Aeon Laboratories LLC
5835 N Genematas Dr
Tucson, AZ 85704


Carbon Extraction & Graphitization Systems

Operating Manual

Contacting Us

"Aeon" is Aeon Laboratories, LLC, Tucson, AZ, USA.

Manufacturer Address

Aeon Laboratories
5835 N Genematas Dr
Tucson, AZ 85704

For ordering information, sales support, or technical assistance, visit Contact Us on

Table of contents

Contact Us
Technical data
Storage and disposal
Accessories and spares


This manual is provided "as is." Its contents are subject to change without notice.

Aeon makes no representation that this documentation is complete, accurate, or error-free. Aeon assumes no responsibility nor liability for errors, omissions, damage or loss that might result from the use of this document, even if all instructions in the document are followed properly.


This manual provides general installation, operation and maintenance instructions for Aeon Carbon Extraction and Graphitization Systems (CEGS). Before installing or operating your CEGS, read this manual carefully. Become familiar with both the manual and your system. The manual contains important information about operator safety and the proper use of the system.


Important safety information is presented in this manual as follows:

A Caution indicates that failing to follow an instruction could result in damage to equipment or failure of the process.
A Warning indicates that failing to follow an instruction could result in injury or death to people.

Warning symbols

Warning -- read documentation for hazard detail.
Warning - electric shock.
Warning - extremely low temperatures.
Warning - hot surface.

General description

Intended use

The CEGS is an automated process control system, intended for extracting carbon from various types of samples, and converting the extracted carbon into a form suitable for radiocarbon (14C) analysis by accelerator mass spectrometery (AMS). The CEGS is intended for operation only by qualified personnel in a laboratory environment.

The correctness and safety of the system software and configuration is the responsibility of the user.

In order to enable unrestricted sample processing research, the fully open-source system software is easily modified by the user. This flexibility gives the user complete control over every aspect of the instrument. Make frequent backups, and exercise extreme care when making software and system configuration changes.


The CEGS 12X features 12 inlet ports and 12 graphite reactors.
The main power switch on the CEGS Control box.
The core process section of the CEGS. After CO2 is liberated from the sample, the coil trap (CT) removes incondensable gases. The variable temperature trap (VTT) purifies the CO2, which is then quantified in the measurement chamber (MC). There, it is split into aliquots, which are sent to graphite reactors (GR) for reduction to solid carbon.

A typical CEGS user interface.

Hovering the mouse over any element displays its description in the status bar at the bottom of the window. Additionally, tool-tip with detailed configuration and state data will pop up for most items. An item-specific context menu is raised when a controllable item right-clicked.

In the main schematic diagram, the colored squares represent valves; red are closed and green are opened. Metering valves are illustrated with a restriction inside; these enable precise flow control. System chambers are formed by tubes and fittings (plumbing) between the valves. Most pressure sensors are illustrated and have numeric displays. Some thermometers are displayed numerically, as well. Other simple rectangles and circles represent heaters or other devices, such as fans. Most light up with an indicating color when in operation.

An array of inlet ports (IPs) connect to the inlet manifold (IM) at the left. The graphite reactors (GRs) are on the graphite manifold (GM) at the right end of the plumbing. The core process section is shown between, comprising a coil trap (CT), a variable-temperature trap (VTT), the measurement chamber (MC), and a small split chamber used for sample-sizing (Split).

Below the process section, the vacuum section includes the vacuum manifold (VM), gas supplies, and the vacuum system. The vacuum system usually operates as an autonomous unit. That is, the user clicks "Evacuate" or "Isolate", rather than directly controlling the vacuum system valves.

Floating at the far right are the liquid nitrogen (LN) and compressed air manifolds. These distribute LN and air to coldfingers (FTCs and the VTC), shown in blue on the main diagram.

At the bottom right is a drop-down list of pre-defined processes which may be selected and started. When a sample is selected or "in process", its data appears at the bottom left.

The Data Visualizer application, displaying a typical VTT CO2 extraction profile.

Technical data

Operating conditions

  • Temperature: +18 °C to +28 °C
  • Humidity: < 60% RH

Storage conditions (stationary)

  • Temperature: -30 °C to +50 °C
  • Humidity: < 95% RH

Mechanical data

Overall dimensions (L x W x H)

  • main CEGS module (bench top): 1250 x 700 x 1120 mm
  • Vacuum Pump System vacuum pump module: 195 x 350 mm
  • UPS: 150 x 195 mm
  • 220 VAC mains power converter option: 250 x 250 mm


  • main CEGS module: 50 to 60 kg, depending on configuration and options
  • vacuum system module: 17 kg
  • UPS: 13 kg
  • 220 VAC mains power converter option: 10 kg

Electrical data

Mains power

  • 120 VAC, 50-60 Hz, single phase, < 1500 VA, or
  • with mains power converter option: 220 VAC, 50-60 Hz, single phase, <1500 VA

Fuses and circuit breakers

  • Control box: 250 VAC, 10A, time-delay or "slow blow" recommended


Many of these performance metrics are profoundly influenced by laboratory conditions and practices, over which Aeon has no control. Others are dependent on the specific system configuration. Therefore, they cannot be guaranteed, and Aeon reserves the right to adjust them at any time without notice. However, the numbers presented here are based on actual factory tests and typical past performance of very similar instruments manufactured by Aeon. As such, they do offer a true and fair representation of the performance capabilities of Aeon's CEGS, and can confidently be used to make meaningful comparisons to alternative approaches.

  • sample constraints
    • total mass: 30 μg to 400 mg
    • carbon content: 30 to 2700 μg C
    • carbon concentration: 0.05% to 100%
    • 14C activity: 0 to 1.3 fM
    • form
      • organic solid or liquid in Aeon combustion tube
      • gas in 6 mm OD x ≤ 150 mm sealed glass ampule
      • gas in septum-sealed vial
  • CO2 collection efficiency: > 97%
  • CO2 transfer efficiency, chamber-chamber: > 97%
  • CO2 quantitification: ± the greater of 1% or 1 μg C, from ~2 to 1200 μg C
  • produced graphite: 30 to 1200 μg C (upper limit configurable)
  • graphitization time: 20 to 180 minutes (typ < 120 min / mg C)
  • graphite yield checked by residual pressure
  • process blank over AMS (aka "system background"): < 0.002 fM (~45,000 years)
  • typical "empty" blank level: below measurement limits
  • sample cross-talk: < 1‰ / mg C
  • throughput: ≥ 1 sample / graphite reactor / day
  • ultimate vacuum: < 5e-5 Torr (typ 1e-6 to 2e-5)
  • furnace temperature control
    • temperature accuracy: ± 10 °C, -196 to 625 °C; ± 20 °C, 625 to 1200 °C
    • repeatability: < 3 °C
    • stability (typical drift full cycle): < ± 3 °C
  • sample step temperature range (recommended): 70 to 850 °C
  • combustion and decomposition temperatures up to ~1200 °C can be used occasionally.
  • variable temperature coldfinger (VTC) for cryogenic purification
    • temperature range: -196 to +50 °C
    • temperature accuracy: ± 5 °C
    • repeatability: < 3 °C
    • stability (typical drift at hold): ± 1 °C
  • trace sulfur removal capability



The person or persons installing the CEGS are responsible for ensuring the safety of the system, themselves, persons nearby, and subsequent users.

The electrical connection of the CEGS to facility power must be made by qualified personnel in accordance with all applicable regulations.

Only trained, qualified personnel may make the gas supply connections to the CEGS.

Only trained, qualified personnel may make the liquid nitrogen and compressed air supply connections to the CEGS.

All personnel participating in the installation and operation of the CEGS must have a full understanding of the hazards presented by the instrument and the substances (gases, liquids) involved. All installation personnel must observe any precautions identified on the material safety data sheets (MSDS).

Voltages up to 120 VAC are present inside the CEGS control box. Do not work on anything inside the control box unless the power cable is unplugged.
Voltages up to 120 VAC are present in some of the cable harnesses attached to the CEGS frame. 120 VAC conductors are always protected with violet (Line) and gray (Neutral) insulation, and their terminals are also fully insulated. Nevertheless, do not touch these wires or their terminals unless the control box power cable is unplugged.

Site requirements

Work area

The CEGS requires a sturdy work surface.

The system is designed to rest on a sturdy work surface, such as a laboratory table or bench top, accessible from at least three sides. The bottom of the CEGS frame fits within a rectangle 1050 mm wide x 520 mm deep. The work surface should be capable of supporting at least 75 kg. The work surface height should ensure convenient access to the inlet ports and graphite reactors by a standing user; typically 760 to 1050 mm is acceptable.

Additional space, typically on the floor below the work surface, is required for the Vacuum Pump System vacuum pumps (395 x 350 mm) and the UPS (150 x 395 mm).

Provide sufficient free space near the liquid nitrogen manifolds for a liquid nitrogen supply cylinder.

Make sure the Control box power switch can be reached at any time.


See Technical Data, Mains power

Liquid nitrogen

The CEGS requires liquid nitrogen. A standard liquid nitrogen cylinder with a 140-240 kPa (22-35 psi) pressure relief valve is suitable. Typical consumption is < 3 liters of liquid nitrogen per sample.

Compressed air

The CEGS requires compressed air: 170 kPa, 140 L/min (> 25 psi, 5 CFM)

Process Gases

The CEGS may require some or all of the following gases to be provided from dedicated pressure-regulated cylinders.

  • Inert gas - Research grade helium or argon; used primarily for displacement of unwanted gases.
  • Oxygen - 99.95% pure O2. The purity of this gas directly affects the minimum achievable organic blank level.
  • Hydrogen - 99.9%+ pure H2. The purity of this gas directly affects the minimum achievable blank level.
  • 14C-free carbon dioxide - Optional. Required for dilution of small samples, to increase the sample mass to meet AMS 14C analysis requirements.

Operating conditions

See Technical data, Operating conditions.


Provision should be made to collect or redirect the condensation that will drip from the various elements of the liquid nitrogen distribution system. The majority of this moisture is generally concentrated in the vicinity of the LN supply cylinder connection.


Initial inspection

Inspect the shipping container for signs of damage, and after unpacking, inspect the CEGS for any indication of mechanical damage that may have occurred in transit. If you suspect the machine was damaged in transit, immediately notify the carrier and Aeon about the damage.


The CEGS is unpacked by disassembling the crate from around it. Begin by removing the crate top. Then detach and remove any accessory containers that may be attached to the hold-down bars. Next remove the bars that secure the CEGS vertically in the crate, and remove the crate sides. Remove the plastic cover from the CEGS. Then, remove any containers or sub-assemblies that are strapped onto to the base plate with the CEGS. Finally, unstrap the CEGS from the base plate.

Heavy, bulky load.

The CEGS is too big and heavy to be handled by one person. At least two people, and preferably more, are needed to lift it from the crate onto the work surface. Do not lift the instrument by the Control box. Lift by the frame.

Once the CEGS is in place, remove the straps from the control box. Remove the control box cover, inspect for loose items, then replace the control box cover.

Carefully remove the zip ties and packing materials that support and secure the inlet port furnace carriages and the graphite reactor furnaces.

Remove the bundle of plastic tubing that is fastened to the CEGS.

Unstrap the wrapped blue foam parts from the CEGS frame and unwrap the devices inside.

Remove the temporary plugs and caps from vacuum system openings. Remove the wire-ties securing loose pressure sensor connectors.

Open each inner container, and unwrap and identify the contents.


Install the Vacuum Pump System valve assembly on the Vacuum Pump System.

Install the measurement chamber (MC) coldfinger and MC FTC.

Install the coil trap with the CT FTC.

Install the VTT coldfinger and the VTC.

Install the FTC air tubes.

Install the LN manifolds:

  • tube retainer
  • FTC inline phase separator tubes and shrouds
  • LN manifold body
  • LN valves
  • TC, TC locator, TC clip
  • LN manifold top

Install the phase separators:

  • absorbent pad
  • phase separator
  • mount
  • duct

Install the FTC LN tubes.

Install the pressure sensors

  • Install the ion gauge, pIG.
  • Install the vacuum manifold high-pressure gauge, pHP.
  • Install the foreline pressure gauge, pForeline.
  • Install the measurement chamber pressure gauge, pMC.
  • Install the coil trap pressure gauge, pCT.
  • If they were removed for shipment, install the inlet manifold and graphite manifold pressure gauges, pIM and pGM.

CEGS connection procedure

Follow this procedure to prepare the CEGS for use at a new location.

Place the UPS beneath the CEGS works surface, near the CEGS control box.

If there is a mains power converter, place it beside the UPS.

Place the Vacuum Pump System beneath the CEGS work surface, so the Vacuum Pump System control panel is readily accessible, and the HV and foreline tubes can be routed to their connection points in the CEGS. Ideally, the HV and Foreline tubes should pass through holes drilled in the work surface.

Connect the HV and foreline tubes between the Vacuum Pump System and the CEGS.

Route the vRvB cable harness along the foreline tube and connect it to the CEGS.

Place the CEGS laptop host computer in a convenient location near the CEGS. The laptop charger power cable must reach the UPS.

If there is a mains power converter, plug the UPS into the converter outlet labeled "CEGS UPS". Otherwise, plug the UPS into a facility 120 VAC outlet.

Plug the following items into Battery + Surge outlets on the UPS:

  • Laptop host computer charger;
    plug the other end into the laptop
  • Control box power cord;
    plug the other end into the control box.
  • Vacuum Pump System power cord;
    plug the other end into the Vacuum Pump System control module.

Plug the CEGS mains detect power cube into a Surge outlet on the UPS (not into a Battery + Surge outlet); plug the mains detect cable into the power cube.

Plug the USB 3.0 SuperSpeed cable into the USB connector of the control box. (Leave the other end disconnected from the laptop for now.

Locate the LN cylinder behind the left or right end of the CEGS. Select the position to ease the routing of the LN supply tubes to the phase separators.

Connect the LN supply plumbing to the LN cylinder.

Route the LN supply tubes to the phase separators. Note: An LN flow restrictor is inserted into the compression fitting at the solenoid valve, before tightening the compression fitting nut.

If necessary, remove the sleeve from the supply line, and use a heat gun to re-form the tube to reach the phase separator.

  • Do not overheat the tube.
  • Do not focus heat on a small area of tube.
  • Instead, warm both the top and bottom of a 15-30 cm section of tube at a time, and form a sweeping bend to direct the end of the tube straight into the phase separator.
  • Form each bend with a somewhat smaller radius than desired, and hold it in that position while it cools. A moist paper towel can be used to cool the tube quickly. The tube will spring back a bit when the holding force is removed.
  • When the tube shape is satisfactory, insert it into the phase separator and gently warm the entire length of tube to relieve stress points along the tube. You should observe the tube relaxing into a natural, low-stress position. During this step, support the tube if needed to avoid excessive sagging.
  • Remove the tube from the phase separator, push the sleeve back onto the tube, and re-insert the tube into the phase separator.
  • Snap the tube into the phase separator support.

Position the LN Overflow sensor on the work surface beneath the LN manifold, and secure it in place with tape.

Place a Yeti cup or other suitable LN container on the work surface under the VTC drain.

Connect the facility air supply line to the CEGS.

Ensure the interiors of the sample and graphite reactor furnaces are free of dust and other foreign material by blowing a moderate stream of compressed air or nitrogen into the bottoms of the furnaces. Use a nozzle long enough to reach the bottom of the furnace well.

Connect the gas supply tubes to the CEGS.

Power up the system according to the CEGS Startup sequence.


Evacuate the gas lines before setting pressures. When adjusting the gas pressures, make sure enough gas is moved to purge the supply lines of air and residual moisture. Set the gas cylinder pressure regulators, using pIM or pGM to check pressure:

  • O2: 1400..1500 Torr
  • He or Ar: 850..900 Torr
  • H2: 1400..1500 Torr
  • CO2: 200..800 Torr

CEGS configuration

The complete system configuration and all state data are stored in the CEGS installation folder, in a single file named "settings.json". When the CEGS is running, the settings file is updated twice per second. The file may be modified using any text editor; however, the CEGS application must be closed while the file is edited; otherwise, the system will overwrite your changes.

Receiving alerts

While the CEGS is running, messages about errors and other important events that require operator attention are transmitted by an alert manager. These messages are sent to the system's own private email account. System operators can configure a remote device, such as a cell phone, tablet, or other computer to receive these messages.

To receive system alerts, you must obtain the system email address and password. These are accessible from within the CEGS application, under Edit > Settings, then AlertManagers > CEGS AlertManager > SmtpInfo. The fields Username and Password contain the system email address and password, respectively. Use these values to set up a new email account on the alert device:

Basic information

System email address: <>
System email password: <gibberish>
Email account type: IMAP
Email "host" or "server":
User name: <use system email address>

Example: Android device, using Samsung Email app

Open Samsung Email
Tap the menu icon ("hamburger") near the upper left,
then the settings icon (gear) in the upper right of the pop-out to open Email settings
from Email settings
Tap + Add account, then tap Other
enter the system email address and password
tap Sign in
select the IMAP account type
Accept all certificates (as many times as needed)
Email sync period: All time
Email sync schedule: Auto (when received)

Example: iPhone

Settings > Mail > Accounts
Add Account > Other > Add Mail Account
On the New Account page, enter:
Name: <any name>
Email: <system email address>
Password: <system email password>
Description: <any description>
then tap Next
Mail will try to set up the account. You may need to confirm:
Account type: IMAP
Host name:
User name: <system email address>
You may need to "Accept all certificates" or similar prompts. To receive alerts instantly, you may need to enable the Push option under Fetch New Data and set the Select Schedule option to Push.


The CEGS is operated from a computer configured specifically for the instrument. The provided software is based on Aeon's Hardware Automation Control System (HACS). HACS is a fully open source (GPL3) software framework designed to enable a programmer to quickly create a Windows application to control a machine or instrument. HACS and the instrument-specific CEGS source code are written in C#, using Microsoft's Visual Studio.

The user can individually control most system elements via the graphical user interface, which resembles a schematic diagram. For example, they could close or open a valve, or adjust the digital filter for a pressure sensor. See User Interface for a brief introduction to the user interface.

However, the user can also select a named process from a drop-down list, and click Start to begin the process. A process is typically a relatively limited task, such as "Admit H2 into the selected graphite reactor", or "Flush the inlet port three times with helium", or "Measure the purified CO2".

Finally, with the Process Sequence Editor, the user can string together a series of processes into a "Process Sequence" which fully processes a sample. For example, the default "Organic" process sequence combusts a sample, collects the gas products, isolates and purifies the CO2, measures the CO2, and then graphitizes it (i.e., using hydrogen to reduce the CO2 gas to solid carbon on an iron catalyst.)

Results are stored in a Sample data text file, and optionally in a user-defined text file for importing into another program.

Additionally, the CEGS continuously monitors temperatures and pressures throughout the system, and records them in a series of log files, which are archived daily. Aeon's Data Visualizer application can present these data in graph form live, or anytime (even years) later.

Startup and shutdown


Follow this procedure to power up the system.

  • Make sure the CEGS application is closed.
  • Make sure the USB cable is unplugged from the laptop host computer.
  • If there is a mains power converter, make sure it is ON.
  • Make sure the UPS is ON.
  • Set the Control box power switch ON.
  • Plug the high-speed USB cable into the Control box USB port.
    Plug the other end into the designated USB port on the laptop host computer.
  • Make sure the laptop host computer is on and start the CEGS application.
  • If the Vacuum Pump System is off:
    • In the CEGS application, set the Vacuum System to Isolate.
    • Ensure the vent valve on the side of the Vacuum Pump System turbo pump is closed.
    • Start the Vacuum Pump System. (Press and hold the power button down for 2-3 seconds.)
    • Wait for the Vacuum Pump System readout to reach 100%.
  • In the CEGS application, set the VacuumSystem to Evacuate.


Follow this procedure to power down the system.

  • In the CEGS application, set the VacuumSystem to Isolate. (Note, this is not required, but it speeds restart pump-down time.)
  • Close the CEGS application.
  • Unplug the CEGS USB cable from the laptop host computer.
  • Set the Control box power switch OFF.
  • Shut down the Vacuum Pump System. (Press and hold the Vacuum Pump System Power button for 2-3 seconds, until the Vacuum Pump System readout displays "Stop". Then press and release the Vacuum Pump System Enter button.)
  • Wait for the Vacuum Pump System readout to reach 0% before doing anything that would admit atmospheric pressure into the vacuum system.
  • Before exposing the interior of any vacuum system plumbing to atmosphere, carefully raise the vacuum system pressure to atmosphere using the vent valve on the side of the Vacuum Pump System turbo pump. Once the flow of gas through the vent valve stops, close the vent valve.

Resuming operations after a significant idle time

If the plug valves are left in the same position for an extended time (more than a week or so), they become increasingly difficult to turn. This happens because the continuous vacuum slowly squeezes the O-ring grease out from between the O-rings and cylinder wall in the plug valve body. To restore normal operation, exercise the plug valves (close and open) several times, to re-lubricate the O-rings.

Starting a process

To start a process, select the desired process from the drop-down list at the bottom right of the user interface, and then click Start. The Start button is hidden while a process is running.

Operator intervention

Even when a process is underway, the operator can directly control the system elements via the user interface. This can be useful in many circumstances. However, this capability also makes it possible for the user to disrupt automatic operations, and can cause the loss of a sample. Therefore, Aeon recommends avoiding manual control of the system while automatic process control is in progress.

Aborting a process

To abort a process, close the CEGS application by clicking the [X] in the upper right corner of its window. Then restart the application. The system state is preserved, but the process is terminated.

Resuming after an abort

After aborting a process, it may be necessary to alter the state of various system devices. For example, a heater may need to be turned off, or a coldfinger might need to be thawed, etc. Typically, these are operations that would have been done by the system, had the process continued normally. In such cases, the operation is usually performed by right-clicking on the device in the user interface to bring up the device's context menu, and then selecting the desired operation from the list presented.

Collected data

Whenever the CEGS application is running, pressure and temperature data are continuously recorded into several system log files. By default, these logs are located in a folder named "log" which resides in the application folder. Each day, most of the log files are archived to a folder named "archive" under the log folder. Aeon's Data Visualizer utility can display the log data in a graph. To view a specific log, open the Data Visualizer, and drag and drop the log file onto the Data Visualizer window. Alternatively, you can use the File > Open menu item and navigate to the desired file to open it.

Aeon recommends compressing old log files into a ".7z" or ".zip" archive on an annual basis. It is also wise to maintain a daily backup of the log folder tree on an independent device or cloud service.

By default, two logs are not archived automatically on a daily basis. These are the system "Event log.txt" and the "Sample data.txt". These files should be archived manually on a regular basis, or when they become excessively large.

Processing samples

The usual course of action to process samples through the CEGS consists of three steps: 1. Prepare the graphite reactors, 2. Load the inlet ports, and 3. "Run" the samples.

Prepare graphite reactors

It is most efficient to combine the unloading of the previously graphitized samples and the loading the new reactor tubes into a single task.

Each graphite reactor accepts two 6 mm borosilicate culture tubes. The vertical tube contains a desiccant, usually anydrous magnesium perchlorate. For brevity, we call this tube "the perchlorate tube". The horizontal tube contains a small amount of powdered metal catalyst, usually iron. For brevity, we call this tube "the Fe tube", as iron is the most common and usually preferred catalyst. When the graphite reaction is complete, the iron powder will be covered, more or less, with the black carbon test sample destined for AMS, but we will still refer to the tube as the Fe tube.

Never touch culture tubes with gloved hands.

Throughout all procedures, when preparing the tubes, and when loading and unloading the graphite reactors, never touch the Fe or perchlorate tubes with gloved hands. This would impart a static charge to the glass, which can easily attract contaminant dust and spoil the sample. You can safely handle the Fe and perchlorate tubes with bare hands. However do not touch within 1 cm of the open ends of the tubes. Any skin oils left there would compromise the O-ring seal in the graphite reactor and could cause the loss of the sample.

Furnaces may be hot.

Raise the graphite reactor furnaces. Do not touch the furnaces or any metal parts on them. Raise and lower the furnaces with the silicone rubber covering on the GR furnace arm. Wait, if needed, for the graphite reactor glass to cool before continuing.

In the CEGS application, start the process "Prepare GRs for new iron and desiccant". When prompted, mark the Fe tubes to clearly identify their contents. Press Ok to continue. After the system back-fills the reactors with inert gas, a message will prompt the operator to replace the Fe and perchlorate tubes.

First, remove the old Fe tubes and cover them with foil caps. Move them as soon as possible to a dust-free area, such as a laminar flow bench, for packing into AMS targets. Then remove the old perchlorate tubes. A gentle tap on the work surface will loosen the spent perchlorate, so that it may be dumped into an intermediate container for subsequent disposal in accordance with regulations.

Into each graphite reactor, install fresh Fe and perchlorate tubes, replacing their O-rings at the same time.

Be sure to re-assemble the graphite reactor correctly.

Take care to avoid misplacing the O-ring seal seat, the circular plastic ring that compresses the O-ring into the graphite reactor fitting. If the seat comes out of the nut, make sure to orient it correctly when returning it to position. The conical face of the seat goes toward the fitting, and the O-ring goes between the seat and the fitting.

To be certain the port is assembled correctly:
  • First place the nut onto the new tube.
  • Then slide the seat, cone side up onto the tube and into the nut.
  • Finally, slide the new O-ring onto the tube.
  • Insert the tube into the correct port on the reactor, slide the nut up to the port threads and turn it until the O-ring begins to compress and hold the tube.
  • Before completely tightening the nut, gently twist and pull the tube out about 1 mm. This is to ensure the rim of the tube doesn't become chipped by the mating metal shoulder in the port.
  • Finally, finger-tighten the nut until it stops. Do not use a wrench.

In the CEGS application, start the process "Precondition GR iron".

Load inlet ports

CEGS inlet ports accept 9 mm or 3/8" diameter tubes.

Organic and other samples that will be combusted to liberate their CO2 are loaded into 9 x 150 mm quartz combustion tubes for processing by the CEGS. The system refers to this inlet port configuration as type "Combustion".

Samples that will be subjected to a wet chemistry procedure to liberate their CO2 can be conveniently processed in septum-sealed vials. To accommodate these, a 3/8" tube to Luer adapter is provided with each inlet port, along with a needle and a silicone stopper. Aeon recommends processing carbonate samples in septum sealed vials for extraction and graphitization by the CEGS. The system refers to this inlet port configuration as type "Needle."

A breakseal adapter, suitable for 6 mm x 125 mm sealed glass ampules, is provided for processing sealed CO2 gas samples. At the appropriate time, the system notifies the operator to release the sample, by bending the adapter, which breaks the ampule. Because operator intervention is required to release the sample, the system refers to this inlet port configuration as type "Manual."

Any port can be independently configured as type Combustion, Needle, or Manual. However, because banks of inlet port furnaces move together, it is best when processing organic samples to process only organic samples together on the same bank. Needle and Manual samples, though, can be intermixed as convenient.

Combustion port

It is important to load the combustion tube as follows:

A column of quartz media is loaded directly into the combustion tube above the sample. During combustion, the quartz is heated to 800 °C to ensure that all carbon is fully oxidized. The fine media "quartz sugar" also mitigates the intrusion of contaminant particles into the vacuum system. Replacing the quartz oxidation bed with every sample helps minimize cross-contamination.
Never touch quartz combustion tubes with gloved hands.

Throughout all procedures, never touch the combustion tube with gloved hands. This would impart a static charge to the glass, which can easily attract contaminant dust and spoil the sample. You can handle the tube with tweezers, with a strip of foil, or even with bare hands if careful. If using bare hands, do not touch the combustion tube within 1 cm of the rim. Any skin oils left there would compromise the O-ring seal at the inlet port and could lead to a lost sample.

Handle quartz durham tubes with clean tweezers only. Never touch with hands.

The durham tubes go into the combustion tube with the sample. Any contaminants on the durham tube will be mixed into the sample CO2 and compromise the sample.

A combustion chamber loading template is provided with the system.

  • Use the template to mark a baked-out combustion tube (9 x 150 mm quartz culture tube).
  • Mark the top and bottom of the quartz sugar region, and the top of the quartz beads.
  • Use the sample loading funnel to transfer a pretreated organic sample into a baked-out durham tube (6 x 25 mm quartz culture tube).
  • With the combustion tube laying on its side on a clean, disposable work surface, slide the durham tube, inverted, into the combustion tube.
  • Then tilt the combustion tube up, so the durham tube with sample falls smoothly to the bottom of the combustion tube.
  • Pour baked-out quartz beads into the combustion tube, up to the bottom mark.
  • Pour baked-out quartz sugar into the combustion tube up to the middle mark.
  • Pour baked-out quartz beads into the combustion tube, up to the top mark.
  • Cover the combustion tube with a foil cap until ready to load it into an inlet port.
  • Be sure to clearly identify the combustion tube contents (e.g., sample Lab ID).

To load the combustion tube into the inlet port, first lower the furnace carriage. Then loosen the nut at the bottom of the port, insert the combustion tube and back it off about 1 mm away from the shoulder inside the port, then tighten the fitting nut.

Needle port

Needle ports are used to process CO2 gas, commonly prepared by acid digestion of carbonate samples. First, lower the furnace carriage. Then insert the needle port adapter, with the needle and stopper attached, into the inlet port and secure it by tighting the fitting nut. The vial must be evacuated before acid digestion. The process "Prepare carbonate sample for acid" does this. Additionally, after digestion, the vial must be loaded onto the needle, while avoiding atmospheric contamination. This is accomplished by running the process, "Load acidified carbonate sample". In both of these processes, it is important to follow the on-screen instructions carefully.

Manual port

Manual ports are used to process CO2 gas in sealed glass ampules. Before loading the ampule into the breakseal, carefully clean the ampule, score it approximately 25 mm from one end, and gently insert it scored end first into the breakseal. Lower the furnace carriage. Then insert the breakseal into the inlet port and tighten the nut. At the appropriate time, the system notifies the operator to release the sample, by bending the adapter, which breaks the ampule.

Run samples

Enter sample information

After the samples have been loaded into inlet ports, use the Sample Editor (Edit > Samples, then New...) to enter the sample information into the CEGS.

  • Lab ID: Enter the sample's Lab ID.
  • Mass: Select your preferred units and enter the pretreated sample mass.
  • InletPort: Specify which inlet port the sample was loaded into
  • Port Type: Select the inlet port configuration.
  • Process: Choose the appropriate Process sequence for the sample.
  • Graphite IDs: Assign up to three Graphite IDs, each on a separate line, according to the number of aliquots the sample should be divided into.
  • Sulfur suspected: If heavy sulfur contamination is expected, check this box. The system will perform a special trace sulfur-trapping procedure before graphitizing the sample. Note that each trace sulfur-trapping procedure uses a graphite reactor, which will no longer be available for samples.

Start the "Run samples" process

To select and run the loaded samples, Start the "Run Samples" process. A sample selection dialog appears with a list of available samples. Select which samples to run, confirm and check-off the conditions in the checklist, and then click Ok to begin the first sample. The system sends a notification when the samples are complete.


Inlet ports

Aeon recommends replacing inlet port O-rings and frits periodically or whenever visible contamination is detected in the inlet port cold trap. This area should be inspected every few weeks, or immediately after any large, dirty sample, such as bulk sediment, has been processed. To inspect the cold trap, remove the nut, ferrule, and O-ring from the bottom of the trap. Moisten a clean cotton swab with isopropyl alcohol and wipe it in a circular motion inside the fitting. If any discoloration appears on the swab, the port needs service. After service, or if none is needed, re-assemble the cold trap for continued use.

To service the port, remove the cold trap (Ultra-Torr fitting) from the tube that enters the inlet port valve. Completely disassemble the cold trap. Thoroughly clean its interior and ferrules with isopropyl alcohol. A a nonwoven abrasive pad may be necessary to remove stubborn deposits. Install a new frit and new, baked-out FKM O-rings. Avoid touching O-rings with your hands (use tweezers) and use absolutely no grease.

Before re-installing a serviced cold trap, moisten a clean cotton swab with isopropyl alcohol and wipe it in a circular motion inside the tube that enters the inlet port valve. If any discoloration appears on the swab, the inlet port tube requires service. After servicing the inlet port tube, or if service is not required, re-install the cold trap for continued use.

Inlet port tube service

Make a mark on the front of the nut that secures the inlet port tube to the inlet port valve; then loosen the nut from the inlet port valve using a 9/16" wrench, taking care to hold the valve body stationary with an adjustable wrench to avoid torquing the inlet manifold above. Remove the nut and tube from the valve. Remove the inlet port screen from within the valve inlet fitting, clean the fitting inlet with cotton swabs and isopropyl alcohol, and replace the inlet port screen with a new one. Do not attempt to clean and reuse a dirty inlet port screen.

Thoroughly clean the interior of the inlet port tube using only isopropyl alcohol and cotton swabs. The interior of the tube is electropolished to a mirror finish. If the tube is not easily restored to its "like new" mirror finish condition, contact Aeon for a replacement. Additionally, if there is any reason to suspect that the inlet port valve may be contaminated beyond the inlet port screen, contact Aeon for guidance; major maintenance may be required.

Do not reinstall the inlet port tube without a new inlet port screen.

The inlet port screen provides critical protection to the inlet port valve, the inlet manifold and the vacuum system. If you must operate the CEGS with an inlet port screen absent (for example, while a new one is on order), then disable the port from its context menu in the CEGS application, and do not use that port or open its valve until the screen has been replaced.

After cleaning the inlet port tube and replacing the inlet port screen, reassemble the inlet port tube into the inlet port valve. Re-tighten the fitting nut only enough to restore the mark to its original position.

Graphite reactors

Aeon recommends replacing both the iron and perchlorate port O-rings between samples. Use only FKM O-rings, preferably baked-out, and never grease.

Plug valves

Service every two years, more often with heavy usage, or if valve performance is degraded.

  • Remove the circlip and valve plug.
  • Clean the valve interior with dry lab wipe.
  • Remove the old O-rings from plug carefully; avoid scratching the O-ring grooves.
  • Clean O-ring grooves and surfaces with dry cotton swabs and lab wipes.
  • Inspect under bright light and magnification and blow off any lint or fibers with compressed nitrogen or clean, dry air.
  • Install new, baked-out FKM O-rings.
  • Re-grease only the accessible surface of O-rings with small dabs of Dow High Vacuum Grease.
  • Reinstall the valve plug and circlip.

Vacuum system (Vacuum Pump System) pumps

Maintain vacuum system pumps in accordance with the manufacturer recommendations. Refer to the individual pump manuals for details.

Storage and disposal



Perform the shutdown procedure.

CEGS disconnection procedure

Follow this procedure to prepare the CEGS for moving to a new location.

  • Shut down the laptop host computer.
  • Shut down the UPS and unplug it.
  • Disconnect the CEGS USB cable from the laptop host computer.
  • Close the LN supply cylinder's liquid valve.
  • Close the facility air supply valve.
  • Close all gas cylinder valves (top of cylinder).
  • Disconnect the LN supply solenoid valve cables from the CEGS.
  • Unclamp and remove the LN supply tubing from the phase separators.
  • Disconnect the LN supply plumbing from the cylinder
  • Disconnect the air supply line from the facility air supply valve at the tee
  • Disconnect the air supply line from the CEGS at the regulator.
  • Disconnect all gas supply lines from the CEGS.
  • Disconnect the vRvB cable harness from the CEGS.
  • Disconnect the foreline and high vacuum tubing from the CEGS.
  • Lock the IP furnace carriages.
  • Lower the GR furnaces.
  • Unplug the following from the UPS:
    • Control box power cord
    • Laptop host computer charger
    • Vacuum Pump System power cord
    • CEGS mains detect
  • Disconnect the USB cable from the Control box.
  • Disconnect the power cord from the Control box.


Throughout the term of storage, ensure that the proper storage conditions are maintained.


Dispose of system in accordance with all applicable safety and environmental regulations. Do not incinerate.

Accessories and spares

Consumable materials

Consumable materials used in the CEGS may be purchased from Aeon, but it may be more economical to purchase readily available items from the OEM or larger distributors.

Commercial, off-the-shelf items

  • iron powder 99.95% 325 mesh 500 g
    for: graphite reactor catalyst
    from: Noah Technologies (, PN 11593
    consumption: ~2.5 .. 2.75 mg / sample
  • magnesium perchlorate chips, anhydrous
    for: graphite reactor desiccant
    from: various chemical suppliers, e.g., Sigma-Aldrich (, PN 222283-500G
    consumption: ~30 mg / sample
  • borosilicate culture tube 6 x 50 mm
    for: Fe and MgClO4 tubes in standard (1/4") graphite reactors
    from: Kimble (, PN 73500-650 N-51A
    consumption: ~2 ea / sample
  • quartz beads (2mm rod x 2 mm)
    for: CO oxidation, particulate combustion product suppression
    from: Quartz Scientific (, PN 3910202
    consumption: ~2.4 g / organic sample
    note: may be cleaned, baked out and re-used
  • O-rings, FKM 75A
    for: elastomeric seals
    from: various industrial supply companies
    SAE AS568-010: 2 ea / sample (standard 1/4" graphite reactor)
    SAE AS568-012: 2 ea @ inlet port when servicing port,
    service frequency depends on samples processed,
    typical is perhaps 2 ea / 30-100 samples
    other sizes as needed infrequently for maintenance (detailed list available)
    note: Aeon recommends baking out FKM O-rings prior to use and storing in desiccated cabinet.
  • needle 22g x 3/4
    for: needle ports for septum-sealed vials
    from: various medical supply outlets
    consumption: very low, perhaps 1 ea / 100 samples
  • plastic or metal frit <20 μm pore size, 6 mm .. 1/4 inch OD
    for: inlet port particulate filter
    from: various chromatography suppliers
    consumption: replace when dirty,
    service frequency depends on samples processed; perhaps 1 ea / 30-100 samples
  • high vacuum grease
    for: lubricating dynamic elastomeric seals (plug valve O-rings)
    from: Dow Corning, PN DC-HI-VAC
    consumption: very little, used only for infrequent periodic valve maintenance;
    one tube will last for years.

Commercially available specialized consumables

  • quartz combustion chamber tube 9 x 150 mm
    for: organic sample combustion
    from: various scientific glassworking companies
    make from standard 9 x 1 mm wall fused quartz tubing
    consumption: 1 ea / organic sample note: may be cleaned, baked out and re-used
  • quartz sample "durham" tube 6 x 25 mm
    for: organic sample combustion
    from: various scientific glassworking companies
    make from standard 6 x 1 mm wall fused quartz tubing
    consumption: 1 ea / organic sample note: may be cleaned, baked out and re-used
  • "quartz sugar" (0.5 .. 0.9 mm crushed quartz chips)
    for: CO oxidation, particulate combustion product suppression
    from: Aeon Laboratories or customer
    consumption: ~0.8 g / organic sample
    note: may be cleaned, baked out and re-used
    To make this item, Aeon purchases recycled crushed quartz, 0.5 mm - 1 mm, PN 7359-05010, from Aeon then sifts the supplied material to select the 0.46 .. 0.86 mm fraction (-24 / +42 mesh). The remaining selected fraction is thoroughly cleaned and dried, and is then ready for bakeout.

Aeon-recommended lab supplies and tools

  • weighing paper 3x3
    for: sample and reagent handling
    from: Chang Bioscience
    PN: HJWP005
    Amazon ASIN: B00OWM4WVA
    What's so great about it:
    This very thin weighing paper is much less likely to accidentally fling your tiny sample or small-quantity reagent than heavier offerings.
  • weighing paper 6x6
    for: clean, disposable work surface
    from: Chang Bioscience
    PN: HJWP007
    Amazon ASIN: B00OWMBVRS
    What's so great about it:
    Lightweight and inexpensive. Place a new one under each sample or between reagent changes at the weighing table to avoid cross-contamination.
  • septum sealed vials
    for: processing carbonate samples
    from: Labco
    PN: 838W
    What's so great about it:
    These 12 mL flat-bottom Exetainer® vials are commonly for storing CO2 samples. With careful handling and proper procedures, they serve well for the acid digestion of carbonates. The pre-evacuated vials stay dry, preventing contamination by dissolved atmospheric CO2 in condensed moisture.
  • for: sample handling and perchlorate loading (keep separate instruments for each task)
    from: Bioquip is permanently closed. Best alternate: DR Instruments Featherweight Entomology Forceps Long Points
    PN: DRENTF01
    Amazon ASIN: B008RBLO8Q
    What's so great about it:
    These super-flexible tweezers provide gentle but reliable grip for fragile materials. They are easily bent to adjust the parallelism between the tips, and the spring force applied to the material being handled. These are much less likely than other instruments to crush the material or let it fly.
  • Jensen Tools Techni-Pro Type 2AD Tweezers
    for: handling weighing paper and general-purpose. These are extremely handy, excellent quality tweezers with numerous uses.
    from: Jensen Tools
    PN: 758TW468
    What's so great about it:
    The 2 mm wide tips taper to a very thin (not narrow) tip. They easily slide under a single piece of weighing paper with no risk catching the edge and bucking your sample into the air. The wide, flat tips solidly grip the paper so it can be easily curled forward or back, without slipping, rotating, crinkling or puncturing.


Spare and replacement parts for the CEGS can be found at If you can't find what you are looking for, please Contact Aeon for assistance.

Special tools

  • blow gun with 1/8 OD x 9" nozzle
    for: flushing dust out of culture tubes
    from: Aeon
    PN: AP-BG705+125x9.0
    Must be used with clean, dry compressed air or nitrogen. Do not connect to ordinary facility-provided compressed air. Recommended pressure: 140 kPa (20 psi).
    Do not allow higher than the recommended pressure. Hold culture tube securely. Blow off the outside top of culture tube first. Then insert nozzle down to bottom of tube. Squeeze and hold trigger while withdrawing the nozzle up and out of the culture tube. Failure to follow these instructions carefully can launch a culture tube with dangerous velocity.
  • Fe powder pickup probe
    for: transferring Fe powder from vial to analytical balance for weighing
    from: Aeon

    Wipe the probe tip with a lab wipe before first use of the session, then blow clean dry air or nitrogen across it to ensure no dust or lint remains on the probe tip. Roll the Fe powder vial between fingers at an angle to loosen the powder and shift it toward the vial opening. Collect a small amount of powder on the probe tip by dipping into the powder. Carefully withdraw the probe from the vial and hold it above the weighing paper in the balance. Gently tap the probe handle to release some powder onto the paper. Close the balance door and wait for the reading to stabilize. If the mass is too low, add more Fe by tapping the probe as before. If it is too high, pick up some of the powder by gently touching the probe tip to the powder on the paper.

    This tool is nothing more than a bent dissecting needle, or teasing needle, which has been magnetized at the tip. Any such needle is suitable as long as its needle is magnetic. Aeon provides this tool only because many dissecting/teasing needles are not magnetic.

  • Fe powder magnet tall
    for: consolidating weighed Fe powder before transfer to culture tube
    from: Aeon
    PN: AP-IPM5

    Stand the magnet assembly on a magnetic work surface near the analytical balance. The larger magnet at bottom of the rod should be stuck to the work surface. The smaller magnet should be stuck to the top of the rod. Make sure a clean, already-flushed 6 x 50 mm pyrex culture tube is ready and within reach.

    Take the weighing paper with the already-weighed Fe powder and carefully place the center of the paper onto the top magnet. The powder should instantly be collected on top of the paper toward the magnet beneath. Hold the magnet rod stationary with one hand and use the other hand to drag one edge of the paper under the powder away from the rod, until the powder approaches the opposite edge of the paper. The powder should remain 5-10 mm away from that edge.

    Continue holding the rod, and with the other hand now under the paper, curl the sides of paper up into a U-shape, with the powder at the bottom of the U. About half way up the sides of the U, above the powder, pinch the sides together between your thumb and fingertip, and lift the paper and powder together straight up off the magnet. All of the powder should remain collected in place on the paper. Do not let the powder fall toward the magnet or shift on the paper.

    With the hand that was holding the magnet rod, take the culture tube and hold it with the top tilted toward the bottom of weighing paper / powder. Place the base of the U by the powder onto the rim of the tube. The edge of the paper should be within the mouth of the tube. Rotate the tube and paper together as a single unit, so the tube becomes vertical, and the powder falls from the paper into the mouth of the tube.

    Holding the tube vertically, place the side of the tube about 10 mm below the rim against the top magnet. Draw the tube upward until it leaves the magnet. All the the iron powder should now be collected at the bottom of the culture tube. Cap the tube with foil and store it in a suitable rack until time to load the graphite reactors.

  • Fe powder magnet
    for: consolidating Fe powder in culture tube after loading into graphite reactor
    from: Aeon
    PN: AP-IPM3

    The larger magnet at bottom of the rod is intended merely to store the tool on a convenient magnetic surface near the graphite reactors.

    After the graphite reactors have been loaded with new Fe tubes: Hold the rod vertically with the small magnet on top. Raise the magnet straight up from below each Fe tube until it contacts the lower surface of the tube beside the metal fitting. Slide the magnet away from the fitting along the underside of the tube. Upon reaching the end of the tube, draw the magnet straight down away from the tube. The powder should form a "flower" at the tip of the tube.

  • Sample loading funnel
    from: Aeon
    for: transferring a sample into a 6 x 25 mm quartz culture tube ("durham" tube)
    PN: MP-SLF

    Prepare a clean, disposable work surface near the analytical balance, for example, by placing down a fresh 6 x 6 weighing paper. Onto the work surface, place a fresh 3 x 3 weighing paper, to catch and recover any spilled sample material.

    Select two clean sample loading funnels. (Aeon recommends cleaning the funnels between uses.)

    Place one funnel, cone side down (i.e., inverted), onto the center of your 3 x 3 paper. Using clean tweezers, take a clean, baked out durham tube from its container. Insert the tube vertically, open end up, into the the inverted funnel. Place the second funnel, cone side up, onto the top of the durham tube.

    Take the weighing paper with the weighed test sample from the analytical balance and place it onto the work surface. Use flat-tipped tweezers to pick up the far edge of the paper and tuck it into the gently pinched thumb and forefinger of your free hand, poised over the sample. Then use the tweezers to pick up the near edge of the paper and tuck it into the same pinch. The paper should form a teardrop shape with the top edges between the thumb and forefinger of your dominant hand, and the sample cradled on the paper beneath the pinch, still in contact with the work surface.

    Lift the paper carefully, and bring the bottom of the paper's free edge into the loading funnel. Keeping the paper's edge within the funnel, carefully rotate the paper to pour the sample into the funnel. If needed, gently tap the paper so that all of the sample leaves the paper and enters the funnel. Discard the paper. If needed, gently tap the side of the funnel with the tweezers so all of the material fall from the funnel walls into the durham tube.

    Slightly lift the top funnel, enough that you can reach between the funnels with the tweezers and take hold the durham tube with them; then, lift the funnel the rest of the way off of the tube and set it aside. Lifting the top funnel without holding the durham tube down may cause the tube to come out of the bottom funnel and spill the sample.

    Lay a clean, baked-out combustion tube on the work surface beside the inverted funnel. Use the tweezers to place the open end of the durham tube into the mouth of the combustion tube. With the combustion tube still laying on its side, use the tweezers to push the durham tube into the combustion tube. Once the closed end of the durham tube is inside the combustion tube, lift and tilt the open end of the combustion tube, so that the durham tube falls smoothly to the bottom of the combustion tube.

    Refer to the Combustion port loading procedure for additional details on preparing the combustion chamber for loading into the CEGS.

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