging Socket ...... 12 Gas Analysis Connections ...... 13 Leaf Cuvette Connection ...... 13 Serial (RS232) Data Connection ...... 14 LCD Display ...... 14 Keypad ...... 15 Absorber Columns ...... 15 Soda Lime ...... 16 Envirogel ...... 16 Powering On TPS-2 ...... 17 TPS-2 Main Menu ...... 17 Measurement of Leaf Gas Exchange ...... 18 1REC (Recording) ...... 18 Warmup Delay ...... 20 Measurement Mode ...... 20 System Checks Prior to Making Measurements ...... 21 Steady-State Recording with a Leaf in the Leaf Chamber ...... 22 Variability of Plant Responses...... 23 Controlling CO2, H2O, and Light (LED) ...... 23 CO2 Control ...... 23 H2O Control ...... 24 Light Control (LED Light Unit) ...... 24 Autozero ...... 25 Differential Balance ...... 26 Single Point Diff-Bal ...... 26 Two Point Diff-Bal ...... 27 Recalculation of Data Based on Leaf Area ...... 28 Additional Main Menu Functions ...... 30
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 3 - Table of Contents
2CAL (Calibration) ...... 30 CO2 Calibration Using a Gas Cylinder ...... 30 H2O Calibration ...... 31 Factory PAR Sensor Calibration ...... 32 Setting the PAR Sensor Gain and Offset Constants ...... 32 PAR Sensor Calibration in Sunlight ...... 33 LED Calibration ...... 33 1 Point Calibration Check ...... 33 LED Scale...... 35 10 Point Calibration ...... 35 LED Initialization ...... 35 3DMP (Dump/Transfer) ...... 35 SCREEN DUMP ...... 36 DATA DUMP ...... 36 4CLR (Clear) ...... 36 5CLK (Clock)...... 36 6DIAG (Diagnostics/Initialize) ...... 37 1:DIAGNOSTICS ...... 37 2:INITIALIZE ...... 38
Using TPS-2 as a Stand-Alone CO2/H2O Analyzer ...... 39 Datalogging and Transfer Software ...... 41 Logging Data via RS232 Interface ...... 41 Transfer of Stored Data via RS232 Interface ...... 42 Data Output ...... 43 Output of Stored Records from Memory ...... 43 Maintenance ...... 44 Air Sampling Pump ...... 44 Air Sampling Pump Replacement ...... 44 Cleaning the Air Sampling Pump ...... 44 Air Inlet Filters ...... 45 12V Lead Acid Battery ...... 45 EPROM ...... 46 Absorber Columns and Desiccants ...... 47 Soda Lime Specifications ...... 47 Envirogel Specifications ...... 48 Error and Warning Displays ...... 53 Photosynthesis Equations Used in TPS-2 ...... 55 Calculations ...... 55 Symbol Definitions ...... 59 Measured Parameters ...... 59 Calculated Parameters ...... 59 Physical Constants Used in Equations ...... 60 Saturated Vapor Pressure of Water from Air Temperature ...... 60 References...... 60 TPS-2 Portable Photosynthesis System Operation Manual Revision Log .. 61
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 4 - Preface
Preface
Notice
This equipment must not be used in situations where its failure could result in injury or death.
For applications where failure of this equipment to function correctly would lead to consequential damage, the equipment must be checked for correct operation and calibration at intervals appropriate to the criticality of the situation.
PP Systems' equipment warranty is limited to replacement of defective components, and does not cover injury to persons or property or other consequential damage.
This manual is provided to help you install and operate the equipment. Every effort has been made to ensure that the information contained in this manual is accurate and complete. PP Systems does not accept any liability for losses or damages resulting from the use of this information.
It is extremely important that you take the time to review this Operator’s Manual prior to installation and operation of the equipment. Otherwise, damage may be caused which is not covered under our normal warranty policy.
This manual and the information contained in it is copyrighted to PP Systems. No part of the manual may be copied, stored, transmitted or reproduced in any way or by any means including, but not limited to, photocopying, photography, magnetic or other mechanical or electronic means, without the prior written consent of PP Systems.
Windows and Excel are registered trademarks of Microsoft.
Documentation Conventions
If viewed electronically, text marked blue acts as Hyperlinks.
User Registration
It is very important that ALL new customers register themselves with us to ensure that our user’s list is kept up to date. If you are a PP Systems’ user, please register yourself electronically on our web site at:
http://www.ppsystems.com/Register.html
Only REGISTERED users will be allowed access to our protected “Users” section of our web site. This section contains important product information including hardware/software updates, application notes, newsletters, etc.
Thank you in advance for your cooperation.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 5 - Preface
Service & Warranty
PP Systems' equipment warranty is limited to replacement of defective components, and does not cover injury to persons or property or other consequential damage.
The equipment is covered under warranty for one complete year, parts and labor included. This, of course, is provided that the equipment is properly installed, operated and maintained in accordance with written instructions (i.e. Operator's Manual).
The warranty excludes all defects in equipment caused by incorrect installation, operation or maintenance, misuse, alteration, and/or accident.
It is the responsibility of the customer to return the equipment to PP Systems or an authorized agent for repair or replacement of the defective part(s).
In order to ensure high quality, accuracy and continued success of your TPS-2 system, it is recommended that your system be returned annually to the factory (or authorized agent) for service. Annual servicing includes inspection of all internal plumbing, replacement of all "O" rings, filters and chemicals, and an electrical check and full calibration of the instrument. Leaf cuvette gaskets and tubing are replaced, and all sensors are checked and calibrated. The entire system is thoroughly serviced and calibrated by factory trained service engineers. Please consult with PP Systems or your local agent for more details regarding this service.
Contact Information
PP Systems, Inc. 110 Haverhill Road, Suite 301 Amesbury, MA 01913 U.S.A. Tel: +1 978 834-0505 Fax: +1 978 834-0545
Sales: [email protected] Support: [email protected] Service: [email protected]
Unpacking Your Equipment
It is extremely important that you check the contents of your equipment immediately upon receipt to ensure that your order is complete and that it has arrived safely. Please refer to the checklist supplied (if applicable) for a detailed list of spares and accessories that are included with your order.
DO NOT DISCARD ANY OF THE PACKAGING MATERIAL UNTIL ALL OF THE ITEMS LISTED ARE ACCOUNTED FOR.
WE RECOMMEND THAT YOU RETAIN THE ORIGINAL PACKING FOR FUTURE USE.
If you suspect that any of the items listed on the appropriate checklist are not included or damaged, you must contact PP Systems or authorized distributor immediately.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 6 - Preface
System Calibration This product is shipped as a factory calibrated system. System calibration is not required upon receipt from our factory. Familiarization with the documentation and calibration procedures is required prior to future recalibration. See section 2CAL (Calibration) on page 30 of this manual. All calibration-related questions may be made directly to PP Systems at:
System Notes
We strongly urge that each user read this manual at least once before getting started. It is also very important to observe the following notes in order to avoid accidental damage to TPS-2.
Never connect TPS-2 to a battery charger without the internal battery fitted to the unit. Only use the battery charger supplied by PP Systems. The 12V battery charger can power TPS-2 and charge the internal battery at the same time. Before changing any absorber columns, please refer to the appropriate section of the manual. The location of the columns can be found on the bottom of TPS-2 main console. TPS-2 AND WATER DO NOT MIX - do not use TPS-2 in conditions where water may be drawn into the unit. Never connect TPS-2 directly to a gas cylinder. Connection must always be via a three-way “T” or “Y” connector with one leg connected to the cylinder, one to TPS-2 and the third to a vent to atmosphere through about 30 centimeters of tubing. A flow meter may be used to show there is surplus flow. If TPS-2 does not start up when switched on, or if the pumps start but there is no display, check that the battery is fully charged. In case of queries, please quote the Eprom version and TPS-2 serial number. This information is displayed when TPS-2 is first switched on. In addition, the serial number of the main console can be located on the bottom of the instrument.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 7 - Technical Specifications
Technical Specifications Main Console
Analysis Method Non-dispersive infrared, configured as an absolute absorptiometer with microprocessor control of linearization.
Measurement Range -1 CO2: 0-2000 µmol mol (Optimal Range) 0-9999 µmol mol-1 (Max. Range)
H2O: 0-75 mb
Corrections are made for temperature, pressure and foreign gas broadening.
Precision CO2: (Absolute) < 1% at 300 ppm o H2O: (Optimal, 25 C) 1.8 to 3% from 10 and 90% RH
Stability (CO2 Analysis) Automatic Zero at regular intervals, corrects for sample cell contamination, source and detector ageing and pre-amplifier gain changes.
Control Range -1 CO2: 0-Ambient µmol mol (6 adjusting steps) H2O: 0-Dewpoint mb (4 adjusting steps)
Response Time Electrical: 0.5 seconds Display/Analog Output: 1.6 seconds Pneumatic: < 5 seconds
Air Sampling 100 cc min-1 using an integral DC pump.
RS232 Output Stored/current data output in standard ASCII format at 1200 baud.
Real Time Clock Accuracy: Better than 1 min/month at 25 oC. Operating Temperature: 0-70 oC.
Recording Options By PC or by the instrument. Automatic logging at user selectable intervals between 10 seconds and 1 hour, controlled by internal real-time clock.
Power Supply Internal, rechargeable 12V battery providing up to 8 hours continuous use.
Integral Cuvette Air Supply Unit 0-500 cc min-1 measured and controlled by a mass flow meter.
Operating Environment 0-50 oC, non-condensing. External air filtration required in dirty environments.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 8 - Technical Specifications
Housing High impact ABS plastic case.
Dimensions 29 cm W x 12.5 cm H x 20 cm D
Weight 5.2 kg.
PP Systems is continuously updating its products and reserves the right to amend product specifications without notice.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 9 - Measurement Background and Theory
Measurement Background and Theory The TPS-2 “Teaching Photosynthesis System” is a completely self-contained portable photosynthesis system for measuring CO2 assimilation (Photosynthesis and Respiration) and transpiration (water loss through plant leaf surfaces). TPS-2 has been designed specifically for use by students in schools and universities, and offers several features similar to instruments designed to satisfy exacting research standards (e.g. CIRAS-2), while greatly simplifying the measurement procedures. The system is supplied with a leaf cuvette which can be used for a wide variety of leaf types, and an LED light unit is available for use with the cuvette to provide control of light intensity using nine manual settings. In all PP Systems documentation we refer to the leaf cuvette as the PLC (Parkinson Leaf Cuvette, in recognition of its original designer/inventor, Dr. Keith Parkinson).
TPS-2 operates on the “Open System” principle. The leaf is placed in a sealed chamber at the head of the cuvette, with a window allowing illumination from a light source. A measured flow of air is passed through this leaf chamber, and the concentrations of CO2 and H2O of the air entering (reference gas) and leaving (analysis gas) are measured. Assimilation and transpiration rates are then calculated from the flow rate of air and the changes in gas concentrations.
To measure these concentrations TPS-2 uses two distinct methods:
1) A high-precision infrared gas analyzer (IRGA) measures CO2, switching between the reference and analysis gas streams by way of a solenoid valve.
2) Two dedicated H2O sensors simultaneously measure water vapor in the reference and analysis gases at their respective intake manifolds.
Though it is designed to supply ambient air to the leaf chamber, TPS-2 can also be used for CO2 response studies. It is possible to introduce high-concentration CO2 gas into the system, and then decrease the CO2 concentration in a series of steps through the TPS-2 control software. A similar provision is made in the control software for water vapor responses, e.g. by creating artificial vapor pressure deficit gradients.
CO2 and H2O Analysis Measurement Principles
Carbon dioxide absorbs infra-red radiation strongly at a wavelength of 4.26 microns. The TPS-2 IRGA uses this absorption spectrum to measure CO2 concentrations. The analyzer consists of a source of infra-red radiation (tungsten filament lamp) at one end of a highly polished, gold plated cell through which gas samples pass. At the other end of the cell is the infra-red photodetector coupled with a filter through which only infra-red radiation at 4.26 microns can pass, therefore the detector responds only to the presence of CO2.
The theoretical analysis range is from 0-100% CO2. However, in practice the absorption characteristics of gases, the absorption path lengths, infrared source intensities, detector sensitivities and the S:N (Signal to Noise) ratio of the system define the effective range. The absorption path length of TPS-2 is optimized for 2000 parts of CO2 per million parts of air – commonly referred to as parts per million by volume, or ppm. (As of 2011 Earth’s atmosphere contains 390 ppm of CO2 on average).
Temperature corrections are not required as the opti-electronics are thermostatted and the air is equilibrated to this temperature before entering the absorption cell. A built-in transducer compensates for absolute pressure changes in the cell.
In part, the excellent stability of TPS-2 is due to regular zeroing when CO2-free air (referred to as Zero) is passed through the IRGA. Zeroing minimizes the effects on span (gas sensitivity), of sample cell contamination, source (lamp) ageing, changes in detector sensitivity, amplifier gains,
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 10 - Measurement Background and Theory
and reference voltages. The TPS-2 default Zero cycle occurs every 20 minutes. The Zero reading is used to compensate for changes in the signal level. From the relationship between absorptance and concentration determined in the factory, and the current calibration factor, the sample CO2 concentration is determined.
TPS-2 measures water vapor using dual capacitive sensors. The sensors are made of silicon with Cu lead-frames, each with an integrated chip containing an amplifier, A/D converter, OTP memory and a digital processing unit. The silicon sensor is in a circuit that measures electrical capacitance. The dual sensor units are installed in the gas inlet manifold, directly in the path of the reference and analysis gas streams. In TPS-2, water vapor concentration is expressed in pressure units of mbar (1 mbar=0.1 kPa=0.001 Atm), representing the partial pressure of water vapor in the sample air mixture.
Both CO2 and H2O measurements give the absolute concentrations for the reference air, and then the difference between the reference and the analysis concentration.
The complete TPS-2 gas circuit with control valves is shown below.
Dual
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 11 - TPS-2 Main Console
TPS-2 Main Console
Power Switch TPS-2 is normally operated in the upright position with the key board/display on the upper surface (referred to in this documentation as TOP) and with the absorber columns on the side of the instrument away from the user.(referred to as BACK). For field measurements, the main console should be housed in the in the custom field carrying case with the shoulder straps adjusted as required for most comfortable operation.
There is an OFF/ON slide switch to the left of the keypad. The legend shows which direction to slide the switch to turn the instrument on or off.
Battery Charging Socket The battery charger input socket is located directly below the OFF/ON slide switch. It features a single phono jack connection for the battery charger. The system is supplied with the appropriate charger and connector. Always ensure that the charger plug is fully inserted into the charger socket when charging TPS-2.
TPS-2 can be powered from its own internal 12V battery, from an external power supply that is simultaneously recharging the internal battery, or from an external battery.
The internal battery is a 12V 7.0Ah sealed Lead-Acid battery. The exact running time of the battery will depend on its state of charge, its capacity (this declines with age) and the ambient temperature (determines the power requirement of the thermostatted cells). The battery is located inside the console case.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 12 - TPS-2 Main Console
THE INTERNAL 12V BATTERY MUST ONLY BE CHANGED AFTER TPS-2 HAS BEEN SWITCHED OFF.
During operation, when the battery voltage drops to 10.5V, TPS-2 will display a low battery warning and, if ignored, will automatically shut down shortly thereafter.
If TPS-2 does not start when switched on, check the battery.
USE ONLY THE BATTERY CHARGER/POWER SUPPLY SUPPLIED BY PP SYSTEMS AS THIS HAS THE CHARGING VOLTAGE SET FOR OPTIMUM OPERATION.
Gas Analysis Connections There are four gas inlet/outlet ports arranged on the left hand side of TPS-2:
The top port marked LINK FOR PLC is where the sample air from TPS-2’s internal smoothing air volume flows as the reference gas along a path to the leaf cuvette. Air from this port may be diverted for certain procedures, such as a user-initiated Differential Balance. For calibration, the calibration gas should be connected via a T-piece direct to this entry. When TPS-2 is being used with the cuvette, a short tube links this to the next port down, marked REF.
REF is the inlet port to the reference line of the analyzer. To ensure a smooth supply of reference air, we strongly recommend keeping the short link tube connected to the inlet directly above. The link tube is supplied as standard.
The following two gas tubes are used for connection to the leaf cuvette:
AN/PLC A is the gas inlet to the analysis line of the analyzer. The tube marked A (analysis air) on the leaf cuvette should be connected to this inlet.
PLC R is the cuvette air supply inlet. The tube marked R (reference air) on the leaf cuvette should be connected to this inlet.
A link tube is also fitted on the TPS-2 console front (near absorber column 1) for additional smoothing of the reference air (see markings on the bottom of TPS-2). When linked, the internal TPS-2 enclosure acts as a smoothing volume. If you prefer to sample air further away from the instrument, you can remove the link tube here and connect a long piece of tubing directly to the Air Supply Inlet only.
Important Note. If you connect directly to the Air Supply Inlet, you must ensure that the sampling point is shielded from any sources that may influence CO2 concentration, and that avoid intake of liquid water.
Leaf Cuvette Connection
The leaf cuvette is connected to the 15 pin D socket on the front panel marked PLC. The following pins are used:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 13 - TPS-2 Main Console
Pin 1 5V reference voltage. This must not be used for purposes other than connecting to the Betatherm 100K6 type thermistor. (See Pin 5). Pin 3 PAR input. 0-1V = 0-3,000 µmol m-2 s-1 Pin 5 Air Temperature Thermistor. A Betatherm type 100K6 thermistor is connected between here and Pin 1 to correctly read the temperature. Pin 7 +12V supply (unregulated at battery voltage) Pin 9-15 Return (0V)
The PLC D-type connector and can only be inserted in one position. Visually locate it and present the connector to the TPS-2 socket in the correct position. Push the connector firmly and secure in place.
To remove the connector, pull upwards on the plug. It is essential to pull upwards on the plug and not on the cable.
For more information on the leaf cuvette refer to Light Control (LED Light Unit) on page 24 or the PLC4(B) Leaf Cuvette Operator’s Manual ver. 2.02.
Serial (RS232) Data Connection
The PC computer connection is the 9 pin D socket on the front panel marked RS232. An RS232 data transfer cable is supplied with each system.
Only 2 pins are used :
9-Pin D Socket (on TPS-2) 9-Pin D Plug (on PC) Pin 2 – Transmit Data Pin 2 – Receive Data Pin 5 – Digital Ground Pin 5 – Signal Ground
RS232 Serial Data Format
Baud Rate 4800 Start bit 1 Data bits 8 Stop bits 2 Parity None
**** WARNING ****
Only the pins specified should be used, as other pins may have dedicated functions and damage may result if these are connected to ground, supply, or any inappropriate load.
LCD Display The LCD display has 2 rows of 16 characters. To the left of the display is a small hole that provides access to a potentiometer that controls display contrast. Contrast can be adjusted with a small screwdriver. At high temperatures, the display gets darker and may ultimately be unreadable, though TPS-2 continues working.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 14 - TPS-2 Main Console
IT IS RECOMMENDED THAT TPS-2 IS KEPT SHADED AT HIGH AIR TEMPERATURES AND HIGH SOLAR RADIATION.
Keypad All key presses should be firm and the user should wait for the instrument to respond. Some menus require entry of numeric data (e.g. recording interval) or may just change the option (e.g. recording type). Press the corresponding key to the number opposite any menu option to change that option. Where numeric data is required, a series of ???? corresponding with the number of digits required will be displayed. Leading zeroes should be entered where necessary (eg. ???? followed by entry of 0500 for 500 ppm).
Press Key To 0-9 Enter a numeric value. Y Accept (Yes) a display/value and move forward to the next display. N Terminate (No) an operation. Go back one step in the menu. 0/R Record the displayed data in memory when in the measurement mode. 4/X Toggle (Exchange) from one display (measured data) to another (calculated data) in measurement mode.
Absorber Columns TPS-2 is fitted with 4 absorber columns. Each absorber contains desiccants for controlling/absorbing CO2 or H2O. With TPS-2 in its normal upright operating position and looking left to right, the absorber columns are:
1 2 3 4
Column Desiccant For: 1 Soda Lime CO2 Control 2 Envirogel H2O Control. 3 Envirogel H2O Control 4 Soda Lime Auto-Zero Control for CO2 analyzer
Please note that the bottom of TPS-2 clearly indicates the layout and contents of all 4 absorber columns for reference purposes. To the left of Absorber Column 1 is the Air Supply Inlet and link tube for making the internal smoothing volume gas connection.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 15 - TPS-2 Main Console
For further information regarding replacement/handling of absorber columns and chemicals, refer to Absorber Columns and Desiccants on page 47.
Soda Lime
Soda lime is used to i) remove CO2 from air entering TPS-2 for zeroing the analyzer and ii) for control of CO2. It is supplied as self-indicating granules (1-2.5mm) which turn from green to brown as they become exhausted. The contents of the absorber column should be replaced when they are no more than 2/3 exhausted. Routine timely replacement of soda lime ensures accurate zeroing and good and repeatable CO2 control. Soda Lime cannot be regenerated and should be discarded after it becomes exhausted.
Envirogel Envirogel is silica gel used as self-indicating pellets (orange changing to green) for drying the air. It can be regenerated by heating in an oven if necessary (above 100° C but not exceeding 150 ºC). However, it is non-hazardous and can be easily disposed of when exhausted.
**** CAUTION ****
WASH YOUR HANDS AFTER HANDLING SODA LIME AND ENVIROGEL
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 16 - Powering On TPS-2
Powering On TPS-2 Before switching TPS-2 on, please make sure of the following:
If TPS-2 is to be used with the leaf cuvette, make sure the 15-pin D Connector is securely attached. TPS-2 will automatically detect if the cuvette is connected when switched on. Check that the reference (R) and analysis (A) tubes of the leaf cuvette are properly fitted to the corresponding ports on TPS-2, and that the necessary TPS-2 tube links are in place. Check the condition of the chemicals in the absorber columns and replace if necessary (see Absorber Columns and Desiccants on page 47). Horizontal operation of the instrument could result in air bypassing the chemical contents of the absorber columns rather than passing through them. The instrument should therefore always be used at an angle sufficient to prevent this from happening. The recommended position is vertical with the display and keypad on top. If the LED light unit is used, ensure that it is fitted properly to the cuvette head and electrically connected to the cuvette. Remember to perform a one point calibration check prior to measurements (see 1 Point Calibration Check on page 33).
Immediately after switching on TPS-2, a copyright statement is displayed, which also shows the instrument serial number and the program version number installed. This should be quoted in any queries.
After about 7 seconds the Main Menu should be displayed. (If either CHECKSUM ERROR or MEMORY CORRUPT appear, see Error and Warning Displays on page 53).
TPS-2 Main Menu After the initial messages are displayed as described in the previous section, the Main Menu will be displayed as follows:
1REC 2CAL 3DMP 4CLR 5CLK 6DIAG
Options are selected by pressing the appropriate key. After selection, pressing key N will return you to the Main Menu. Main and sub-menus are described in detail in the sections that follow.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 17 - Measurement of Leaf Gas Exchange
Measurement of Leaf Gas Exchange
1REC (Recording)
For purposes of this manual, we assume that you are using the standard PLC4(B) leaf cuvette with TPS-2 for leaf-level gas exchange measurements. Therefore, all leaf gas exchange parameters are measured, displayed and recorded by TPS-2. After selecting 1REC, the next four menus displayed are used to set up the system configuration. After checking/changing any of the system configuration data, press key Y to advance to the next menu. Key “N” to go back one level in the menus.
Please Note: If a leaf cuvette is not used and TPS-2 is being used as a stand-alone analyzer, only two of the following menus (Menu 2 without FLOW rate and Menu 4) will be displayed before entering the Measurement Mode. After selecting 1REC, the message “NO CUVETTE ANALYZER ONLY” message will be displayed.
From the Main Menu, press key 1 (1REC):
Menu 1
SET PLC 1:BROAD 2:UNIVERSAL
Press Key To 1 Instructs TPS-2 that you are using the PLC4 (B) broadleaf type cuvette. For all new TPS-2 users, this is the style cuvette being supplied with all instruments. This cuvette has a circular chamber with a diameter of 18mm. 2 Instructs TPS-2 that you are using an older PLC (U) or PLC2 (U) universal style leaf cuvettes.
Each cuvette has slightly different characteristics (i.e. cuvette window, location of PAR sensor, etc.). TPS-2 measurements and calculations will be based on the cuvette selected here. If you have any questions as to which cuvette type you have, contact PP Systems ([email protected]) by email and provide us with the serial number of your cuvette.
After selecting the cuvette, the next three menus display the current configuration of the system:
Menu 2
1REC:M 2INT: 0 FLOW:300
Press Key To 1 Toggle between automatic (A) and manual (M) recording. For leaf gas exchange measurements, we recommend manual recording so that measurements can be recorded when the leaf reaches equilibrium. 2 To set the automatic recording interval. If automatic (A) recording is selected, press key 2 (2INT) to set the recording interval (1-250) minutes. If manual (M) recording is selected, 2INT is set to 0 minutes by default.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 18 - Measurement of Leaf Gas Exchange
Remember to use leading zeros when entering the recording interval. For instance, an entry of 002 is required for an automatic recording interval of 2 minutes.
The cuvette flow rate (FLOW) is set to 300 cc min-1 by default and cannot be changed.
Key Y to advance to the next menu to select the light source used and to set leaf area:
Menu 3
1: LIGHT = SUN (or LAMP/LED) 2: LEAF AREA = 02.5
Press Key To 1 Toggle between Sun or Lamp/LED. If natural sunlight is used for measurements, press key 1 until SUN is displayed. For measurements using the LED light unit supplied with the PLC4 (B), press key 1 until LED is displayed. A 10 Point Calibration is required before using the LED light unit (see 10 Point Calibration on page 35).
If you selected “Universal” for the leaf cuvette, you have the option of selecting “Lamp” if using our quartz halogen light unit. For measurements using the quartz halogen light unit, press key 1 until LAMP is displayed. If you selected “Broad” for the leaf cuvette, you have the option of selecting “LED”.
Proper selection of the light source used is required to set the value of the constants (i.e. TRANS factor) used to convert PAR measurements to the energy absorbed by the leaf. 2 Set the projected leaf area (cm2). Set a value as close as possible to the actual leaf area. To assist in determining leaf area, the total window sizes for our cuvettes are as follows:
PLC4 (B) Broad Leaf Cuvette: 2.5 cm2 PLC2 (U) Universal Leaf Cuvette: 4.5 cm2 PLC (U) Universal Leaf Cuvette: 10.35 cm2
Data may be recalculated based on actual leaf area using a simple recalculation program offered by PP Systems.
Press Key Y to advance to the next menu for selection of plot number and to view the number of records available for storage:
Menu 4
1P:01 R:01 FREE RECORDS 820
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 19 - Measurement of Leaf Gas Exchange
Press Key To 1 Set the plot number used to identify stored records. To change the displayed value, press key 1 and enter the desired value (1-99).
R refers to the record number associated with the plot number. This is reset to 1 when the plot number is changed and increments up to a maximum value of 89. It will recycle to 1 after the 89th record is taken.
FREE RECORDS refers to the the number of records that can be taken before the memory is full. The maximum number of records that can be saved is 820.
Press Key Y to advance into the Measurement Mode.
Warmup Delay
If the system has not come to operating temperature (55 ºC) a display similar to the following will appear:
WARM UP DELAY 47.7 C dT=10
The current TPS-2 IRGA temperature is displayed. The value following dT refers to rate of temperature change as the IRGA approaches steady state. When the rate of change falls to 0, TPS-2 will complete an Autozero and then enter Measurement mode.
Measurement Mode If TPS-2 is switched off then quickly turned on again the following message may be displayed for a short period as TPS-2 checks itself:
Then the display will show measured data:
Cnnnn +/-nnn Qnnnn Hnn.n +/-nn.n Tnn.n where:
Upper Row C Reference CO2 concentration (ppm). Range: 0000-9999 Differential CO2 concentration (ppm). This is the difference between +/-nnn the air entering the leaf cuvette (reference) and the air leaving the leaf cuvette (analysis). PAR (µmol m-2 s-1). Range: 0000-2500. If LED is selected in Menu 3 Q described earlier, Q will display the LED lookup table value. If SUN or LAMP is selected, the corrected PAR sensor reading is displayed. Lower Row H Reference H2O concentration (mb). Range: 00.0-75.0 Differential H2O concentration (mb). This is the difference between +/-nnn the air entering the leaf cuvette (reference) and the air leaving the leaf cuvette (analysis). T Cuvette temperature (oC)
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 20 - Measurement of Leaf Gas Exchange
To view the calculated data associated with the measured data press the 4/X key:
Enn.nn Gnnnn Tnn A+/-nn.n CInnnn where:
Upper Row E Transporation rate (mmol m-2 s-1) G Stomatal conductance (mmol m-2 s-1) T Leaf temperature (oC) based on energy balance. Lower Row A Assimilation (net photosynthetic) rate (µmol m-2 s-1) -1 CI Intercellular CO2 concentration (µmol mol )
Every 4.8 seconds, both measured and calculated data are transmitted from the RS232 port. Data can also be viewed on a PC, if desired. To do so, connect the serial cable provided with the system between the 9 pin RS232 port on the top of TPS-2 and the serial or USB port on the PC. Using the software provided by PP Systems (or hyperterminal on your PC), you can view the output on the PC (see Logging Data via RS232 Interface on page 41).
While you are in the measurement mode, the following key presses are available to the user:
Press Key To R Record a measurement Change recording type (manual or 1 automatic). To return to Measurement Mode, press key Y. Change light type and leaf area. To return 2 to Measurement Mode, press key Y. Change the plot number. To return to 3 Measurement Mode, press key Y. Toggle between measured and calculated 4/X data. Y Set CO2, H2O and LED Control Return to Main Menu. Always return to N the Main Menu prior to powering down TPS-2.
System Checks Prior to Making Measurements Before proceeding with measurements, we always recommend performing the following system checks (with measured data displayed) to ensure that the system is operating properly:
With the leaf cuvette closed and connected to the TPS-2 main console as described earlier in this manual, perform the following basic system checks:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 21 - Measurement of Leaf Gas Exchange
System Checks Yes No
Reference CO2 value (C) should be stable (+/- 1ppm). If outdoor ambient, the value should read approximately 390 ppm. If the CO2 reading is unstable, check that the work area is isolated from CO2 influences such as vehicles, ventilation, individuals (breathing), etc. A smoothing volume may be required in some cases. It may take the instrument 5-10 minutes to stabilize at ambient levels. Differential CO2 value (+/-nnn) should be 000 (+/- 001ppm). PAR value (Q) should read the approximate value. On a day with clear skies values should be in the 1,500-2,000 range. Reference H2O value (H) should be stable (+/- 00.1 mb) and be reading the approximate set concentration. Differential H2O value (+/-nnn) should be 000 (+/- 001 mb). Cuvette temperature (T) should read similar to the ambient temperature.
If you have answered yes to all of the above system checks, your system is working properly and you are ready to begin making measurements.
Steady-State Recording with a Leaf in the Leaf Chamber Squeeze the open/close lever mechanism beneath the cuvette handle to fully open the cuvette. You will notice an increase in the differential CO2 concentration (signified by a +nnn value) as a result of outside air entering the cuvette. Choose a leaf of sufficient size to completely fill the cuvette head opening around the closed cell foam gaskets. This is the only way to ensure that a consistent leaf area is sampled. If possible, approach the leaf from the side, not the tip. Be sure that you have changed the display from measured data to calculated data by pressing the 4/X key.
With the leaf enclosed in the cuvette you should notice a series of dynamic leaf responses, assuming ideal physiological conditions. Sub-stomatal CO2 concentration (Ci) will decrease, and with Ci
Immediately after pressing the R key, a message similar to the following will be displayed:
RECORD rrr TAKEN PLOT= pp nn where:
rrr Number of records stored so far (up to 820) pp Current plot number nn Record ID
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 22 - Measurement of Leaf Gas Exchange
The display now returns to the measured data – press the 4/X key to again view the calculated data display, or simply press the R key to record another measurement. Several records per leaf are recommended to satisfy statistical data assumptions.
Variability of Plant Responses Even with environmental conditions inside the leaf chamber held constant, certain physiological responses, especially A, CO2 differential and gs (stomatal conductance), may continue to change as the leaf approaches a stable state. This can occur over approximately 45-60 seconds, and as long as a several minutes. The duration of this process depends largely on the preconditioned state of the plant relative to the environmental conditions inside the leaf chamber.
A useful illustration of this can be seen in highly shade-tolerant plants which are suddenly exposed to strong light intensities. In this case, delayed gas exchange responses can be expected compared to a plant (or leaf) accustomed to more intense light conditions. Likewise, plants of temperate zone provenances measured in wintertime, although indoors, are often in a protracted phase of physiological maintenance controlled by hormonal signalling. Innate physiological changes range from significant down-regulation of photosynthesis to nearly complete quiescence.
TPS-2 tests conducted with apparently healthy plants, sampled under dry, indoor, winter conditions produced results indicative of both stomatal closure and shutdown of photosynthesis in winter. Whenever there is no detectable carbon dioxide or water vapor exchange between the plant and cuvette air, TPS-2 may return system firmware values of zero or 9999 for the interrelated parameters A, E, gs, Ci, as expected from the gas exchange algorithms. However, it is possible to detect at least some low-level physiological activity for some indoor plants measured under ideal conditions in winter. For example, many temperate zone plants respond under climate controlled (temperature, humidity) greenhouse conditions, using a 16 hour photoperiod supplemented by artificial lighting.
We assume that all PP Systems customers are well informed, either through direct research experience or the literature, regarding the biology of their plant species of interest. However, in certain cases a familiar plant species may not respond as expected. The researcher or student should remain aware that plant gas exchange technology cannot by itself overcome biologically hard-wired limitations, and that lack of a “typical” plant response may be unrelated to instrumentation, hardware and technological issues. This may be true even though the enclosure inside the leaf chamber is capable of simulating summer-like conditions.
Controlling CO2, H2O, and Light (LED)
TPS-2 offers manual control of CO2, H2O and Light (when LED light unit is used). With the measured or calculated data displayed as described earlier, press the Y key and the following control submenu will be displayed:
CONTROL SETTINGS 1CO2 2H2O 3LED
CO2 Control
Press key 1 to select CO2 CONTROL and the following is displayed:
CO2 STEP n (MAX=6) N=CHANGE Y=OK
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 23 - Measurement of Leaf Gas Exchange
CO2 control can be set in 6 steps where n is the current step (default value = 6). The following table illustrates the approximate values of CO2 per each step:
Step CO2 Concentration (% of Ambient) 6 100 5 75 4 60 3 45 2 25 1 0
Press key N to change from step to step. If step 6 is selected there will be no absorption of CO2 and the reference supply of CO2 to the cuvette will be the ambient CO2 concentration. If step 5 is selected, the reference supply of CO2 to the leaf cuvette will be partially absorbed (through the soda lime) so that approximately 75% of the ambient CO2 concentration is provided to the cuvette, and so on.
Please be aware of the following affect when controlling CO2: When reference air is passed through soda lime, CO2 is removed. However, water vapor is evolved and added to the gas stream. To counter this effect TPS-2 uses an internal water vapor equilibrator. Depending on the ambient humidity, setting a lower CO2 control setting may still result in a higher air humidity.
Press key Y to return to the measurement mode when completed.
H2O Control
Press key 2 to select H2O CONTROL and the following is displayed:
H2O STEP n (MAX=4) N=CHANGE Y=OK
H2O control can be set in steps of 4 where n is the current step (default value = 4). The following table illustrates the approximate values of H2O per each step:
Step H2O Concentration (% of Ambient) 4 100 3 80 2 60 1 35
Press key N to change from step to step. If step 4 is selected there will be no absorption of H2O and the reference supply of H2O to the cuvette is the ambient H2O concentration. If step 2 is selected, the reference supply of H2O to the leaf cuvette will be reduced (through the Envirogel desiccant) so that approximately 60% of the ambient H2O concentration is provided to the cuvette, and so on.
Press key Y to return to the measurement mode when completed.
Light Control (LED Light Unit) Press key 3 to select LED for control of light intensity and the following is displayed:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 24 - Measurement of Leaf Gas Exchange
LED LEVEL n=xxxx PRESS 0-9 OR Y where:
Refers to the Level Number (0-9). n This is the last value set by the user. Refers to the light intensity (PAR) xxxx corresponding to Level n (PPFD µmol m-2 s-1).
Pressing keys 0-9 will change the current level and PAR value associated with it. The user can step through all levels to see the corresponding light levels if required. Select the light level required for your measurements and make sure that the light intensity indicator on the LED light unit is also set to the same LED level selected on the display.
Light Intensity PAR Electrical Indicator Sensor Connector for (0-9) Holder Light Unit Securing Clip for light unit
Note, if LED is not selected in the setup menu, a message “LED NOT SELECTED” will flash on the display. See page 18 under Menu 3. The LED light unit must be selected in order to manually control light intensity.
Important Note It is important that you perform a simple one point calibration of the LED light unit on a daily basis prior to the start of measurements. (See 1 Point Calibration Check on page 33).
Autozero TPS-2 performs a zero air test automatically at 20 minute intervals. At the Main Menu press key 8 to set the Autozero cycle from 1 to 20 minutes:
ZEROTIME = xx CORRECT (Y-N)?
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 25 - Measurement of Leaf Gas Exchange
Enter the desired interval, leading zeros are necessary, i.e. enter 05 for a 5 minute interval. The selected setting is not saved in non-volatile ram, so this interval will need to be reset each time TPS-2 is started.
You can force an autozero sequence at any time by pressing key 8 from the measure mode. No measurements should be made during the Autozero until the system returns to a stable condition. For 20 seconds the display will read:
AUTOZERO PLEASE WAIT
When Autozero completes the system returns to the normal measurement display. A brief recovery period (45-60 sec) following any Zero is required for the system to return to a stable condition. If the operator is logging data there will also be a 25 second break in the output of data on the RS232 line during an Autozero.
Differential Balance
With two independent humidity sensors, there is a possibility that the same gas input into both sensors will read slightly different humidities due to accuracy limitations of the sensors. To eliminate this condition TPS-2 offers a Differential Balance feature. This feature is completely user controlled – the user decides when to perform a Diff-Bal, the user initiates the Diff-Bal manually, and the user sets up gas connections so that identical gas streams enter the REF and AN inlets. Single Point Diff-Bal
The Diff-Bal is achieved in one of two ways:
Press Key 7 from the Measurement Mode screen.
Or
From the Main menu, Press 2 CAL, 2:H2O, 2:DIFF-BALANCE, 1:SINGLE PT.
The display will read:
MB R:05.1 A:05.2 KEY0 WHEN STEADY
The displayed values are the vapor pressure in millibar for the REF and AN humidity sensors. Note that these are corrected values using the previous Diff-Bal factors and not the result of the current operation. To see previously stored Diff-Bal factors use the 3:SET option (see below).
The inlet ports must now be reconfigured to both receive air from the same source. Three simple options exist to achieve this:
1. Remove the cuvette gas tubing from both REF and AN PLC A inlet connections - the same ambient air will be present at both inlets.
2. Create a T-fitting with some spare tubing (do not use silicone tubing) – attach the single tube of the T-fitting to the reference gas (LINK FOR PLC). Attach the two tubes from the T-fitting to the REF inlet and the AN PLC A inlet.
3. Use the standard PLC4 cuvette gas connections, but with no leaf in the chamber. Assuming there is no gasket leak or other imperfection in the cuvette or gas connections, water vapor entering the REF gas inlet should be the same as that entering the AN PLC A gas inlet.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 26 - Measurement of Leaf Gas Exchange
When the readings are steady, press key 0 and the firmware will calculate a new DBOFFSET factor to make the two readings equal. The new DBOFFSET factor is displayed briefly on the display. The Diff-Bal can be easily executed from the Measurement menu at any time and for differing humidity conditions. The DBOFFSET is saved in non-volatile memory, so it does not have to be performed at each power-up.
Two Point Diff-Bal For those cases when performing a Diff-Bal during a series of measurements is not easily accomplished, and where the series of measurements may include a wide range of humidity conditions, there is a second Diff-Bal option. The Two Point Diff-Bal allows a Diff-Bal at low humidity and a Diff-Bal at higher humidity to be recorded. The firmware will then interpolate the correct correction factor at all other humidity conditions. This can eliminate the need to repeatedly perform the Single Point calibration during changeable humidity conditions.
The differential balance correction is computed as follows:
CF = DBOFFSET + DBGAIN x (Uncorrected Analysis MB) Corrected Analysis MB = (Uncorrected Analysis MB) + CF The correction is always applied to the Analysis sensor reading. When a Single Point Diff-Bal is performed, only the DBOFFSET is affected, and the DBGAIN is not changed. Therefore, a user could set up a Two Point Diff-Bal to cover a range of humidities, and still use a Single Point Diff- Bal to optimize at a specific humidity. The steps to perform a Two Point Diff-Bal are:
From the Main menu, Press 2 CAL, 2:H2O, 2:DIFF-BALANCE, 2:TWO POINT Then, the display will briefly read:
LOW HUMIDITY GAS TO REF AND AN indicating that identical low humidity gas should be connected to the REF inlet and AN PLC A inlet.
The display will read, e.g.:
MB R:05.1 A:05.2 KEY0 WHEN STEADY
When the readings are steady, press key 0 and the display will briefly read:
HI HUMIDITY GAS TO REF AND AN indicating that identical high humidity gas should be connected to the REF inlet and AN PLC A inlet.
The display will read, e.g.:
MB R:20.1 A:21.2 KEY0 WHEN STEADY
When the readings are steady, press key 0 and the firmware will calculate and briefly display the new DBOFFSET and DBGAIN factors, e.g.:
DBOFFSET=+/- xx.x DBGAIN=+/- xx.xxx
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 27 - Measurement of Leaf Gas Exchange
TPS-2 now returns to the Main Menu.
An additional feature of the H2O Calibration menus is the ability to directly display and enter DBOFFSET and DBGAIN. This is useful if you previously recorded values for DBOFFSET and DBGAIN and you want to return to those settings without actually performing the Diff-Bal operations. Also note that if a user chooses to perform a Single Point Diff-Bal, then DBGAIN should be set to 0. The menu path for this manual setting is:
From the Main menu, Press 2 CAL, 2:H2O, 2:DIFF-BALANCE, 3:SET. The display will read:
DBOFFSET = +/- xx.x OK (Y-N)
Press the N key to change the offset, the display reads:
DBOFFSET = +??.? 1 for pos, 2=neg Enter the desired sign and values.
Press the Y key to advance to the gain display:
DBGAIN = +/- xx.xxx OK (Y-N)
Press the N key to change the gain, the display reads:
DBGAIN = +??.??? 1 for pos, 2=neg
Enter the desired sign and values. TPS-2 now returns to the Main Menu.
If the Dual H2O Sensor board malfunctions in any way, an error message is displayed during the power-up sequence that reads:
ERROR READING DUAL H2O SENSORS
This message is also displayed continuously during a Single Point Diff-Bal. TPS-2 will otherwise function normally with the humidity readings all set to zero. This will allow the user to capture CO2 measurements when the humidity sensor is not operational.
Recalculation of Data Based on Leaf Area There may be cases when the actual leaf area is not known at the time of measurement, for example, when measuring plants with small leaves that do not fill the leaf chamber opening. Accurate leaf area determination is essential to the final calculation of photosynthesis and other calculated parameters. The leaf area entered in 1REC sub-menu 3 must be a close approximation of actual leaf area. After measurements are completed sampled leaves should be measured using a suitable method (i.e. portable leaf area meter, image analysis, etc.), to determine the true leaf area. Also, check the TESTED label attached to the leaf cuvette to see if factory-determined boundary layer resistance (rb) is the same as the default value (0.2 m2 s mol- 1). If not, rb can be changed using a recalculation program.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 28 - Measurement of Leaf Gas Exchange
Operators may use their own program, or the TPS-2 Data Recalculation Software Program or Excel recalculation spreadsheet can be used to correct data for these and other factors. Recalculation software and instructions are available to all registered users from our web site. If you are not registered with us, we strongly encourage you to do so by visiting:
http://www.ppsystems.com/Register.html
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 29 - Additional Main Menu Functions
Additional Main Menu Functions
2CAL (Calibration) From the Main Menu, press key 2 to check and calibrate the CO2 analyzer, H2O sensor, PAR sensor and LED light unit (if used).
1:CO2 2:H2O 3:PAR 4:LED
CO2 Calibration Using a Gas Cylinder
Under normal operating conditions TPS-2 should NOT require CO2 recalibration. However, as a part of routine system maintenance, we recommend that you check the CO2 calibration against i) a standard calibration gas or ii) ambient air (away from CO2 sources such as vehicles, liquid-fuel powered generators, breathing, etc).
In order to carry out a proper CO2 calibration, the following items are required:
A certified CO2 calibration gas* (recommended +/- 1% accuracy) with a regulator valve Soda lime in the TPS-2 zero column (column 1) must be new TPS-2 must have been switched on for at least 30 minutes
*This must be between 100 and 2,100 ppm. For optimal accuracy, the concentration should be slightly higher than the maximum concentration of CO2 that you intend to use, i.e. if you intend to work only at ambient CO2, then a calibration gas of 400 ppm would be ideal. NEVER calibrate with a gas concentration much lower than the anticipated CO2 measurement levels. For example, do not use a 200 ppm standard gas when measuring around 500 ppm.
Disconnect the PLC leaf cuvette and power on TPS-2. Press key 1 to select CO2 calibration:
CO2 CONC = nnnn CORRECT (Y/N)? nnnn is the setting of the current/most recent calibration concentration. Press Y if this is correct. To enter a new value based on the concentration of your gas cylinder, press N and enter the new calibration concentration.
On completion of the concentration selection the display will show:
CO2 CONC = nnnn KEY0 WHEN STEADY
The gas connection is made to the REF inlet on the top of TPS-2. The calibration gas cylinder must not be connected directly to TPS-2, but through a T or Y connector.
Connect an appropriate length of non-silicone tubing to the gas cylinder’s regulator. To the other end of the calibration gas tubing connect a, e.g. Teflon T or Y piece. On the top of TPS-2, remove the LINK FOR PLC tube from the REF inlet. Connect one leg of the T or Y connector to the REF inlet. The other leg should vent to atmosphere through a short length of tubing.
Pressure must be carefully regulated and must not exceed standard atmospheric pressure (1 atm, 100 kPa). The flow rate from the gas cylinder should be set initially to no more than 300 cc
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 30 - Additional Main Menu Functions
min-1, and there should be excess flow venting to atmosphere. Verify the excess flow by connecting a flowmeter to the vent tube.
In-line “T” piece, vent to atmosphere
Regulated pressure from
TPS-2 REF inlet CO2 tank
CO2 gas cylinder
Wait until TPS-2 gives a steady reading. When the concentration reading is steady, press key 0. Any other key will abort the calibration. When 0 is keyed the display reads:
INPUT ACCEPTED and the calibration factor is calculated and stored in memory. TPS-2 returns to the Main Menu. If the display continues to show “Input Accepted“ for a longer period:
1. Switch off TPS-2. 2. Switch TPS-2 on again, and when the Main Menu is displayed, press key 6 (6:DIAG). 3. Press key 2 (2:INITIALISE) and when prompted with ????, enter 0462. 4. From the Main Menu, press key 2 and attempt another calibration.
If there is a significant (10%) difference between the calibration gas concentration from your cylinder and TPS-2 reading, try the following:
1. Quit the calibration by pressing key N.
2. Check TPS-2 CO2 zero absorber column and ensure that it is fresh (green color).
3. Next, measure the outside CO2 concentration away from all CO2 influencing sources (i.e. automobiles, ventilation, breathing, etc.). If TPS-2 reads correctly (approx. 390 ppm) then the standard gas concentration may be suspect. To abort a calibration at any time and return to the Main Menu, press N.
H2O Calibration Press key 2 to select H2O calibration to see the following display:
H2O MB = nn nn is the current setting of the calibration concentration. If this is correct press Y. To enter the new value based on the actual concentration, press N and enter the new calibration concentration. This must be between 10 and 50 mb.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 31 - Additional Main Menu Functions
On completion of the concentration selection the display will show:
H2O MB = nn KEY0 WHEN STEADY
Next, connect the humidity calibration source with gas flowing through the T or Y piece described above, wait until TPS-2 gives a steady reading. When the concentration reading is steady, press key 0. Be sure to press 0, any other key will abort the calibration. When 0 is pressed, “Input Accepted” is displayed and the calibration factor is calculated and stored in memory. TPS-2 returns to the Main Menu.
If the display continues to show “Input Accepted“ for a longer period:
1. Switch off TPS-2. 2. Switch TPS-2 on again and when the Main Menu is displayed, press key 6 (6:DIAG). 3. Press key 2 (2:INITIALISE) and when prompted with ????, enter 0462. 4. From the Main Menu, press key 2 and attempt another calibration.
If there is a significant (10%) difference between the H2O source concentration and TPS-2 reading, quit the calibration and try again. If the problem continues, contact PP Systems. To abort a calibration at any time and return to the Main Menu, press N.
Factory PAR Sensor Calibration Press key 3 to select PAR sensor calibration on the leaf cuvette – the following display appears:
RAW= 7COR= 7 LED OK (Y-N)?
Both the raw PAR reading and the corrected PAR reading are displayed as above. The PAR sensor is calibrated at the factory and under normal conditions, maintains its accuracy for the life of the instrument. Some cuvettes can utilize the PAR Calibration routine to adjust the PAR readings to match a customer’s laboratory standard or another PAR sensor reading.
PAR readings are processed in TPS-2 as follows:
COR = (RAW – OFFSET) * GAIN where:
COR Is the corrected PAR reading used in all calculations and data recording. RAW Is the raw PAR reading directly from the cuvette. OFFSET Is a user-entered constant between 0 and 200 (factory default = 0). GAIN Is a user-entered constant between .5 and 1.999 (factory default = 1.000).
Setting the PAR Sensor Gain and Offset Constants With the following displayed:
RAW= 7 COR= 7 CORRECT (Y-N)?
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 32 - Additional Main Menu Functions
Position the cuvette in a known light environment of various levels and note the two readings. If the readings are correct, press Y to return to the calibration menu. To set the Gain and Offset constants (or to see what they are currently set to), press N, and the following will be displayed:
1:OFFSET 000 2:GAIN 1.000
To set the Offset constant, press 1, then a three digit number between 000 and 200. To set the Gain constant, press 2, then a four digit number between 0.500 and 1.999. Press any other key to return to the display of current PAR readings.
PAR Sensor Calibration in Sunlight Some cuvettes that work with TPS-2 (e.g. PLC4(B)) have integral zero and span potentiometers inside the cuvette handle that can be used to adjust the PAR readings. This can be used to set the cuvette’s PAR sensor to match a customer’s laboratory standard PAR sensor.
TPS-2 should be in normal Measurement Mode with the measured parameters displayed, not in the 2CAL menu. Be sure that SUN is selected at configuration Menu 3 of the TPS-2. Refer to TPS-2 Operator’s Manual.
Place the cuvette PAR sensor and a reference PAR sensor in an open, non-shaded position in full sunlight within two hours of noon. Ensure both PAR sensors are in the same horizontal plane and at the same angle to the sun. Both PAR sensors must be directly in the sunlight, not under the cuvette’s Calflex window. Be careful not to move the PAR sensors during the adjustment.
The cuvette’s zero and span potentiometers are adjusted by using a small flat bladed screwdriver to engage with the slot in the screws that can be seen through the holes in the cuvette handle. The zero potentiometer is located inside the front hole towards the cuvette head. The span potentiometer is located inside the rear hole towards the end of the cuvette handle. If adjustment of the potentiometers is difficult through the access holes, it may be necessary to remove the cuvette’s handle to gain easier access to the potentiometers (contact [email protected]).
Cover the cuvette head and PAR sensor with an opaque cloth and adjust the zero potentiometer until the reading alternates between zero and a small positive value. This will ensure that there is no negative offset in low light or dark conditions. Adjust the span potentiometer to match the value on the reference PAR sensor.
The PAR calibration is now complete. The PAR (Q) reading will be approximately the same as the reference PAR sensor in all levels of sunlight.
LED Calibration Press key 4 to select LED calibration.
1: 1 POINT CHECK 2: 10 LEVEL CAL
1 Point Calibration Check Pressing key 1 will allow you to perform a simple one point calibration (Level 7) check of the LED light unit. If TPS-2 is supplied with an LED light unit, PP Systems will perform a full calibration at the factory. The calibration values are stored in non-volatile memory. However, we still highly recommend performing a one point calibration check of the LED light unit on a daily basis prior to measurements since it is expected to drift from day to day. Make sure that the indicator on the LED light unit is set to 7.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 33 - Additional Main Menu Functions
Important Note
Never look directly into the LED light unit when it is powered on (even at low intensities).
In order to perform this one point calibration check, the LED light unit must be fitted to the leaf cuvette and the cuvette lower head plate must be detached in order to position the PAR sensor below the LED light unit. To perform this calibration:
1. Remove the thumb screw on the right side of the cuvette handle by turning it counter- clockwise until it is loose enough to slide out (see below).
Thumb Screw
2. Once the thumb screw is removed, the bottom head plate will drop down allowing access below the light unit. 3. Secure the cuvette in a horizontal fixed position, for example, using a laboratory clamp. 4. Remove the PAR sensor from its holder on the side of the cuvette and place it in a fixed position beneath the upper head plate. Again, a laboratory clamp can be used to accomplish this. The PAR sensor cannot be held by hand for an accurate calibration – it must be steady and level, and centered beneath the cuvette window. 5. Assuming that the light unit intensity indicator is set to 7, wait for readings to stabilize. Record the value(s) – take the average if several values are returned.
The display will appear as follows:
SENSOR nnnn LEVm TABLExxxx 1/2/3 where: nnnn Is the actual value being measured by the PAR sensor (µmol m-2 s-1) m Refers to the Level number (7) xxxx Is the stored value for PAR for Level 7(µmol m-2 s-1)
From here:
Press Key To: 1 To keep the stored TABLE value. If the SENSOR value is similar to the TABLE value (within 20 µmol m-2 s-1), press key 1 (or Y). You will be returned to the main menu. 2 If the SENSOR value is much different (> 20 µmol m-2 s-1) than the TABLE value. A new LED Scale factor is calculated and stored that makes the LEVEL 7 table value match the current PAR SENSOR reading. When matched, press key 1 (or Y) to return to the main menu.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 34 - Additional Main Menu Functions
3 To display the current LED Scale. A new value can also be manually entered between 0.500 and 1.999 if required. N Exit to main menu
LED Scale The LED Scale is a multiplier applied on all values in the LED lookup table. It is forced to 1.000 on initialization and whenever any 10 Point Calibration value is entered or changed. Whenever TABLE values are displayed and/or used in the firmware for computation, the LED Scale is applied. When satisfied with your entry, press Y to return to the main menu.
10 Point Calibration Press key 2 to perform a 10 point calibration. The 10 point calibration is required before selecting LED from Menu 3 in Measurement Mode.
The following display is shown:
SENSOR nnnn LEVm TABLE xxxx 1/2/3 where: nnnn Is the actual value being measured by the PAR sensor (µmol m-2 s-1) Refers to the Level number (0-9). During this process, Level 0 will be displayed m first. xxxx Is the stored value for PAR for Level m (µmol m-2 s-1)
The steps needed to perform a 10 point calibration are the same as those for the one point check described in the previous section. However, for a 10 point calibration each individual light level is checked, starting at 0 (lowest level) and continuing through 9 (highest level).
Begin the calibration by ensuring that the light intensity indicator on the LED light unit is set to 0. With the PAR sensor positioned level and centered beneath the cuvette window, note the sensor reading. If the sensor value is similar to the TABLE value (within 20 µmol m-2 s-1), press key 1 and the display will automatically move to the next light level. If the sensor value is much different than the TABLE value (>20 µmol m-2 s-1), press key 2. The new TABLE value should now match the sensor reading, and will replace the current TABLE value for that LEVEL.
Continue to the next level, making sure that the light intensity indicator on the LED light unit is manually changed to match the LEVEL on the TPS-2 display. After completing LEVEL 9 the display will automatically return to the main menu.
LED Initialization The LED light unit can be set back to factory default settings if required. Initializing TPS-2 will force all the current table values to 0 and will require a full 10 point calibration before entering the Measurement Mode.
3DMP (Dump/Transfer) Press key 3 (3DMP) from the Main Menu to display or transfer stored records in the database. Note that internal records are not erased during this process using either option described below.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 35 - Additional Main Menu Functions
1: SCREEN DISPLAY 2: DATA DUMP 1-2?
SCREEN DUMP Press key 1 to view stored data on the TPS-2 LCD display starting with the most recent record. The following display is shown:
PLOT 01 REC 01 23-07 12:19 plot number, record number, date (day-month) and time of measurement (hh:mm) are displayed.
To view the measured data associated with the displayed plot and record number, press Key 7. To view the calculated data (if a leaf cuvette was used with TPS-2) associated with the same record, press Key 7 again. Press the Y key to view the next most recent record in storage, and the next plot number, record number, etc. will be displayed. Note - where there are two further displays, as for leaf cuvette measurements, the displays will scroll around on this keypress. Key N returns to the Main Menu.
When all the records have been viewed then TPS-2 displays:
NO MORE RECORDS IN STORE followed by a return to the Main Menu.
DATA DUMP
Press key 2 (2:DATA DUMP) to transfer stored data from TPS-2 to an external PC via the serial (RS232) port. The oldest data is transferred first. The RS232 protocol and the data format is described in detail in Output of Stored Records from Memory on page 43.
4CLR (Clear) Used to clear the database. Press key 4 to clear the database and remove all previously stored records. To ensure that this cannot be done inadvertently, several key presses are required. The following is displayed:
CLEAR DATABASE (YY-N)?
Press YY and then key 0 to confirm. A “DATABASE CLEARED” message will briefly display before returning you to the Main Menu.
5CLK (Clock) Used to set the clock to the correct time and date. Press key 5 to view the current time and date settings. Press key N to accept the settings or key Y to change:
RESET TIME (Y-N)? 12-02-11 14:00
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 36 - Additional Main Menu Functions
The date is shown as day-month-year and the clock is based on a 24 hour clock (i.e. 2:00PM should be set to 14:00). The clock settings are always retained by the internal battery.
6DIAG (Diagnostics/Initialize) This features are available to users, but are intended primarily for testing and maintenance. After pressing Key 6 the display will show:
1:DIAGNOSTICS 2:INITIALIZE
1:DIAGNOSTICS Press key 1 to view system diagnostics. Shown are the 16 bit readings of the A/D converter measuring the CO2 infra-red sensor output in Reference/Analysis and Zero modes. Zero should always be the largest reading – in CO2-free air there is no infra-red absorption, therefore the detector output is largest.
DISPLAY 1 CR: NNNNN A:NNNNN Z:NNNNN ZC:NNN
CR:NNNNN A/D read for CO2 Analyzer Reference. Expected between 42000-49000 (at approx. 500 ppm CO2) if working properly. A:NNNNN A/D read for CO2 Analyzer Analysis. Expected between 42000-49000 (at approx. 500 ppm CO2) if working properly. Z:NNNNN A/D read for CO2 Analyzer ZERO. Expected to be higher than the Reference and Analysis A/D reads - between 46000-54000 if working properly. ZC:NNN Zero cycle countdown in 4.8 sec intervals.
Press key Y to go to the next display in Diagnostics:
DISPLAY 2 HR: NNNNN NNNNN HA: NNNNN NNNNN
HR:NNNNN RH read for H2O Sensor Reference (reading in % x 103) NNNNN A/D read for H2O Sensor Reference
HA:NNNNN RH read for H2O Sensor Analysis (reading in % x 103) NNNNN A/D read for H2O Sensor Analysis
Press key Y to go to the next display in Diagnostics:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 37 - Additional Main Menu Functions
DISPLAY 3 LCT NNN PAR NNNN
LCT:NNN A/D read for leaf cuvette temperature (oC x 10) PAR:NNNN Sensor read for PAR
Press key Y to go to the next display in Diagnostics:
DISPLAY 4
RHT NNNNN ANT NNN ATP NNNN AUX
RHT: NNNNN A/D read for H2O sensor (x 10) ANT: NNN A/D read for analyzer temperature (x 10). ATP: NNNN Atmospheric pressure in the analyzer sample cell. AUX: Not Used (should be blank)
Press key Y to exit Diagnostics and return to the Main Menu. When stepping through the Diagnostics menus, a key press of N will return you to the Main Menu.
2:INITIALIZE
Download stored data from TPS-2 before using this function. Initialization will permanently remove all stored data from internal memory.
This option is used for initial calibration of the instrument in the factory, and can be used by the user to reset the TPS-2 analyzer calibration back to factory defaults if the memory has been corrupted. Initialization should be followed by a CO2 calibration, since the analyzer should be recalibrated rather than leaving it set to the factory default (see 2CAL (Calibration) on page 30). The following prompt appears after pressing key 2:
REINITIALIZE ALL MEMORY (YY-N)?
To proceed with initialization, press YY, then key 0 to confirm. The display will read “DATABASE CLEARED” for approximately 2 seconds, and then return to the Main Menu.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 38 - Using TPS-2 as a Stand-Alone CO2/H2O Analyzer
Using TPS-2 as a Stand-Alone CO2/H2O Analyzer
TPS-2 can be used as a stand alone CO2/H2O analyzer if required. No leaf cuvette should be connected to TPS-2 for the stand-alone analyser application. In addition, the menu structure is different than that described earlier. Power on TPS-2 and the Main Menu will appear:
1REC 2CAL 3DMP 4CLR 5CLK 6DIAG
Press key 1 to begin. A message “NO CUVETTE ANALYZER ONLY” message will be displayed followed by: 1REC:M 2INT: 0
Press Key To 1 Toggle between manual (M) and automatic (A) recording. 2 To set the automatic recording interval (1-250 minutes). If manual (M) is selected, 2INT is set to 0 by default.
Remember to use leading zeros when entering the recording interval. For instance, an entry of 002 is required for an automatic recording interval of 2 minutes.
Press key Y to advance to the next menu for selection of plot number and to view the number of records available for storage:
1P:01 R:01 FREE RECORDS nnn
Press Key To 1 Set the plot number (P) used to identify stored records. To change the displayed value, press key 1 and enter the desired value (1-99).
R refers to the record number associated with the plot number. This is reset to 1 when the plot number is changed and increments up to a maximum value of 89. Note, this will recycle to 1 after the 89th record is taken.
FREE RECORDS refers to the the number of records that can be taken before the memory is full. The maximum number of records that can be saved is 820. Press key Y to advance to Measurement Mode. When TPS-2 is used as a stand-alone CO2/H2O analyzer, only the measured data is displayed as follows:
Cnnnn +/-nnn Qnnnn Hnn.n +/-nn.n Tnn.n where:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 39 - Using TPS-2 as a Stand-Alone CO2/H2O Analyzer
Upper Row C Reference CO2 concentration (ppm). Range: 0000-9999 +/-nnn Differential CO2 concentration (ppm). The difference between the air entering the leaf cuvette (reference) and the air leaving the leaf cuvette (analysis). Q PAR (µmol m-2 s-1). Range: 0000-2500 (Not used) Lower Row H Reference H2O concentration (mb). Range: 00.0-75.0 +/-nnn Differential H2O concentration (mb). The difference between the air entering the leaf cuvette (reference) and the air leaving the leaf cuvette (analysis). T Cuvette temperature (oC) (Not used)
While in Measurement Mode, the following key presses are available to the user:
Press Key To R Record a measurement. 1 Change recording type (manual or automatic). To return back to the measurement mode, press key Y. 3 Change the plot number. To return back to the measurement mode, press key Y. N Return to Main Menu. Always return to the Main Menu prior to powering down TPS-2.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 40 - Datalogging and Transfer Software
Datalogging and Transfer Software The TPS-2 system is designed optimally for use with Windows-based transfer and logging software. An installation CD is provided with each new system, and the software is available for download from the Registered Users Area of our website at:
http://www.ppsystems.com/Register.html
Instructions and help menus are embedded in the software – steps for logging and data transfer procedures are outlined below:
Logging Data via RS232 Interface
1. Using the RS232 data transfer cable, connect the 9 pin D-connector to the 9 pin socket marked RS232 on the TPS-2 top panel. 2. Connect the other end of the cable to the 9 pin plug serial port of your PC, or to a USB port if using a USB-to-Serial adaptor with the cable. 3. Power on TPS-2. With the Main Menu displayed, press key 1REC and proceed to Measurement Mode. 4. Execute the Transfer Software on the PC (Start-All Programs-PP Systems-Transfer). For first time users, you will need to set up the Transfer Software for use with TPS-2. Select File – Preferences and then choose TPS from the “Instrument Type” dropdown list. Select the proper COM Port being used to log the data – to verify look in Device Manager, Ports. 5. As instructed on the screen, click the Log button on the lower left hand corner of your computer screen. 6. You will then be asked to name the data file (.dat extension). Enter a name and file location on the PC here, and click the Save button.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 41 - Datalogging and Transfer Software
You will then be presented with logging options which can be set according to your preferences. The following options exist:
Auto Logging To automatically record measurements (per settings under File - Preferences) Manual Logging To manually record measurements (using the record key (0/R) Capture All Records To log all records. View Only To view TPS-2 data on your computer screen
Up to 4 different variables can be selected for viewing real-time color-coded plots on the screen:
CO2 Ref. Reference CO2 concentration (ppm) CO2 Diff. Differential CO2 concentration (ppm) H2O Ref. Reference H2O concentration (mb) mb Diff. Differential H2O concentration (mb) PAR PAR (photosynthetically-active radiation) (PPFD µmol m-2 s-1) Air T Air Temperature (oC) Flow Flow rate (cc min-1) Evap. Transpiration rate (mmol m-2 s-1) Leaf T Leaf temperature (oC) PN Net photosynthetic rate (µmol m-2 s-1) -1 Ci Intercellular CO2 concentration (µmol mol )
Choose the variables to be displayed by selecting the check boxes. The button in the upper right hand corner of the screen indicates the currently selected Y-axis variable being displayed. Click on this button to toggle from one variable to the next. Click the Stop button at the bottom of the screen to end data logging.
Transfer of Stored Data via RS232 Interface
To transfer stored data from TPS-2 memory main console to your local computer:
1. Using the RS232 data transfer cable, connect the 9 pin D-connector to the 9 pin socket marked RS232 on the TPS-2 top panel. 2. Connect the other end of the cable to the 9 pin plug serial port of your PC, or to a USB port if using a USB-to-Serial adaptor. 3. Power on TPS-2. With the Main Menu displayed, press key 3 (DMP) and then key 2 (Data Dump). The TPS-2 display will read “CONNECT TO PC ANY KEY TO SEND”. 4. Execute the Transfer Software on the PC (Start-All Programs-PP Systems-Transfer). For first time users, you will need to set up the Transfer Software for use with TPS-2. Select File – Preferences and then choose TPS from the “Instrument Type” dropdown list. Select the proper COM Port being used to transfer the data – to verify look in Device Manager, Ports. 5. As instructed on the screen, click on the Transfer button on the lower left hand corner of your computer screen. 6. You will then be asked to name the data file (.dat extension). Enter a name and file location on the PC here, and click the Save button. 7. On the TPS-2 main console, press any key to transfer the stored data. Upon completion of the transfer, the message “NO MORE RECORDS IN STORE” is displayed on TPS-2. 8. TPS-2 returns to the Main Menu.
For more information on transferring/logging data, graphing preferences and system setup, refer to the help menus.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 42 - Data Output
Data Output
Output of Stored Records from Memory TPS-2 data is output via the RS232 serial port every 4.8 seconds. During normal operation records are saved to memory, and later downloaded, in ASCII delimited .dat format. Once the raw data file is opened in a, e.g. Excel, spreadsheet the complete record(s) appears on a single line with the following variable headings:
TPS-2 Data Plot Record Day Month Hour Minute CO2 CO2 PAR Software Version =1.05 Ref Diff
Mb Mb Air Leaf Flow EVAP GS Leaf PN C Int Ref Diff Temp Area Temp
The position of each character in the string is numbered to facilitate string handling in any user program. The following describes each variable in the transferred data record.
TPS-2 Data Recording/data capture method; Windows Transfer software version number Plot Plot number (00-99) Record Record number (1-89) Day 01-31 Month 01-12 Hour 01-24 CO2 Ref Reference CO2 concentration (ppm) +/- CO2 Diff Differential CO2 concentration (ppm) PAR PAR (photosynthetically-active radiation) as measured by PAR sensor attached to leaf chamber or LED setting (PPFD µmol m-2 s-1) Mb Ref Reference H2O concentration (mb) +/- Mb Diff Differential H2O concentration (mb) Air Temp Leaf cuvette air temperature (oC) Leaf Area Leaf Area as entered by the user (cm2) Flow Flow rate measured by the internal mass flow meters (cc min-1) EVAP Calculated transpiration rate from the leaf (mmol m-2 s-1) GS Calculated stomatal conductance (mmol m-2 s-1) Leaf Temp Calculated leaf temperature (oC) +/- PN Calculated assimilation rate (µmol m-2 s-1). + reading indicates photosynthesis (CO2 uptake); – reading indicates respiration (CO2 evolution). -1 C Int Calculated sub-stomatal CO2 concentration (µmol mol )
If data capture is via data logging the stored output format is slightly different, and a single record appears as below, with the additional calculated variable ATMP included.
Logged TPS-2 Data Plot Record Day Month Hour Minute CO2 CO2 PAR Software Version =1.05 Ref Diff
Mb Mb Air Leaf Flow EVAP GS Leaf PN C Int ATMP Ref Diff Temp Area Temp
ATMP Atmospheric pressure (mb)
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 43 - Maintenance
Maintenance
Air Sampling Pump The TPS-2 air sampling pump is a rotary vane style pump. Rotary vane pump components wear with prolonged use, and material from the vanes may build up within the pumps. This can eventually reduce the pumping efficiency or even cause the pump to seize. The normal signs of a bad pump are:
1. Noise - a worn pump usually sounds rough or vibrates. 2. Temperature - the outer casing is hot (not warm) to the touch.
Air Sampling Pump Replacement Follow these simple procedures to replace the air sampling pump. Open the TPS-2 case by removing the two corner covers, then remove the 4 screws that secure the outer case. Slide the back part (side opposite the desiccant columns) of the two-piece case out completely. The pump is visible in the middle, above the battery. Trace the red/black electrical wire pair from the pump, and disconnect the 2-pin connector from its terminal on the TPS-2 circuit board. Please note the orientation of the red/black wire and connector for correct re-installation of the pump. The pump itself is secured in position by a clip. Remove the tubing from the inlet and outlet ports on the pump and lift out. Mark the tubing if necessary so they can be reattached in the correct positions.
Fit the new pump making sure that:
1. The back part of the pump is pushed securely into its clip. 2. Connect the inlet tubing to the inlet port and the outlet tubing to the outlet port on the pump. 3. Reconnect the 2-pin electrical connector in the correct orientation.
Cleaning the Air Sampling Pump During prolonged operation, the vanes inside the pump will wear and deposit material inside the pump. It is sensible to clean the pump by periodically flushing it with isopropyl alcohol.
1. Connect the pump to a 6-12V source and fit a 30 mm tube to the pump inlet - TPS-2 can be used to supply power via the pump electrical connector. It is, however, essential that the flushing is performed outside of the instrument).
2. Hold the pump above a beaker of isopropyl alcohol and dip the inlet tube into the alcohol. Run the pump to draw alcohol through it. A small roll of cotton wool in the inlet tube can act as a filter for the re-circulating alcohol.
If the pump is seized, it may be freed by tapping it on a bench or by briefly reversing the voltage to run it backwards (done by reversing the connector’s polarity).
3. Run alcohol through the pump for a minute or two to ensure that any material is removed. When finished, run the pump in air for at least 15 minutes to allow any residual alcohol to evaporate. Ideally, let the pumps dry outside of TPS-2 overnight. If the pumps are reconnected prematurely, the absorber chemical (soda lime) will be exhausted quicker than usual.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 44 - Maintenance
connector
inlet
outlet pump
Air Inlet Filters The air inlets are protected by hydrophobic filters. Periodically check them and replace if dirty. The filters are located immediately beneath the REF and AN PLCA gas inlets on the top panel.
Lift up gas inlets to remove filters
12V Lead Acid Battery The 12V 7.0 Ah sealed, rechargeable, lead acid battery should last for several years if properly maintained. Based on manufacturer’s data, the battery is non-spillable (qualified to non-spillable UN2800 standards) and can be used in any orientation. It has a float design life of 5 years. It should be checked periodically to ensure that it takes up charge. Measure the voltage across the terminals of the battery after it has been charged overnight to assess this.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 45 - Maintenance
Please note - the internal 12V battery should always be fully charged before long-term storage. If the battery is stored in a low or discharged state, it is possible that it will become deep- discharged. If this occurs, the charge capacity of the battery will be permanently reduced and the battery will require replacement.
EPROM The firmware and factory measured calibration factors for TPS-2 are stored on a memory chip commonly referred to as an EPROM. This should only require replacement if the system is upgraded or new firmware is released.
The EPROM that is used in TPS-2 must be protected from static electricity. As a result, there are several precautions that the customer should take before removing the EPROM. The risk of damage can be minimized by grounding both the operator and the lab bench surface. This can be done by covering the surface of the bench with a conductive material (e.g. aluminium foil) that is electrically connected to a grounding point, such as a metal water pipe. The operator should be grounded using a wrist strap or by holding a wire that is connected to the same grounded point. Please contact PP Systems for further information.
Once suitably grounded, the TPS-2 enclosure can be opened to gain access to the circuit board containing the EPROM. The position of the EPROM is shown above.
Each EPROM is located in a specific orientation. Before starting to remove the chip, note the position of the notch on the end of the chip relative to the rest of the instrument. Using a small, flat screwdriver, gently pry the EPROM up until it is removed from its socket. When fitting the new EPROM to the socket, be careful not to bend any pins. Place the EPROM in the socket (noting the notch on one end of the EPROM) and gently press down to secure in place.
Important note - After replacing the EPROM, you should reinitialize the instrument before use (see 2:INITIALIZE on page 38).
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 46 - Maintenance
Absorber Columns and Desiccants
The condition of the chemicals within the absorber columns must be regularly checked, and the chemicals replaced as necessary. To remove any of the columns, first lay TPS-2 on its back so that you are looking down on the columns. Hold both ends of the column firmly, and pull upwards. Do not lever out one end only, as this will damage the end fitting.
One end cap and foam disk can then be removed and the contents emptied. The foam disks are there to stop the contents spilling out if the end caps are inadvertently pulled off during removal. When replacing the soda lime (columns 1 and 4), the columns should be lightly tapped to ensure settling of the contents, and the foam replaced as found.
Take care when replacing the end fittings as the "O" rings can roll up and out of the groove. This will give rise to leaks and TPS-2 will not work properly. There can be a very tight fit between the tubes and end fittings. Pushing the end fittings on without proper care can cause the tubes to crack. Again this will allow air to leak in and out of the column. The "O" rings on the end caps should be occasionally lightly smeared with silicone grease to aid ease of fitting.
Soda Lime Specifications
Chemical Composition Components: % W/W Calcium Hydroxide: (Ca(OH)2) > 75.5% Sodium Hydroxide: (NaOH) < 3.5% Water: < 21.0% Indicator (Inorganic Salt): < 0.2% Physico-Chemical Data Form: Granules Color: Green (Exhausted: Brown) Odor: None Bulk Density: 0.9 g/cm3 Solubility in Water None pH in Water 12-14 Incompatible Substances Acids, Chloroform, Trichlorethylene. Hazardous Products None Decomposition Protective Measures, Storage Conditions Clean dry environment. Storage & Handling Preferred temperature range 0-35 oC Store away from direct heat/sun.
Protective Measures Avoid inhaling dust. Wash hands after handling.
Industrial Hygiene Keep containers closed. Keep contents dry.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 47 - Maintenance
Measures In Case Of Spillage Contain material. Accidents & Fires Sweep up or vacuum. Transfer solids to metal or plastic container for disposal. Wash down spillage with water.
Suit. Extinguishing Media Water, CO2, Powder, Foam, Halon.
First Aid Inhalation Remove from exposure. Obtain medical attention if discomfort persists.
Skin Contact Drench with clean water. Obtain medical attention if skin becomes inflamed.
Eye Contact Irrigate thoroughly with clean water. Obtain medical attention.
Ingestion Wash out mouth thoroughly. Drink water. Obtain medical attention.
Hazard Labelling Transport Codes None required. Hazard Classification None.
Envirogel Specifications
1. Product Identification Name Envirogel
Company Brownell Ltd Address Unit 2, Abbey Road Industrial Park Commercial Way Park Royal, London NW10 7XF
Telephone number +44 (0)20 8965 9281 Fax number +44 (0)20 8965 3239 Emergency phone +44 (0)20 8838 8408
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 48 - Maintenance
2. Composition of the components
Chemical Description Orange to Green Indicating Silica Gel Formula SiO2 CAS (R Phrase Classification) 112926-00-8 amorphous silica 98.2%, activated coloring agent 0.2% max.
3. Health Hazard Identification
Do not breathe dust or exceed the exposure limits
4. First Aid Measures
Inhalation Remove from source of exposure. Wash spillage from skin with soap and Skin Contact water. Eye Contact Wash immediately with large amounts of
water and obtain medical attention. Ingestion Wash out mouth with water. Seek medical attention if large amount swallowed or symptoms develop.
5. Fire Fighting Measures Ex tinguishing Media Not applicable. Inorganic compound. Not combustible.
6. Accidental Release Measures Personnel Precautions Do not inhale. Wear appropriate protective clothing. Dust mask essential if conditions are dusty. See section 8 for exposure limits. Spillages Contain spillage. Collect in suitable containers for recovery or disposal. During collection avoid creating dust.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 49 - Maintenance
7. Handling and Storage Handling Avoid creating any dust. Do not smoke. During handling electrostatic charges can accumulate (see BS 5958 for advice on the control of static.)
Storage All containers must be closed air tight and kept in a dry place.
8. Exposure Control / Personal Protection Occupational Exposure Standards: Synthetic amorphous silica Silica amorphous, total inhalable dust: UK EH40: OES 6mg/m3 8h TWA. Silica amorphous, respirable dust: UK EH40: OES 2.4mg/m3 8h TWA. Silica Gel: ACGIH: TLV 10mg/m3 8h TWA. Activation agent: ACGIH: 0.5mg/m3 8h TWA. Engineering Control Measures Engineering methods to prevent or control exposure are preferred. Methods include process or personnel enclosure, mechanical ventilation (dilution and local exhaust), and control of process conditions. Respiratory Protection Avoid inhalation of dust. Wear suitable respiratory protective equipment if working in confined spaces with inadequate ventilation or whenever there is any risk of the exposure limits being exceeded. Hand Protection Wear protective gloves. Eye Protection Wear suitable eye protection. Protection During Application Handle in well ventilated conditions in accordance with good industrial hygiene and safety practices.
9. Physical and Chemical Properties Aspect Beads Colour Dry: yellow/orange Saturated: Green Odour Odourless pH 2-10 at 5% w/w in water Melting Point (oC) >1000 Boiling Point Not Applicable Flash Point Not Applicable Explosion Limits Not Applicable Bulk Density 720kg per cu meter (typical) Solubility in Water less 1.0% in weight Thermal Decomposition Stable except when saturated water released during regeneration
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 50 - Maintenance
10. Stability and Reactivity
Stability Hygroscopic Conditions to Avoid High temperatures in excess of 155oC Materials to Avoid None known Hazardous Decomposition Hygroscopic material
11. Toxicological Information Toxicity The lethal dose for humans for synthetic amorphous silica is estimated at over 15,000mg/kg. Health Effects Inhalation Synthetic amorphous silica gel has little adverse effect on lungs and does not produce significant disease or toxic effect when exposure is kept below the permitted limits. However existing medical conditions (eg asthma, bronchitis) may be aggravated by exposure to dust. Effects of dust may be greater, and occur at lower levels of exposure in smokers compared to non-smokers. Eye Contact Dust may cause discomfort and mild irritation. Skin Contact Dust may have a drying effect on the skin. Carcinogenicity Amorphous silica is not classifiable as to its carcinogenicity to humans (Group 3).
12. Ecological Information
Synthetic amorphous silica is virtually inert and has no known adverse effect on the environment.
Ecotoxicity
13. Disposal Product Disposal Product can be reactivated in an oven for re-use. This material is not classified as hazardous waste under EEC Directive 91/689/EEC. Dispose of in accordance with all applicable local and national regulations. This material is not classified as special waste under UK Special Waste Regulations 1996.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 51 - Maintenance
14. Transport Information
UN Class Not classified as dangerous goods under the United Nations Transport Recommendations.
15. Information on Regulation EC Classification This product is not classified as dangerous. S phrases Handle in accordance with good industrial hygiene and safety practices. Avoid inhalation of dust. EINECS Listing Preparation – all components listed TSCA Listing Mixture – all components listed AICS Listing Mixture – all components listed DSL/NDSL (Canadian) Listing Mixture – all components listed
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 52 - Error and Warning Displays
Error and Warning Displays
The Error and Warning displays are listed in alphabetical order.
BATTERY VOLTS 10 = XXX
Indication Battery voltage < 10.5v
Remedy Re-charge battery. If it then immediately re-occurs check the battery charger voltage.
CALCULATION NOT COMPLETED
Indication Record key pressed too rapidly after previous recording and the measurements have not been updated.
Remedy Wait a few seconds until previous measurement is updated before making next recording.
CHECKSUM MEMORY ERROR SEE MANUAL
Indication Memory corruption is generally caused by failure to turn off TPS-2 when changing an EPROM. Also could be caused by a misread of an EPROM on data/address lines.
Remedy Initialize, recalibrate and clear the memory. If it regularly re-occurs then contact your agent.
DATABASE FULL PRINT AND RESET
Indication 820 records have been taken. Further records overwrite last record.
Remedy Dump data and then clear memory.
ERROR CODE NN
Indication Calculation error. Should rarely be seen as most errors have been trapped. Please report circumstances of its display and the error code (NN) to PP Systems.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 53 - Error and Warning Displays
Remedy Press any key to return to the main menu. Reset all set-up values in record menus.
ERROR READING DUAL H2O SENSORS
Indication Humidity sensor board failure. Board disconnected.
Remedy Check status of board connector, reconnect if possible. Contact PP Systems.
MEMORY CORRUPT PLEASE RESET
Indication TPS-2 has 2 pointers to its record store. One is to the number of records currently stored, the other is the address of the next free record. The pointers can get out of line if TPS-2 is switched off in the middle of recording. Therefore, always return to the Main Menu before switching off. Another possible cause is failure of the battery that maintains memory power when TPS-2 is switched off. On start up, TPS-2 checks that the pointers agree. If they do not, then this message is displayed.
Remedy Clear the memory. If the message is repeated after switching off, then contact your agent.
NO MORE RECORDS IN STORE
When transferring stored records from TPS-2 to a PC, this is displayed when all the records have been sent.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 54 - Photosynthesis Equations Used in TPS-2
Photosynthesis Equations Used in TPS-2
Calculations
Step 1.0
Calculate the mass flow of air (W) per unit leaf area entering the cuvette
The mass flowmeter is calibrated to read the volume flow at 20 °C and 1013.25 mb (V20). Molar volume is 22.414 at 0 °C and 1 standard atmosphere (STP). Therefore:
2 -1 Where: a is projected leaf area (cm ). The V20 term is calculated above using cc sec , but is converted from cc min-1 (TPS-2 default flow rate set to 300 cc min-1).
Step 2.0
Calculate transpiration rate (E) from the partial pressures of water vapor of the air entering (ein) and leaving (eout) the cuvette
(2.1) The molar flow of water vapor (mol m2 s-1) into the cuvette is:
(2.2) The molar flow of air out of the cuvette (due to the addition of transpired water) is (W+E). Therefore, the molar flow of water vapor out of the cuvette is:
(2.3) However, the difference between the molar flows into and out of the cuvette must equal the transpiration, so:
(2.4) Therefore:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 55 - Photosynthesis Equations Used in TPS-2
Clarification of nomenclature:
i) ein is defined as the partial pressure of water vapor of dry reference air supplied to the cuvette, but not yet inside the cuvette, and therefore uninfluenced by the cuvette stirring fans or the leaf itself. Its partial pressure is determined by the Reference humidity sensor.
ii) eout is defined as the partial pressure of water vapor of air inside the cuvette, surrounding the leaf. This air is both highly mixed by the stirring fans and influenced by transpirational water vapor. Its partial pressure is determined by the Analysis humidity sensor.
As relates to the measured values in TPS-2 output:
Step 3.0
Calculate leaf temperature (Tleaf) from the energy balance
(3.1) From Reference 1 the difference between air and leaf temperature is:
Where:
H = incident radiation absorbed by the leaf
= latent heat of vaporization of water
E = transpiration rate
Ma = molecular weight of air
Cp = specific heat at constant pressure
rb = boundary layer resistance to water vapor transfer, empirically determined for each cuvette by the pseudo-leaf (filter paper) method. 0.93 converts it to that for heat transfer.
σ = Stefan Boltzmann constant
Tc = cuvette air temperature
H is calculated from the photon flux incident on the cuvette (Q), taking into account the ratio of infrared to PAR in the light source, transmission through the cuvette window (Trans), and reflection/absorption by the leaf: (H = Q x Trans).
The following approximation is made in the program:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 56 - Photosynthesis Equations Used in TPS-2
(3.2) From this we derive:
Step 4.0
Derive i) saturated vapor pressure at leaf temperature (eleaf) from Tleaf and ii) stomatal resistance (rs)
(4.1) From Reference 2:
(4.2) Stomatal resistance (to water vapor) is derived by:
(4.3) An alternative expression of Step 2.4 is:
(4.4) Because,
(inverse of equation 2.4)
(4.5) Then,
(4.6) It follows that stomatal conductance is the inverse of stomatal resistance:
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 57 - Photosynthesis Equations Used in TPS-2
Step 5.0
Determine the rate of net photosynthesis (A) from the difference between CO2 concentrations entering (Cin) and leaving (Cout) the cuvette
(5.1) IRGA CO2 readings are corrected for water vapor, temperature, and atmospheric pressure. The addition of transpirational water vapor dilutes the air leaving the cuvette (Cout), and this is compensated for in the calculation:
(5.2) Therefore,
TPS-2 calculates and displays the CO2 difference (Cout - Cin). As relates to the calculated values in the TPS-2 output:
Step 6.0
Calculate CO2 concentration in the sub-stomatal cavity (Ci) using the equation derived by von Caemmerer & Farquhar (Reference 3)
(6.1)
(6.2) Where:
Please note: These calculations are based on the following assumptions:
i) the leaf is exposed on both upper and lower leaf surfaces
ii) the upper and lower boundary layer resistances are similar
iii) stomata are evenly distributed on both upper and lower leaf surfaces.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 58 - Photosynthesis Equations Used in TPS-2
Symbol Definitions
Measured Parameters Symbol Measured Parameter Unit
3 -1 V20 Mass flow of dry air into cuvette at STP cm sec
a Projected leaf area cm2
2 -1 rb Boundary layer resistance to water vapor m s mol
P Atmospheric pressure mb
Q Photon flux density incident on cuvette µmol m-2 s-1
Tc Cuvette air temperature °C
Calculated Parameters Symbol Calculated Parameter Unit
W Mass flow of dry air per unit leaf area mol m-2 s-1
ein Partial pressure of water vapor of air entering cuvette mb
eout Partial pressure of water vapor of stirred cuvette air mb
E Transpiration Rate mmol m-2 s-1
es Saturated vapor pressure at cuvette air temperature mb
eleaf Saturated vapor pressure (inside the leaf) at leaf temperature mb
Tleaf Leaf Temperature °C
Δt Temperature difference between the air and the leaf °C
H Radiation absorbed by the leaf W m-2
2 -1 rs Stomatal resistance to water vapor m s mol
-2 -1 gs Stomatal conductance to water vapor mmol m s
-1 Cin CO2 concentration of air entering cuvette µmol mol *
-1 Cout CO2 concentration of air inside and exiting the cuvette µmol mol *
-2 -1 A Rate of CO2 assimilation (Net Photosynthetic Rate) µmol m s
-2 -1 gc Total conductance to CO2 transfer mmol m s
-1 Ci CO2 concentration of sub-stomatal cavity µmol mol
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 59 - Photosynthesis Equations Used in TPS-2
*Determined by IRGA. Temperature and pressure corrected for water vapor effects on measurement and analyzer temperature.
Physical Constants Used in Equations
Volume of one kg mole of gas =0.0224 m3, at 1013.25 millibars of pressure and 273.15 °K
Latent heat of vaporization of water ( ) = 45064.3 - (Tc x 42.9)
Molecular weight of air (Ma) = 28.97
-1 -1 Specific heat at constant pressure (Cp) = 1.012 kJ kg K
Stefan Boltzmann constant (σ) = 5.6704 x 10-8 W m-2 K-4
Saturated Vapor Pressure of Water from Air Temperature
Modified from Reference 1 to optimize the fit in the temperature range of 0-50 °C, above 0 °C:
References
1. Parkinson, K.J. 1983. Porometry in S.E.B. Symposium of Instrumentation for Environmental Physiology. Cambridge University Press.
2. Buck, A.L. 1981. New equations for computing vapour pressure and enhancement factor. Appl. Meteorol., Vol. 20:1527-1532.
3. von Caemmerer, S. and G.D. Farquhar 1981. Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves. Planta, Vol. 153:376-387.
4. Parkinson, K.J., W. Day and J.E. Leach 1980. A Portable System for Measuring the Photosynthesis and Transpiration of Graminaceous Leaves. J. Expt. Bot., Vol. 31:1441- 1453.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 60 - TPS-2 Portable Photosynthesis System Operation Manual Revision Log
TPS-2 Portable Photosynthesis System Operation Manual Revision Log
Revision Date Changes
2.01 January 30, 2007 Created for v1.1 firmware to include LED light unit.
2.02 May 27, 2011 Changes to Initialization section/Water vapour expression. Changed A/D readings. Describes changes related to ver. 2.1 firmware, including Dual Humidity Sensors, Autozero and Differential Balancing.
TPS-2 Portable Photosynthesis System Operator's Manual – Version 2.02 - 61 -