David Manura

For anyone attending ASMS 2014, I'll be available at the Scientific Instrument Services, Inc. booth #1 (except Thu) to answer user questions on SIMION. There's a long list of SIMION related ASMS posters at http://simion.com/docs/asms2014posters.pdf . Recent advancements to SIMION are summarized at http://simion.com/advances . Some important advances have been made to SIMION this year including - Initial Fly'm parallelization - multicore and multi-machine. The former isn't stable yet for the meeting, but the latter will be on display. - OpenGL on the View screen. - Native Linux binaries (non-GUI), which are good for HPC clusters. Also Intel Xeon Phi binary of SIMION (soon to be tested). - Further work on magnetic support and extensive integration with magnetic packages like QuickField and Poisson Superfish. - New GUI dialog library for creating GUI's in SIMION.

For anyone attending ASMS 2012, I'll be available Mon-Wed at Scientific Instrument Services, Inc. booth #32 to answer user questions on SIMION. There's a long list of SIMION related ASMS posters at http://simion.com/docs/asms2012posters.pdf . The latest 8.1 service pack capabilities (v8.1.1.x releases) are concisely summarized graphically at http://simion.com/docs/simion811_changes.pdf . Important progress has been made in SIMION over the last year. One 8.1 feature that is among the most important in years, but as-of-yet has not been widely utilized, pertains to order-of-magnitude accuracy improvements in Refine; you can look forward to 8.1.1.x software updates in the coming days and weeks that move this feature into the mainstream. Various other changes (a full list of which is at http://simion.com/changes ) render some assumptions about SIMION no longer valid. CAD import is more accurate. Voltage and geometry optimization can be programmed more robustly. We are now dabbling with dielectrics, improving space-charge, permeability, magnetic vector potential, asymmetric grid cells, 64-bit/multicore, and now surface enhancement. Custom plots can be made in the 3D window. Refines can be triggered from within a fly'm and PA's nested and refined dependently. The info web site and supplemental documentation have merged and multiplied in size. They'll be a new VM and text editor. The roadmap for the next major upgrade is also being planned out, recently reopening early access in preparation for trying out the next generation of capabilities (to-be-announced). We also have developments from one of our SIMION distributors who created the specialized SIMION add-on and CFD solver named Virtual Device; this application continues to mature, recently multiplying performance and in the upcoming release adding slip boundary conditions and improving usability. The vision for 8.0 was a SIMION that modernized the user interface and laid a groundwork of programmability, upon which many interesting new examples developed. The vision for 8.1 has been a SIMION that on the surface looked fairly similar but internally was faster, more accurate, and more versatile (with emphasis on core Refine enhancements, APIs, and yet more examples/documentation). Looking forward, the next major version will continue a lot of these themes though probably have a stronger emphasis on user interface than 8.1 and perhaps introduce other themes.

SIMION 8.1 (rev 8.1.0.18) started shipping Aug 23. A summary of changes from 8.0 is at [1]. For customers who purchased SIMION 8.0 after the Jan 1, 2011 price update, a free upgrade package will ship to you starting tomorrow. Please remember to use the "Check for Updates" button in SIMION from time-to-time. SIMION is presently under heavy development, and the SIMION 8.1.0.18 release is only the beginning of the 8.1.x version release cycle. For example, a new 8.1.0.20 full production release is planned in a couple days (as seen, production releases are becoming more frequent), and a preview of its upcoming changes are listed in [2]. A number of 8.0 updates are also being released concurrently as bugs discovered in the 8.1 development/testing are being cleared out. [1] http://simion.com/info/simion81.html [2] http://simion.com/changes

An important change has been made in SL Tools to improve the accuracy of the STL -> PA conversion. This change now permits exact grid-unit alignment when using STL files, which previously was only really achievable with GEM, Modify, and programming approaches to geometry definition. Details are in http://simion.com/issue/339 . The change affects version 8.0.7-TEST11 (side note: the version number scheme for SL Tools has also been changed to correspond to SIMION version numbers). Some screenshots are attached. The picture on the left shows two_cylinder.stl, which is a recent addition to the SIMION "geometry" example set (you can download "simion8-geometry-20110805.zip" from the "Check for Updates" button on the SIMION 8.0 main screen). The conversion was done at a very low resolution so that it's easier to observe the accuracy. It's important to note that during the conversion process I used the option "Solid strategy" = "No extra solid points" (most accurate), which causes surfaces to be treated as ideal 100% tranmission grids in the PA. It can be observed with the mouse that all the dimensions, including the inner hole radius, exactly match the original STL file (apart from the "inherent" defect at non-orthogonal angles of the cylinder renderd in a 3D rectangular PA). The picture on the right shows another STL file of a single triangle with corners at vertices of a cube. Again, this was converted using the "No extra solid points" option, so the triangle is treated as an ideal 100% transmission grid. Since electrode points that are not solid points do not always display in the 3D view, in order to visualize this PA, I enabled the "Points" option. The "Points" option has been changed in the latest version to display all grid points that are electrode points but not inside the solid. (The Points feature can also be useful to visualize the grid density.) You can observe that, unlike in earlier version of SL Tools, the spacing between points is very regular, and remains so even if we don't use the "No extra solid points" option. The algorithm for rendering the has been improved and more thoroughly tested for topological properties. Additional "Solid strategies" may be added later. However, "No extra solid points" will provide the best accuracy. Although major new features are now only going into SIMION 8.1, I considered this more of a defect correction rather than a new feature, so it's made available in 8.0 as well. A future planned update to SL Tools, whicht will only be available in 8.1, will be to support the 8.1.x enhanced refine accuracy option hinted in http://simion.com/info/simion81.html , which will will work toward reducing the "inherent defect" mentioned above.

The list of ASMS2011 posters related to SIMION is at [1]. I'll be at ASMS to support SIMION users, so you can also likely find me at Scientific Instrument Services, Inc. booth #115 if you want to discuss anything SIMION. The major news is that SIMION 8.1.0 is approaching release in a month, and we are taking orders for the upgrade now. 8.1.0-TEST2 (pre-release) will be made available right after ASMS to all users who have purchased SIMION (or an 8.1 upgrade) this year. We have big plans for SIMION in evolving core areas. [1] http://simion.com/docs/asms2011posters.pdf [2] http://simion.com/info/simion81.html

As usual, here's the list of ASMS 2010 posters and sessions related to SIMION, or at least mentioned in the abstract (SIMION users have been busy): http://simion.com/docs/asms2010posters.pdf Scientific Instrument Services, Inc. will be at booth #84. I'll be available there also (Mon-Wed only), so you're welcome to stop by and discuss anything on your mind about SIMION or otherwise. SIMION development versions will start emphasizing some enhancements to Refine. A major new version of Virtual Device will also be coming out. --- copy of first page summary list --- Session: MP28, Ion Sources: ESI Time Slot/Poster: 609, Monday, Poster Hall Improving and Coupling Electrospray Ion Funnel Interface to Ion Mobility-Mass Spectrometry; Junho Jeon; Chaminda M. Gamage; David H. Russell; Texas A&M University, College Station, TX ________________________________________ Session: MP30, Ion Activation/Dissociation: General Time Slot/Poster: 647, Monday, Poster Hall Investigation of fast unimolecular dissociation reactions using surface-induced dissociation implemented in a modified commercial MALDI-TOF; Sung Hwan Yoon; Mowei Zhou; Arpad Somogyi; Chaminda M. Gamage; Vicki H. Wysocki; University of Arizona, Tucson, AZ ________________________________________ Session: MP31, Instrumentation: FTMS Time Slot/Poster: 651, Monday, Poster Hall Design Considerations for External Ion Injection FT-ICR MS at 21 Tesla; Steven C. Beu 1; Christopher L. Hendrickson 2; Alan G. Marshall 3; 1 S C Beu Consulting, Austin, TX; 2 National High Magnetic Field Laboratory, Tallahassee, FL; 3 Ion Cyclotron Resonance Prog, Tallahassee, FL ________________________________________ Session: MP31, Instrumentation: FTMS Time Slot/Poster: 653, Monday, Poster Hall Characterization of axial motion frequency analyses in harmonized cylindrical Penning traps as potential mass spectrometry method; Eugene Nikolaev 1; Ivan Boldin 1; Pavel Ryumin 1; Igor Popov 2; 1 Institute for Energy Problems of Chemical Physics, Moscow, RUSSIAN FEDERATION; 2 Russian Academy of Sci, Moscow, RUSSIAN FEDERATION ________________________________________ Session: MP31, Instrumentation: FTMS Time Slot/Poster: 655, Monday, Poster Hall Injection of Externally-Generated Low Mass Ions into High Magnetic Field in Q/FT-ICR Instruments: SIMION Simulations and Experimental Observations; Behrooz Zekavat; Touradj Solouki; University of Maine, Orono, ME ________________________________________ Session: MP31, Instrumentation: FTMS Time Slot/Poster: 657, Monday, Poster Hall Effects of ion introduction in the FT ICR cell on frequency shifts, mass accuracy, and resolution; Andriy Kharchenko; Ron M.A. Heeren; FOM Institute for Atomic and Molecular Physics, Amsterdam, NETHERLANDS ________________________________________ Session: MP31, Instrumentation: FTMS Time Slot/Poster: 658, Monday, Poster Hall Investigation of collision cross section effects on ion motion in ICR cell under influence of bath gas and quadrupolar excitation; Alexander Misharin 1; Alexander Popov 2; Vladimir Doroshenko 1; 1 MassTech, Inc., Columbia, MD; 2 MSU, Moscow, Russia ________________________________________ Session: TP29, Ion Mobility I Time Slot/Poster: 650, Tuesday, Poster Hall A Periodic-focusing DC-only Ion Funnel for a Cryogenic Ion Mobility- Mass Spectrometer ; Joshua Silveira 1; Chaminda M. Gamage 1; Jody May 2; David H. Russell 1; 1 Texas A&m University, College Station, TX; 2Vanderbilt University, Nashville, TN ________________________________________ Session: TP30, Instrumentation: TOF Time Slot/Poster: 671, Tuesday, Poster Hall Doughnut Multi-reflecting Time-of-Flight Mass Spectrometer; Vyacheslav Shchepunov 1; Alexander Berdnikov 2; Hideaki Izumi1; Roger Giles 1; Nicolay Gall 2; 1Shimadzu Research Laboratory, Manchester, United Kingdom; 2 Institute for Analytical Instrumentation of RAS, St. Petersburg, Russia ________________________________________ Session: TP30, Instrumentation: TOF Time Slot/Poster: 682, Tuesday, Poster Hall A Serpentine Extraction Ion Source for a Laser Desorption Postionization Microprobe Imaging MS; Jerry F. Moore 1; Gerald Gasper 2; Artem Akhmetov 2; Luke Hanley 2; 1MassThink LLC, Naperville, IL; 2 University of Illinois at Chicago, Chemistry, Chicago, IL ________________________________________ Session: WP23, Homeland Security Time Slot/Poster: 506, Wednesday, Poster Hall Investigation using SIMION on the implementation of a cubic ion trap as an ionization chamber on a GC/LIT; Sarah Vitcher 1, 2; Claude Beaugrand 3; Laurens Dudragne 2; Roberta Collino 2; Jean-Claude Tabet 1; 1 University Paris VI (UPMC), Paris Cedex O5 , FRANCE; 2THALES SECURITY SOLUTIONS & SYSTEMS, Vélizy-Villacoublay, FRANCE; 3ALPHA-MOS, Toulouse, FRANCE ________________________________________ Session: WP28, Ion Sources: API Time Slot/Poster: 606, Wednesday, Poster Hall Modular computational toolset for atmospheric pressure ionization method development: SIMION meets FEM; Walter Wissdorf1; Larissa Pohler 1; Thorsten Pöhler 2; Herwart Hönen 2; Klaus J. Brockmann 1; Thorsten Benter 2 1University of Wuppertal, Wuppertal, Germany; 2 RWTH Aachen, Aachen, Germany ________________________________________ Session: WP31, Instrumentation: New Concepts I Time Slot/Poster: 679, Wednesday, Poster Hall Optimization of the Electrodynamic Ion Funnel for Enhanced Low Mass Transmission: Influence of Funnel Operational Pressure on Ion Transmission; Paul Momoh; Michael Ugarov ; Mark Werlich; Tom Knotts; Alex Mordehai; Agilent Technologies, Santa Clara, CA ________________________________________ Session: ThOC am, Recent Developments in Ion Mobility MS Time Slot/Poster: 09:10, Thursday, Ballroom BDF A Novel, Modular Ion Mobility Drift Cell; Ryan Blase ; Chaminda M. Gamage; Joshua Silveira; David H. Russell; Texas A&M University, College Station , TX ________________________________________ Session: ThOD pm, Novel Developments in Instrumentation Time Slot/Poster: 3:30, Thursday, Room 155 Development of a portable mass spectrometer for operation at 1 Torr; Glen Jackson; Ohio University, Athens, OH ________________________________________ Session: ThP23, Computer Analysis Time Slot/Poster: 530, Thursday, Poster Hall Numerical simulation of ion dynamics in collision multipole ion guides; Victor Laiko 1; Craig M. Whitehouse 2; 1 Perkin Elmer, Inc., Branford, CT; 2 PerkinElmer, Branford, CT ________________________________________ Session: ThP23, Computer Analysis Time Slot/Poster: 532, Thursday, Poster Hall Accelerated Trajectory Simulations for SIMION with a Beowulf Cluster; Peter Williams; Agilent Laboratories, Santa Clara , CA ________________________________________ Session: ThP27, Instrumentation: New Concepts II Time Slot/Poster: 630, Thursday, Poster Hall Development of Tripole-Multipole Rotational Ion Mobility Mass Spectrometer by Ion Simulations; Takanori Harada; Tsutomu Masujima; Hiroshima Univ. BioMed., Hiroshima, JAPAN ________________________________________ Session: ThP28, Instrumentation Quadrupoles and Traps Time Slot/Poster: 644, Thursday, Poster Hall A tightly curved collision cell with high MSMS efficiency; Felician Muntean; Varian Inc., Walnut Creek, CA ________________________________________ Session: ThP28, Instrumentation Quadrupoles and Traps Time Slot/Poster: 646, Thursday, Poster Hall A new linear quadrupole ion trap with axial ejection; David Langridge; Jason L Wildgoose; Waters Corporation, Manchester, UNITED KINGDOM ________________________________________ Session: ThP28, Instrumentation Quadrupoles and Traps Time Slot/Poster: 655, Thursday, Poster Hall A Digital Linear Ion Trap based on Ceramic Printed Circuit Boards; Mu Hui ; GongYu Jiang; Tao Lin; XiaoHui Yang; JunSheng Zhang; Li Ding; Shimadzu Research Laboratory (Shanghai), Shanghai , CHINA ________________________________________ Session: ThP28, Instrumentation Quadrupoles and Traps Time Slot/Poster: 657, Thursday, Poster Hall Short-Pulse Ion Extraction from a Quadruple Ion Trap into a Time-of-Flight Mass Spectrometer for Trapped Ion Cloud Diagnostics; Beni B. Dangi; Nicholas A. Sassin; Kent M. Ervin; University of Nevada, Reno, Reno, NV ________________________________________ Session: ThP28, Instrumentation Quadrupoles and Traps Time Slot/Poster: 661, Thursday, Poster Hall Kinetic energies of ions ejected radially from LIT at high q; Viatcheslav V. Kovtoun; Thermo Fisher Scientific, San Jose, CA ________________________________________ Session: ThP28, Instrumentation Quadrupoles and Traps Time Slot/Poster: 662, Thursday, Poster Hall Optimization of Multipole Components in a Planar Paul Trap; Zhiping Zhang; Ying Peng; Hannah Quist; Junting Wang; Brett J. Hansen; Aaron R. Hawkins; Daniel E. Austin; Brigham Young University, Provo, UT ________________________________________ Session: ThP28, Instrumentation Quadrupoles and Traps Time Slot/Poster: 663, Thursday, Poster Hall Miniaturization of an axially focusing linear ion trap for mass spectrometry; Gareth Dobson1; Christie Enke2; 1SRI International, Menlo Park, CA; 2University of New Mexico, Albuquerque, New Mexico

As usual, SIS will be at the ASMS meeting, which is next week in Seattle, Washington. Last year, we announced our acquisition of the SIMION development license from Idaho National Labs, and so this year, we are formally announcing the production release of SIMION 3D 8, which is shipping end of Q3 2006: SIMION 3D 8 Announcement http://www.simion.com/news/20060527.pdf In summary, SIMION 3D 8 is a mix of user interface improvements, new capabilities, and performance enhancements. Previously referred to as 7.1, its list of committed changes is now substantial enough to warrant the 8.0 version number. Like the SL Toolkit, and unlike the static 7.0, 8.0 is planned to be continuously enhanced for a year or more, with free upgrades downloadable from simion.com, to incorporate additional capabilities users have requested. The latest 8.0beta version will be there for demonstration. At this time, we'd like to also recognize the following ASMS posters and sessions related to SIMION. ASMS can be a good place to meet other users doing SIMION simulations and solving related problems in particle optics. Abstracts and schedules on these items can be obtained from the following ASMS web page: ( http://www.asms.org/Default.aspx?tabid=54 ) by doing a "full text search" for "SIMION". ===== MOC pm, 03:20, Distance-of-Flight MS - Exploratory implementation in a Q/oTOF mass spectrometer, Christie Enke(1), Gareth Dobson(1), (1)University of New Mexico, Albuquerque, NM MOF pm, 03:20, It's all about the fields., James E. Bruce(1), Saiful Chowdhury(1), Nathan K. Kaiser(1), Xiaoting Tang(1), Si Wu(1), Wei Yi(1), Kai Zhang(1), (1)Washington State University, Pullman, WA MOF pm, 03:40, Theory and Practice of the Orbitrap Mass Analyzer, Alexander A. Makarov(1), (1)Thermo Electron (Bremen) GmbH, Bremen, Germany MP08, 155, Development of a Hybrid Quadrupole-Linear Ion Trap-Ion Mobility-TOFMS for Structural Mass Spectrometry, Jody C. May(1), John A. McLean(1), David H. Russell(1), (1)Texas A&M University, College Station, TX MP09, 175, Improving Mass Resolution in ortho-TOF Mass Spectrometer, Vadym D. Berkout(1), Vladimir M. Doroshenko(1), (1)MassTech, Inc., Columbia, MD MP09, 183, A Novel Ion Gate Comprising a Small Orthogonal TOF With Ion Mirror, Jeffery M. Brown(1), Daniel J. Kenny(1), Robert H. Bateman(1), (1)Waters Micromass MS Technologies, Manchester, UK MP09, 196, A Direct Comparison of a Resitive Glass and Stacked-Ring Reflectron, Stephen M. Ritzau(1), Bruce N. Laprade(1), Sharon R. Mrotek(1), Ray Leffingwell(1), (1)Burle Electro-Optics, Sturbridge, MA MP09, 197, Simple Template-Based Method to Fabricate Bradbury-Nielson Gates and Applications in Mass Spectrometry [1], Oh Kyu Yoon(1), Ignacio A. Zuleta(1), Matthew D. Robbins(1), Griffin K. Barbula(1), Richard N. Zare(1), (1)Stanford University, Stanford, CA MP10, 199, Modification of ICR Trapping Potential to Generate a Local Electrostatic Field Minimum to Improve Signal Resolving Power, Sunghwan Kim(1), Myoung Choul Choi(1), Seung Yong Kim(1), Jong Shin Yoo(1), Hyun Sik Kim(1), Greg T. Blankney(2), Christopher L. Hendrickson(2), Alan G. Marshall(2), (1)Korea Basic Science Institute, Daejeon, Korea, (2)National High Magnetic Field Laboratory, Tallahassee, FL MP10, 210, Coaxial multi-electrode FTICR cell for high-sensitivity detection at a multiple frequency: main design and modeling results, Alexander Misharin(1), Roman Zubarev(1), (1)Uppsala University, Uppsala, Sweden MP10, 212, SIMION Modeling of Image Charge Detection in FT-ICR MS, Steven C. Beu(1), Christopher L. Hendrickson(2), Alan G. Marshall(2), (1)S C Beu Consulting, Austin, TX, (2)ICR Group at NHMFL, Tallahassee, FL MP10, 213, A New Open Cylindrical ICR Cell with Electrodes of Different Diameters, Karl P. Wanczek(1), Basem Kanawati(1), (1)Inorganic & Physical Chemistry, University, D-28334 Bremen, Germany MP10, 217, Progress Toward Real Time Bioerosol Analysis Using the Novel Fourier Transform Ion Cyclotron Resonance Bioaerosol Mass Spectrometer, Richard Seipert(1), Xin Cong(1), Gregg Czerweineic(1), Carlito Lebrilla(1), (1)University of California, Davis, Davis, CA MP10, 220, Simulation Study to Improve Ion Transmission Efficiency through the Gate Valve for an External Ion Injection FTICR-MS, Myoung Choul Choi(1), Hyun Sik Kim(1), Sunghwan Kim(1), Jong Shin Yoo(1), (1)Korea Basic Science Institute, Daejeon, Repurblic of Ko ThP04, 048, Aperture Arrays for Atmospheric Pressure Sources, Edward W Sheehan(1), Ross C Willoughby(1), (1)Chem-Space Associates, Inc., Pittsburgh, PA ThP09, 141, Surface Induced Dissociation (SID) in a Quadrupole Time of Flight Mass Spectrometer - Towards the Study of Larger Biomolecules, Asiri S. Galhena(1), Shai Dagan(1), Christopher M. Jones(1), Richard L. Beardsly(1), Vicki H. Wysocki*(1), (1)University of Arizona, Tucson, Arizona ThP09, 146, Applying Superfluid Helium Nanodroplets to the Study of Ions: New Possibilities, Travis M. Falconer(1), William K. Lewis III(1), Aaron M. Johnson(1), Raymond J. Bemish(2), Gary L. Glish(1), Roger E. Miller(1), (1)University of North Carolina, Chapel Hill, NC, (2)Pfizer Inc., Groton, CT ThP09, 150, Surface-Surface (Ping-Pong) Neutralization-Reionization Mass Spectrometry, Luke E. Adams(1), Xinli Yang(1), Frantis(ek Turec(ek(1), (1)University of Washington, Seattle, WA ThP16, 262, Kinetics of surface induced dissociation using laser desorption of C60 and silicon nano powder assisted ionization of N(CH3)4+, Sung Hwan Yoon(1), Dylan Boday(1), Chaminda Gamage(1), Wiujuan Wen(1), Kent Gillig(1), Shai Dagan(1), Vicki Wysocki(1), (1)University of Arizona, Tucson, AZ, Wenjian Sun(1), David H. Russell(1), (1)Texas A&M University, College Station, TX TP23, 406, A novel SID/TOF source for MALDI-IM-SID-oTOF MS, Wenjian Sun(1), David H. Russell(1), (1)Texas A&M University, College Station, TX WP14, 263, Micro-Cylindrical Ion Trap Mass Spectrometers, Ashish Chaudhary(1), Friso H.W. van Amerom(1), Robert T. Short(1), (1)University of South Florida, St. Petersburg, Florida WP14, 267, Computer Simulation of a New, AC three rods (tripole), Ion Optic with High Focusing and Mass Filtering Capabilities, Gary Abdiel Salazar(1), Tsutomu Masujima(1), (1)Hiroshima University, Hiroshima, Japan WP15, 303, Novel Ion Trap Focusing Techniques for use with Distance of Flight (DOF) Time of flight (TOF) Mass Spectrometry (MS)., Gareth S. Dobson(1), Christie G. Enke(1), (1)University of New Mexico, Albuquerque, NM =====

SIMION user Dr. Sergei Koltsov of the Russian Academy of Sciences (Institute for Analytical Instrumentation) announces a new version 16 of his "Virtual Device" accessory software for SIMION. === Dear User of SIMION software, I would like to present a fresh version of Virtual Device. It is version 16. I am glad that my software is already used by above 100 people from different countries. Thanks for your suggestions and remarks. Version 16 is the last version which is for free. I also continue to work on the next version. What will be in next versions. First of all, I will add the possibility to create 3D geometries of spheres/half spheres and grid as a single object. I also add the possibility to create the 3D geometry of any axial symmetry system. If you a have text file with two columns, which describes the shape of electrodes, you can recreate these electrodes as a 3D geometry in my software and of course transform these electrodes into SIMION. This feature is very important for scientists who deal with the simulation of energy analyzers. One of the main problems in the simulation of energy analyzers is the problem of electrode shape. If you like to prove the resolution you need to change the shape of the analyzer. By using my software you can do this very easy and quickly. The other direction of my software is connected to the simulation of ion movement in special gas flow. The main problem is in arranging the description of gas flow in SIMION. Many articles devoted to this problem are addressed to a resting gas. But if you like to simulate supersonic gas in some 3D geometry, what are you going to do? I see only one way. You will try to simulate gas flow in some CFD software and then transform the results of the simulation to a SIMION PRG file. But, does commercial software actually give correct results? I just checked CosmosFlowWorks and 3D Flow. Both of them give completely wrong results for a supersonic jet. I would like to remind that one of main directions in mass-spectrometry is the investigation of the ESI source and coupling this source to mass-spectrometer. The simulation of ion movement in different pressure regions is one of problems of such coupling. Therefore, I developed my own software, which simulates gas flow in 3D geometry in Virtual Device. The results of the simulation are arrays of pressure, density, temperature, and velocity distribution of gas in a 3D geometry. This geometry can be easily transformed to a SIMION geometry, and the user can use those arrays in a PRG file. I like to stress that my CFD software is tested with experimental results, which is of course very important. Therefore simulation of gas-dynamics task in SIMION becomes very simple. Sincerely yours, Dr. Sergei Koltsov Laboratory of mass-spectroscopy Institute for Analytical Instrumentation, Russian Academy of Sciences kol-sergei(-at-)yandex.ru === Further information and screenshots of the Virtual Device software are available at ( http://www.simion.com/docs/virtual_device.html ). To request a copy of the software, contact Sergei via e-mail.

Hello SIMION users, The SIMION Ion Optics Users Group and SL Toolkit Users Group have now been officially moved from Yahoo! to simion.com. The new forums can be accessed here: http://www.simion.com/discuss The site is currently structured into three main forums: SIMION Announcements -- SIMION Announcements (low volume, read only). For infrequent announcements by simion.com. SIMION Users -- Questions and discussions on using SIMION (moderate volume) For most discussions. SIMION Development -- Development of SIMION. Bugs, feature requests, suggestions, beta testing, ... (higher volume) For those users more particularly interested in the future software development of SIMION. All previous Yahoo! messages (including SL messages) have been imported largely into the "SIMION Users" forum (a task that took some effort, but I think it was largely successful). The old Yahoo! forums will be effectively disabled today. I hope you like the new format. I have a few notes about it: - Currently, you must register to view/post messages (like the old Yahoo! forums, but much simpler and far fewer questions). I had considered not requiring regitration, but this reduces the chance of abuse by bots and such. - You can elect to receive "e-mail notifications" whenever a message is posted on the forums. You can alternatively elect to receive "e-mail digests" of all messages posted on the forums in the last day or week (which some users may prefer as it may send far fewer e-mails). You can choose to receive notifications only in the forums you are interested in. Of course, you can alternately elect to receive no such e-mail. - Currently you must post messages from the web page (reply via e-mail does not work). - You can attach images or certain files (e.g. screenshots or SIMION files) into your messages. These can only be viewed via the web page (not via e-mail). - There is a search function. Please let me know if you have any questions or comments on the new forum structure. I intend to post some comments in the coming days, e.g. on feedback from ASMS, development, etc.

To SIMION Users, I have some long awaited news on SIMION. As you may know, there has not been a major new release of SIMION in some years following the retirement of lead SIMION developer David Dahl at what is now Idaho National Labs (INL). Still, SIMION remains widely used and its user base continues to grow at a steady rate. Obviously, as in any piece of software, customers desire changes and improvements. As a distributor of SIMION for INL, our company Scientific Instrument Services, Inc. (SIS) has heard feedback from many users, comments of where SIMION gets things right (the simplicity/directness, interactiveness to aid intuition, affordability, and it's a ability/flexibility to solve a wide variety of real problems) and where it falls short (e.g. the user interface and programming interface are due for an overhaul and some nagging quirks like the file directory limit need fixed). It's obvious that SIMION needs an active maintainer. SIS has pursued this issue for some time and with some difficulty, and in the meantime we had started up simion.com and developed the toolkit accessory package. The good news is that the SIS has completed the required contract, and its rights to maintain the SIMION source code become effective July 1, 2005. My main job over the year (and possibly much longer) will be to manage this project and bring about SIMION 8.0 (and likely 7.x or development/beta releases along the way, which will require testers). In the meantime, some planning is being done, and we appreciate all feedback as to what you would like to see improved in SIMION, whether in general or on very specific points. After all, you are the users of the software, and it is your requirements that must be met. (Vacuum conditions may be desirable for ion optics, but for software development it is not.) You may post comments on the discussion board or call/e-mail me. I will also be at the ASMS meeting in San Antonio Texas next week, and we can discuss anything there as well. SIS will be at booth #61, and I will plan to stop by at some of your posters. Also, as in last year, you may stop by and ask some question on using SIMION (I will bring a laptop with SIMION and even CPO and other such software). Over the coming month, new tools will be added to the SIMION web site to better support the development process. For example, this SIMION discussion group will be moved to simion.com to better manage multiple levels of discussion (e.g. Announcements, User Support, and Development). The new forum is at http://www.simion.com/discuss (Some changes may be made in the forum in the next few days as things are finalized and existing messages are imported, but you are welcome to try it out.) Additional details will follow. For those attending ASMS, below is the list of all posters that are related to SIMION (or at least have SIMION mentioned in the abstract). ==== ASMS Posters on SIMION ==== Session Code Title MOFam 11:35 Implications of miniaturising Linear Ion Trap arrays for portable detectors (includes CPO) MP16 258 Performance and Modeling of a Small TOF Mass Spectrometer used in Aerosol Sampling MP16 261 Countering the turn-around time effect in orthogonal TOF MS MP16 266 Advantages of a Three-Field Source Over a Two- Field Source in a Multipurpose Tandem Time of Flight Mass Spectrometer MP16 268 The Development of Novel Resistive Glass Technology for Tailoring Electric Fields in Ion Mobility and Mass Spectrometer Applications. MP16 270 Single Particle Analysis of MALDI using Bio-Aerosol Mass Spectrometry MP16 271 Electrospray Ionization Time-of-Flight Mass Spectrometry (ESI-TOFMS) with microfabricated Beam Modulation Devices ThOEam 11:15 The Ion Conveyor: A New Ion Optical Device for Improved Focusing and Sensitivity ThP12 173 Developing Electrospray Charge Detection Mass Spectrometry as a Nanoparticle Injector for X-ray Free Electron Laser Diffraction Imaging ThP12 174 An Advanced Laser Desorption Ionization Ion Source with Controlled Superposition of Electric and Pneumatic Fields ThP12 177 Surface Induced Dissociation (SID) in a Quadrupole Time of Flight Mass Spectrometer ThP12 180 Surface-Surface (Ping-Pong) Neutralization-Reionization Mass Spectrometry ThP13 199 Axial Field Characteristics in an RF-only Linear Ion Trap with End Lenses ThP13 200 Strategies to reduce the effects of field imperfections in quadrupole ion traps ThP13 214 Miniaturization of mass spectrometers based on sub millimeter cylindrical ion traps TODpm 03:40 Kinetic Investigation of Peptide Fragmentation in a MALDI TOF SID TOF Mass Spectrometer TODpm 04:20 Linear Ion Trap with Axial Ejection as a Source for a TOF MS TP11 199 Efficient Ion Transmission Through a Quadrupole Mass Filter and into a Linear Octopole Trap TP11 201 Physical Characterization and Optimization of Electron Capture Dissociation in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry TP11 212 Octopole Ion Guide Transmission Efficiency in a High Magnetic Field for FT-ICR MS TP11 215 SIMION Modeling of Methods to Control Time-of-Flight Dispersion of Externally Generated Ions in High Field FT-ICR MS TP12 223 Electron Capture Dissociation in RF Quadrupole devices: A New Method to Trap Ions and Low-Energy Electrons TP12 247 SIMULATION OF INTERNAL ENERGY DISTRIBUTION OF PEPTIDES IN ELECTROSPRAY IONIZATION WOFam 10:15 Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: Overview of Recent Technique and Instrumentation Developments WP08 122 Ion Motion Control in the Orbitrap Mass Analyzer WP08 126 Fabrication of Cylindrical Ion Traps Using Selectively Plated Non-Conducting Materials WP08 127 Ion Funnels for the Masses: Experiments and Simulations with a Simplified Ion Funnel WP08 128 Toward Single Cell Detection-Development of A Novel Bioaerosol Fourier Transform Mass Spectrometer WP08 136 Beam Dynamics in a High Resolution Multi-Pass Time of Flight Mass Separator WP08 138 Transmission of Ions Through Laminated Conductance Pathways from Atmospheric Pressure WP19 342 3D Particle-In-Cell Code for Simulations of Ion Motion in the Presence of Magnetic Field For full abstracts on these posters, go to the ASMS web site at http://www.asms.org/abstracts/webform1.aspx Click "Search", in "Full Text Word Search" enter "simion", click "Begin Search", and click "Print View". ==== News Flash ==== INL and SIS Agree to Develop SIMION Ion Optics Software The U.S. Department of Energy's Idaho National Laboratory and Scientific Instrument Services Inc. (SIS) of Ringoes, NJ have joined in a new license agreement to develop and maintain the software code for the SIMION suite of ion optics modeling software. The agreement will allow SIS to enhance, update and maintain the software, to satisfy the needs of the user community, benefit the industrial partner and the government. SIMION 3D, originally developed by INL employee David Dahl, is an award-winning Windows PC based program, widely used by manufacturers and designers of mass spectrometers, electron microscopes, electron multipliers and other scientific instruments to study the optics of charged particles through electric and magnetic fields in two and three dimensions. SIMION is designed to provide direct and highly interactive methods, balancing ease-of-use, speed, accuracy, and affordability in order to simulate a variety of real-world ion optics problems. SIMION can model complex problems using a workbench strategy that can hold up to 200 2-D and/or 3-D electrostatic or magnetic field arrays, each of up to 50,000,000 points, which the user can visualize in 3D and cut away to inspect ion trajectories and potential energy surfaces to gain intuition and collect quantitative data. SIMION is so pervasive, and so influential that in 1998, the American Society for Mass Spectrometry (ASMS) recognized that "the application of SIMION has been invaluable to the design of mass spectrometers (the kinds of machines that SIMION simulates) for the last decade." SIS has distributed SIMION since 1996 and has more recently developed accessory tools to expand the capabilities of SIMION to include the importation of CAD files directly into SIMION, a new compiler and other tools requested by customers. Similar features along with an updated user interface are planned for inclusion in the next major release of SIMION. SIS has also established a SIMION web site (www.simion.com) to provide customers with information and support on SIMION. SIS warmly welcomes any comments or suggestions from the SIMION community on the future direction of the SIMION software. Established in 1978, Scientific Instrument Services specializes in supplies and services for mass spectrometers and related scientific and medical equipment. The company distributes its products via a catalog and through its web site (www.sisweb.com). SIS also designs and manufactures filaments, probes and other instrument accessories for OEM's in the scientific and medical market. With more than 30 employees, SIS's staff includes sales, technicians, machinists, engineers, programmers and product development/support specialists. The INL is a science-based, applied engineering national laboratory dedicated to supporting the U.S. Department of Energy's missions in environment, energy, science and national security. The INL is operated for the DOE by Battelle Energy Alliance, LLC. ===== I look for forward a long and productive collaboration with the SIMION community, David Manura Scientific Instrument Services, Inc. 908-788-5550 x831, dm.oohay[-at-]sisweb.com, www.sisweb.com / www.simion.com (<< Supplies and Services for Mass Spectrometers, Gas Chromatographs and Liquid Chromatographs)

A new web resource "SIMION Model Exchange (SIME)" is now online for testing: http://www.simion.com/sime.html Description: SIMION Model Exchange (SIME) is a repository of SIMION models and source files (e.g GEM/PA/PRG/SL/IOB/STL/CAD) freely contributed by users or made commercially available. In this light, SIME's purpose is similar in nature to that of Perl's CPAN or 3D CAD Browser.com. SIME is currently quite new, and not many files are yet listed (but contributions are most welcome). If anyone has SIMION model files they'd like to share with other users (for free or for charge), posting them or links to them would be most appreciated. If SIME expands significantly, a search function, a streamlined file upload, and other features could be added. David Manura Scientific Instrument Services, Inc. 908-788-5550 x831, dm.oohay[-at-]sisweb.com, www.sisweb.com

The SIMION SL Toolkit v. 1.2.0 (http://www.simion.com/sl/) is now available for download at simion.com. This is a significant update with a number of new components and that is more mature overall. To summarize: - SL Libraries much expanded and more robust. - SL Tools included (release v. 1.0.0) - SL Editor included - Revamped documentation and packaging. A more complete list of changes between this version and the previous (1.0.2) is provided in the "Change Log" page. Feedback is greatly appreciated, and changes have been made upon request. From this point on, I plan to make much more incremental changes to the toolkit (e.g. v. 1.2.1, 1.2.2, ...) and possibly release these more often. Release number will follow the scheme 1.x.y, where even numbered x are stable releases, and odd numbered x are less stable development releases (if released at all). I also want to make it more possible to download components individually (currently only the SL Tools can be downloaded separately). Best regards, David Manura Scientific Instrument Services, Inc. 908-788-5550 x831, dm.oohay[-at-]sisweb.com, www.sisweb.com

We have a new "patools.exe" utility under beta testing that provides the following functions: - import 3D CAD files into SIMION (STL --> PA conversion) - import 2D bitmap (BMP/PNG/GIF/PNM) files into SIMION as 2D potential arrays. - export potential and field maps from refined PA files as text. - export PA files into CAD (PA --> STL conversion). - quickly view PA and STL files from Windows Explorer (OpenGL) Check out the tutorial first: "Potential Array Tools Tutorial: Importing/Exporting PA Files" [ http://www.simion.com/sl/pa_tut.html ] Existing SL customers may download this utility free, as part of the upgrade plan. The final version of patools.exe will be part of the upcoming SL toolkit v.1.1. Feedback is greatly appreciated, especially during this beta testing stage. Any very technical feedback should probably be directed to the SL users group (http://groups.yahoo.com/group/simion-sl/) or to myself. Best regards, David Manura Scientific Instrument Services, Inc. 908-788-5550 x831, dm.oohay[-at-]sisweb.com www.sisweb.com (<< Supplies and Services for Mass Spectrometers, Gas Chromatographs and Liquid Chromatographs)