Covaris E220 evolution User manual

Covaris E/LE220
Service Manual

410072 E/LE-series Service Manual Rev E
CONFIDENTIAL FOR INTERNAL USE ONLY
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Table of Contents
1. Scope of this Manual 3
2. Safety & Compliance 3
3. Introduction 4
4. Maintenance & Repair 7
Daily Maintenance 7
Periodic Maintenance 7
Troubleshooting 8
Ineffective Treatment Topics 9
Repair Procedures 13
Aligning Motion Stages 13
Center Position 22
LE Center Position 25
Cabinet Disassembly 28
Servicing the X, Y, Z, & Z-prime Stage Assemblies 33
Stage Replacement Procedures 35
Z Stage 36
X/Y Stage 37
Z-prime Stage 39
Motion Controller Board 41
Degas Pump Replacement 42
5. Diagnosing & Replacing PCBs 45
Theory of Operation 45
RF Power Board 47
RF Controller Board 51
Capacitor Reserve Board 55
Transducer & Matching Network 57
Accessing Instrument Configuration Settings 60
6. Power Calibration Verification 62
7. Installing SonoLab Software 63
8. Tools and Fixtures 63
9. Appendix 64
Spare Parts 64
List of Service Notes 65

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1. Scope of this Manual
This manual is intended provide Covaris service personnel the necessary information to
perform effective fault finding and corrective actions for the Covaris E/LE220-series
sample preparation instruments, running SonoLab version 6.2.
The following definitions apply in this manual:
NOTE: Inconvenience only if disregarded –no damage or personal injury will result
CAUTION: Equipment damage may occur, but not personal injury.
WARNING: Personal injury may occur –DO NOT DISREGARD.
2 Safety and EMC Compliance Information
2.1General Instrument Safety
2.1.1 Acoustic Safety
The Covaris E-Series instruments generate a focused high-power
acoustic field in the water bath. Potentially hazardous acoustic
energy exists in the water bath, including the entire sample vessel
(above and below the water level). Service personnel who run the
instrument with the safety system defeated must not touch the
water bath or the sample vessel.
WARNING: Service personnel who run the instrument with the safety system defeated
must not touch the water bath or the sample vessel.
2.1.2 Safety and Electromagnetic Compatibility (EMC)
Standards
Safety: Meets Low Voltage Directive 73/23/EEC with Amendment
93/68/EEC. Tested to EN/UL/CSA 61010-1:2004 Safety
Requirements for Electrical Equipment for Measurement, Control
and Laboratory Use, Part 1: General Requirements EMC: Meets
EMC Directive 2004/108/EC. Tested to EMI emissions
requirements for Industrial Scientific or Medical (ISM) equipment
EN55011:1998 + A2:2002 Class A Group1 and EMC requirements
- Electrical Equipment for Measurement, Control, and Laboratory
Use EN 61326-1:2005 Table 2,EN61000-3-2:2004 and EN61000-
3-3:1995 +A1:2001

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3 Introduction
The Covaris Adaptive Focused Acoustics process works by sending
converging acoustic energy wave packets from a dish-shaped transducer to
a small, localized area. Mechanical energy is thus applied to the sample,
without directly contacting the sample. At low energy intensities, gentle
mixing is affected. At high energy intensities, intense shock waves result
in cell lysing or tissue disruption. The E-series accomplishes this via the
following subsystems, under the control of the Covaris SonoLab software.
3.1 Transducer
The transducer converts an electrical signal into an acoustic signal.
Specifically, a burst of electrical sine-waves is converted into a series
of acoustic pressure waves. The transducer is focused such that the
pressure waves converge at a focal point inside the treatment vessel.
The primary mechanism to process a sample or compound is the
growth and collapse of cavitation bubbles within the acoustic focal
zone, inside the sample vessel. The collapse of the bubbles results in
an intense, localized jet of solute acting upon the sample.
3.2 Interlock Subsystem
Safety interlocks prevent motion and energizing of the transducer
when doing so might result in damage to the transducer or injury to
operators.
3.3 Degassing System
In order for the acoustic process to function properly, the level of
dissolved gas in the water bath must be reduced. A positive-
displacement degassing pump pulls vacuum on an inlet tube
submerged in the water bath. This inlet tube has 6 small holes through
which the bath water enters. The sudden pressure drop inside the tube
causes dissolved gasses to come out of solution and form bubbles. The
water and the bubbles flow through the pump to the outlet tube before
the gas can re-dissolve in the water. The bubbles float to the surface
and vent to the atmosphere.
3.4 Motion Control System
The Covaris E-series is designed to treat multiple samples placed in a
tray, without further operator intervention once the run is started. The
system automatically positions each sample at the transducer’s focal
point.
The motion of the tray is implemented by stepper motors driving three
mechanical stages, one for each axis: x, y, and z. The x-axis is front to
back motion, the y-axis is left to right, and the z-axis is up and down.

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The x and y stages consist of a single assembly, which, if necessary,
must be replaced as a unit. The z axis is a separate stage, bolted to the
x and y assembly. An additional stage, z` (z-prime), raises and lowers
the transducer assembly into and out of the water bath.
The E-series robotic incorporates an additional shuttle stage and
modified enclosure, allowing the sample tray to interface with a
customer supplied sample handling robot.
A Galil brand motion controller interfaces between the SonoLab
software and the hardware stages.
The E-series robotic option adds a Trinamic single axis stepper card,
controlled via a digital I/O port on the Galil controller. This Trinamic
board drives a stepper motor which positions the shuttle stage
described above.
Motion Control Electronics at Rear of Enclosure.
3.5 Control Electronics System
The control electronics are mounted at the top, rear of the instrument
enclosure and connect to components located in the treatment area via
bulkhead connectors. A 24 volt DC power supply provides power for
the low voltage and digital components on the following assemblies:
the RF Power Board, the RF Controller Board, the degassing pump,
the cooling fan, the interior cabinet lamp, and the Galil motion
controller. Additional voltages are derived from the main 24 volt

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supply. A single 48volt DC power supply in conjunction with a
capacitor storage assembly provide power to the transducer, via the RF
Power board. See Figure below.
The operation of the control electronics is detailed later in this manual.
Boards and Power Supplies in Upper Rear Enclosure
RF Power Board
RF Controller Board
Capacitor Board
24 Volt Power Supply
48 Volt Power Supply
Matching Network

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4. Maintenance and Repair
4.1 Recommended Daily Maintenance
WARNING: The water bath is heavy when filled. Use caution when moving it.
At the start of each day, fill the water bath as follows:
•Click the “Service Bath” button on the main screen. This will
move the mechanics to the service position.
•Fill the water bath tank with AFA grade distilled or deionized
water only.
•Slide the bath into position in the instrument.
At the end of the day, the bath should be emptied as follows:
•Click the “Change Bath” button on the main screen. This will
move the mechanics to the service position.
•Slide the water bath out of the instrument and empty it.
•Replace the empty water bath, and run the degas pump a few
seconds to empty the pump lines.
•Empty the bath, and wipe it down with a soft cloth.
•Sponge off the transducer with a soft cloth or sponge, and
allow it to dry.
The above steps can be changed from daily to monthly if customer
uses a Covaris Water Conditioning System (WCS).
4.2 Periodic Maintenance Procedures
Periodic maintenance (PM) service involves cleaning, inspection, and testing of the various
instrument subsystems. Refer to Covaris document PN 440192 for the formal procedure.

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4.3 TROUBLESHOOTING
System Trouble Analysis Chart
SYMPTOM
PROBABLE CAUSE
POSSIBLE SOLUTION
Error message “Unknown
Instrument Type”
Device Com ports were
assigned incorrectly
See Figure in Appendix B in
this manual for COM Port
assignment verification.
Degassing system not
generating bubbles.
1. Degassing dip tube may be
clogged
2. Pump not working
1. Remove and backflush
under running water. Use
fine wire to unclog holes.
2. Replace pump.
Incorrect positioning,
inconsistent treatments
1. Home position lost, system
misalignment
2. Wrong Well Plate Definition
used
1. Reinitialize system by
clicking ‘Home’ on the Ctrl-
shift-F1 screen (SonoLab 6)
or clicking ‘Home’ on the
‘Run’ screen (SonoLab 7).
2. Verify correct Well plate
definition selected
Safety interrupt
1. Water tank is misaligned
2. Door is open.
3. STOP button is depressed
4. Door interlock is bypassed
1. Check tank alignment
2. Check door
3. Check safety interlock
4. Correct Door Interlock
Homing/Initializing not
completed successfully
1. Stage limit switch failure
2. Stage motor stalling
1. See section on stage and
limit switch service in this
manual.
2. Ensure nothing obstructs
stage movement
Values for Dithering and
Vertical Sweep are different
from the values that were
entered
Values entered are larger than
the limits for a particular Well
Plate
Use lower values

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4.4 Ineffective Treatment Topics
Water Bath, Degassing, and Transducer Issues
•Buzzing Noise
A loud buzzing noise indicates that cavitation is occurring
on the outside of the treatment vessel rather than on the
inside. Cavitation on the outside of the vessel prevents the
acoustic energy from getting through the vessel to the
sample. In order for the water bath to effectively conduct
the energy to the sample it must be degassed and clean.
•Degassing
Degassing takes a minimum of 60 minutes in room
temperature water; do not attempt to degas chilled water.
The dissolved oxygen level should be 3.5 parts per million
or less in room temperature water; it will be somewhat
higher at temperatures below 10 degrees C. While oxygen
is not the only gas dissolved in the bath, it is not practical to
measure them all. Covaris has determined that a dissolved
oxygen reading of less than the described limits indicates
that the total dissolved gas is sufficiently low to allow
satisfactory operation of the acoustic process.
Test the dissolved oxygen level with either a dissolved
oxygen meter (see list of tools and equipment) or with
Covaris’ Degas System Verification Kit, part number
520143.
Service Note 410076, included with the kit and available
separately, describes the testing procedure.

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Sensors and inlet tubes mounted on transducer bracket
If the pump is running, but there are no bubbles coming from
the outlet tube, the small holes in the inlet tube may be
clogged. Raise the transducer arm in the service position and
slide out the inlet tube. Unblock the holes by rinsing, or, if
necessary, by using a fine wire.
End of inlet tube
showing small openings.
Once the tube is cleaned, slide it into the bracket, working it
past the o-ring seal until it bottoms. A tube that is not seated
properly will result in excessive bubbling.
Water Level Sensor
Degas Inlet Tube
Degas Outlet Tube
Temperature Sensor

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Contamination
The water bath can become contaminated from the growth of
biofilm in the tank or from debris on sample vessels.
Contamination does not have to be visible to affect processing.
If there is any doubt about the cleanliness of the water bath, it
should be changed. Wipe down the inside of the tank and all
submerged surfaces, including the transducer, with a soft, lint-
free cloth before refilling with distilled or de-ionized water.
Bath Temperature
A chiller is required to remove heat from the acoustic treatment
and the degassing system. For high-power operation, the bath
temperature should be set according to the recommendations in
Covaris Protocol section on the website. Covaris can supply or
specify an appropriate chiller.
Position of Treatment Vessel
If the treatment appears to be missing the treatment vessel,
make certain that you have selected the correct tray type in
your process setup. If this is correct, and the treatment misses
the vessel in all tray positions and all treatments, the motion
system may have lost its position. Reset the motion system by
clicking the “Home” button on the “Run” screen (SonoLab 7)
or the “Home Stage” button on the Ctrl-Sh-F1 screen (SonoLab
6).
Water Level Errors
If water level errors are not resolved by cleaning the sensor and
eliminating any sources of stray ambient light, the sensor
should be replaced. Raise the transducer bracket assembly to
the service position. Referring to Figure 5 below, remove the
water level sensor retaining screw and remove the sensor
assembly from the transducer bracket. Disconnect the sensor’s
cable at the bulkhead. Reverse the process to install the new
sensor. Dress the sensor’s cable to the other cables using a
cable tie

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Water level sensor assembly
Testing Acoustic Power
Follow the acoustic power test procedure described in Section
6.
Transducer
If the software graphics indicate higher power than normal
while the bath and sample vessel little activity, the transducer
may be failing. Perform the acoustic power checks described
in Section 6, and replace the transducer if necessary.
Interlock Errors
The primary interlocks in the E-series are the magnetic sensor
which verifies that the water tank is in place and the red lock
securing the access door when acoustics are active. If the door
is closed, but the software indicates that it is not, the interlock
may have been deactivated. Re-activate the interlock using the
special tool mounted to the rear of the instrument cabinet. See
the figure below.
Over-riding the door interlock

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Communication Errors
In the event of communication errors, verify that the problem is not
a defective USB cable. Verify that the internal USB cable is
secure.
4.5 Repair Procedures
Aligning Motion Stages
Note: for SonoLab 7 instruments, refer to sections 9 through
12 of document 440144, E_LE220 Alignment Procedure.
Current motion parameters will be maintained in the 440144
document. The procedures are generally the same as described
below, but include alignment of the E220 evolution.
SonoLab 7 motion parameters are accessed through the SonoLab 7
‘Motion’ tab, while SonoLab 6 motion is controlled from the
‘Control-Shift-F1’ screen. Functionality is very similar, though
some buttons will be named slightly differently. For instance, the
SonoLab 6 ‘Go to Center’ button is equivalent to the SonoLab 7
‘Center Position’ button. Instructions below will refer generically
to “the motion screen”, and assume that service personnel
understand these small differences.
Any time a motion stage, transducer bracket, or tray bracket is
installed, crashed, or disturbed in some manner, the mechanical
alignment must be checked, and corrected as necessary. Aligning
the mechanics requires the calibration fixture set described in the
appendix and/or appropriate well plates, depending on software
version. See section, “Using the SonoLab Software to Control
Motion”, elsewhere in this chapter, for specific instructions on
operating the motion system.

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Aligning the Sample Holder
Dial Indicator and Holding Fixture
Potential Alignment Tools Required
3/32 Hex Allen Wrench
7/64 Hex Allen Wrench
5/32 Hex Allen Wrench
1/8 Hex Allen Wrench
Alignment Kit p/n 500313
Alignment Plate PN 900809 (E220 evolution only)
Height Gauge Plate PN 900810 (E220 evolution only)
Use the arrow controls on the motion screen to move the plate
holder and transducer assembly as required. Step sizes can be
edited by clicking in the middle box and selecting from the step
increments listed.
Installing Dial Indicator
Access the motion screen.

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Using the Z arrow, move in steps of 10mm downward until there is
clearance for the Alignment Bracket (PN 900067) and dial
indicator (PN 900080).
Attach the alignment bracket (PN 900067) to the transducer
manifold using two pins to line up the fixture and tighten using the
thumbscrews provided.
Slide the dial indicator up through the Alignment Bracket until
flush with top surface and adjust side screw to tighten in place.
Dial Indicator Mounted to Manifold
NOTE: Step size will be the number of millimeters the stages
travel in any given direction. You may have to change step
numbers during this process.
Leveling the Sample Holder
Leveling the sample holder fore/aft
Twist the dial indicator PN 900080 so the contact point is facing
the top left edge of the sample holder (see figure below for
orientation).
Adjust the Step Size in SonoLab as needed and press the
appropriate X or Y arrows until the far left corner of the well plate
holder is aligned beneath the dial indicator actuating pin.
Adjust the Step Size and slowly press Z ‘UP’ arrow to raise well
plate holder so that it starts to approach contact with the dial
indicator pin.

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Adjust step size to 0.1 or 0.2 and then raise the plate holder until
the indicator’s contact point is centered in its travel.
The extent of travel for the dial indicator can result in one full
revolution on the gage. Ideally, the Z height should be adjusted
such that the dial makes close to a half revolution (near the 15 tick
mark if starting from 0).
When the appropriate location is set, gently twist the dial indicator
outer metallic ring clockwise so the dial pointer is now at ‘0’. See
images below.
Dial Indicator before Well Plate
Holder makes contact with actuating
pin.
Dial Indicator after contact with plate
holder. “Z” Height for well plate holder is
adjusted in SonoLab until actuator pin is
centered in travel.

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MEASUREMENT: Adjust X Axis step size to ‘10’ or ‘5’ and
move plate holder away from you (X-UP Arrow) along the edge of
the sample holder. Verify the deflection on the dial indicator is less
than +/- 0.003”.
If the deflection significantly exceeds +/-0.003”, adjust the sample
holder to correct the issue.
To raise the front of sample holder, tighten BOTTOM two set
screws on mating block an equal number of turns using a 3/32” hex
wrench.
To lower the front of the sample holder, tighten the TOP two set
screws on mating block.
Sometimes, it may be necessary to loosen the four mounting bolts
to perform the adjustment. Be certain to retighten the mounting
bolts after completing alignment and recheck alignment after
securing the mounting bolts.
Dial Indicator in same position as above; but
outer metallic ring has been rotated so dial
hand is now at ‘0’ reference position.
Plate Holder Direction of
Movement

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X Axis Alignment Screws
If adjustments are made, repeat the alignment measurement steps
as needed to verify the plate holder now meets specification.
Leveling the sample holder horizontally (Left-to-Right)
Use the Z-Down arrow to slightly lower the plate holder enough to
allow for adjustment of the dial indicator pin.
Rotate the dial indicator about 90° clockwise so that it sits in the
Alignment Bracket (PN 900067) as shown.
Use the X and Y arrows in SonoLab as necessary to move the plate
holder into position so that the left upper corner of the plate is
again just under the dial indicator pin.
Click on the Z-UP arrow in small step sizes until the dial indicator
contact touches the sample holder on the top surface of the rear
horizontal edge (as shown).

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Make necessary adjustments to center the dial indicator pin (as
described in previous section) and set to ‘0’.
MEASUREMENT: Enter a step size of ‘10’ and click on the Y-
LEFT arrow to move the plate holder to the left. Upon moving the
plate holder 50-75% across the length of the holder, verify that the
dial indicator deflection does not exceed +/- .003”.
If the deflection significantly exceeds +/-0.003”, adjust the sample
holder to correct the issue.
To rotate the plate holder Clockwise, tighten the left-most top set
screw with 3/32” wrench. To rotate CCW, tighten the right-most
top set screw.
Bolts for Leveling Y Axis
If adjustments are made, repeat the alignment measurement steps
as needed to verify the plate holder now meets specification.
Important: when adjustment is complete, to ensure that left-to-
Plate Holder Direction of
Movement

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right level is secure, verify that both set screws contact surface of
support block below.
Sample Holder Parallelism (with respect to manifold block)
Drop the well plate holder using SonoLab arrows (Z-DOWN) so
the dial indicator can once again be rotated in the Alignment
Bracket (900067).
When there is sufficient clearance, rotate the dial indicator in the
Alignment Bracket in the orientation shown. Also adjust the pin
angle so it is more vertical (and slightly angled toward the dial) as
shown below.
Use the X, Y and Z arrows in SonoLab as necessary to move the
plate holder into position so that the pin is close to touching the
outer edge of the left leg of the plate holder (at the end furthest
from you).
Click on the Y-LEFT arrow in small step sizes until the dial
indicator contact touches the sample holder on the outer left
surface.
Plate Holder Direction of
Movement