Dainius Simelevicius

Modelling of Amperometric Biosensor Used for Synergistic Substrates Determination

In this paper the operation of an amperometric biosensor producing a chemically amplified signal is modelled numerically. The chemical amplification is achieved by using synergistic substrates. The model is based on non-stationary reaction-diffusion equations. The model involves three layers (compartments): a layer of enzyme solution entrapped on the electrode surface, a dialysis membrane covering the enzyme layer and an outer diffusion layer which is modelled by the Nernst approach. The equation system is solved numerically by using the finite difference technique. The biosensor response and sensitivity are investigated by altering the model parameters influencing the enzyme kinetics as well as the mass transport by diffusion. The biosensor action was analyzed with a special emphasis to the effect of the chemical amplification. The simulation results qualitatively explain and confirm the experimentally observed effect of the synergistic substrates conversion on the biosensor response.

The CMS Timing and Control Distribution System

The Compact Muon Solenoid (CMS) experiment operating at the CERN (European Laboratory for Nuclear Physics) Large Hadron Collider (LHC) is in the process of upgrading several of its detector systems. Adding more individual detector components brings the need to test and commission those components separately from existing ones so as not to compromise physics data-taking. The CMS Trigger, Timing and Control (TTC) system had reached its limits in terms of the number of separate elements (partitions) that could be supported. A new Timing and Control Distribution System (TCDS) has been designed, built and commissioned in order to overcome this limit. It also brings additional functionality to facilitate parallel commissioning of new detector elements. The new TCDS system and its components will be described and results from the first operational experience with the TCDS in CMS will be shown.

Computational Modeling of Mediator Oxidation by Oxygen in an Amperometric Glucose Biosensor

In this paper, an amperometric glucose biosensor is modeled numerically. The model is based on non-stationary reaction-diffusion type equations. The model consists of four layers. An enzyme layer lies directly on a working electrode surface. The enzyme layer is attached to an electrode by a polyvinyl alcohol (PVA) coated terylene membrane. This membrane is modeled as a PVA layer and a terylene layer, which have different diffusivities. The fourth layer of the model is the diffusion layer, which is modeled using the Nernst approach. The system of partial differential equations is solved numerically using the finite difference technique. The operation of the biosensor was analyzed computationally with special emphasis on the biosensor response sensitivity to oxygen when the experiment was carried out in aerobic conditions. Particularly, numerical experiments show that the overall biosensor response sensitivity to oxygen is insignificant. The simulation results qualitatively explain and confirm the experimentally observed biosensor behavior.

The FEROL40, a microTCA card interfacing custom point-to-point links and standard TCP/IP

In order to accommodate new back-end electronics of upgraded CMS sub-detectors, a new FEROL40 card in the microTCA standard has been developed. The main function of the FEROL40 is to acquire event data over multiple point-to-point serial optical links, provide buffering, perform protocol conversion, and transmit multiple TCP/IP streams (4x10Gbps) to the Ethernet network of the aggregation layer of the CMS DAQ (data acquisition) event builder. This contribution discusses the design of the FEROL40 and experience from operation

CMS DAQ current and future hardware upgrades up to post Long Shutdown 3 (LS3) times

Following the first LHC collisions seen and recorded by CMS in 2009, the DAQ hardware went through a major upgrade during LS1 (2013-2014) and new detectors have been connected during 2015-2016 and 2016-2017 winter shutdowns. Now, LS2 (2019-2020) and LS3 (2024-mid 2026) are actively being prepared. This paper shows how CMS DAQ hardware has evolved from the beginning and will continue to evolve in order to meet the future challenges posed by High Luminosity LHC (HL-LHC) and the CMS detector evolution. In particular, post LS3 DAQ architectures are focused upon.

DAQExpert - An expert system to increase CMS data-taking efficiency

The efficiency of the Data Acquisition (DAQ) of the Compact Muon Solenoid (CMS) experiment for LHC Run 2 is constantly being improved. A significant factor affecting the data taking efficiency is the experience of the DAQ operator. One of the main responsibilities of the DAQ operator is to carry out the proper recovery procedure in case of failure of datataking. At the start of Run 2, understanding the problem and finding the right remedy could take a considerable amount of time (up to many minutes). Operators heavily relied on the support of on-call experts, also outside working hours. Wrong decisions due to time pressure sometimes lead to an additional overhead in recovery time. To increase the efficiency of CMS data-taking we developed a new expert system, the DAQExpert, which provides shifters with optimal recovery suggestions instantly when a failure occurs. DAQExpert is a web application analyzing frequently updating monitoring data from all DAQ components and identifying problems based on expert knowledge expressed in small, independent logic-modules written in Java. Its results are presented in real-time in the control room via a web-based GUI and a sound-system in a form of short description of the current failure, and steps to recover.

The CMS Data Acquisition - Architectures for the Phase-2 Upgrade

The upgraded High Luminosity LHC, after the third Long Shutdown (LS3), will provide an instantaneous luminosity of 7.5 × 10 cm−2s−1 (levelled), at the price of extreme pileup of up to 200 interactions per crossing. In LS3, the CMS Detector will also undergo a major upgrade to prepare for the phase-2 of the LHC physics program, starting around 2025. The upgraded detector will be read out at an unprecedented data rate of up to 50 Tb/s and an event rate of 750 kHz. Complete events will be analysed by software algorithms running on standard processing nodes, and selected events will be stored permanently at a rate of up to 10 kHz for offline processing and analysis. In this paper we discuss the baseline design of the DAQ and HLT systems for the phase-2, taking into account the projected evolution of high speed network fabrics for event building and distribution, and the anticipated performance of general purpose CPU. Implications on hardware and infrastructure requirements for the DAQ ”data center” are analysed. Emerging technologies for data reduction are considered. Novel possible approaches to event building and online processing, inspired by trending developments in other areas of computing dealing with large masses of data, are also examined. We conclude by discussing the opportunities offered by reading out and processing parts of the detector, wherever the front-end electronics allows, at the machine clock rate (40 MHz). Presented at CHEP 2016 22nd International Conference on Computing in High Energy and Nuclear Physics 1) DESY, Hamburg, Germany 2) CERN, Geneva, Switzerland 3) University of California, Los Angeles, Los Angeles, California, USA 4) University of California, San Diego, San Diego, California, USA 5) FNAL, Chicago, Illinois, USA 6) Massachusetts Institute of Technology, Cambridge, Massachusetts, USA The CMS Data Acquisition Architectures for the Phase-2 Upgrade J-M Andre5, U Behrens1, J Branson4, P Brummer2, O Chaze2, S Cittolin4, C Contescu5, B G Craigs2, G-L Darlea6, C Deldicque2, Z Demiragli6, M Dobson2, N Doualot5, S Erhan3, J F Fulcher2, D Gigi2, M G ladki2, F Glege2, G Gomez-Ceballos6, J Hegeman2, A Holzner4, M Janulis2a, R Jimenez-Estupiñán2, L Masetti2, F Meijers2, E Meschi2, R K Mommsen5, S Morovic2, V O’Dell5, L Orsini2, C Paus6, P Petrova2, M Pieri4, A Racz2, T Reis2, H Sakulin2, C Schwick2, D Simelevicius2a, and P Zejdl5b 1 DESY, Hamburg, Germany 2 CERN, Geneva, Switzerland 3 University of California, Los Angeles, California, USA 4 University of California, San Diego, California, USA 5 FNAL, Batavia, Illinois, USA 6 Massachusetts Institute of Technology, Cambridge, Massachusetts, USA a also at Vilnius University, Vilnius, Lithuania b also at CERN, Geneva, Switzerland E-mail: emilio.meschi@cern.ch Abstract. The upgraded High Luminosity LHC, after the third Long Shutdown (LS3), will provide an instantaneous luminosity of 7.5 × 10 cm−2s−1 (levelled), at the price of extreme pileup of up to 200 interactions per crossing. In LS3, the CMS Detector will also undergo a major upgrade to prepare for the phase-2 of the LHC physics program, starting around 2025. The upgraded detector will be read out at an unprecedented data rate of up to 50 Tb/s and an event rate of 750 kHz. Complete events will be analysed by software algorithms running on standard processing nodes, and selected events will be stored permanently at a rate of up to 10 kHz for offline processing and analysis. In this paper we discuss the baseline design of the DAQ and HLT systems for the phase-2, taking into account the projected evolution of high speed network fabrics for event building and distribution, and the anticipated performance of general purpose CPU. Implications on hardware and infrastructure requirements for the DAQ ”data center” are analysed. Emerging technologies for data reduction are considered. Novel possible approaches to event building and online processing, inspired by trending developments in other areas of computing dealing with large masses of data, are also examined. We conclude by discussing the opportunities offered by reading out and processing parts of the detector, wherever the front-end electronics allows, at the machine clock rate (40 MHz). This idea presents interesting challenges and its physics potential should be studied. The upgraded High Luminosity LHC, after the third Long Shutdown (LS3), will provide an instantaneous luminosity of 7.5 × 10 cm−2s−1 (levelled), at the price of extreme pileup of up to 200 interactions per crossing. In LS3, the CMS Detector will also undergo a major upgrade to prepare for the phase-2 of the LHC physics program, starting around 2025. The upgraded detector will be read out at an unprecedented data rate of up to 50 Tb/s and an event rate of 750 kHz. Complete events will be analysed by software algorithms running on standard processing nodes, and selected events will be stored permanently at a rate of up to 10 kHz for offline processing and analysis. In this paper we discuss the baseline design of the DAQ and HLT systems for the phase-2, taking into account the projected evolution of high speed network fabrics for event building and distribution, and the anticipated performance of general purpose CPU. Implications on hardware and infrastructure requirements for the DAQ ”data center” are analysed. Emerging technologies for data reduction are considered. Novel possible approaches to event building and online processing, inspired by trending developments in other areas of computing dealing with large masses of data, are also examined. We conclude by discussing the opportunities offered by reading out and processing parts of the detector, wherever the front-end electronics allows, at the machine clock rate (40 MHz). This idea presents interesting challenges and its physics potential should be studied.

Performance of the CMS Event Builder

The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider (LHC) assembles events at a rate of 100 kHz. It transports event data at an aggregate throughput of 100 GB/s to the high-level trigger (HLT) farm. The CMS DAQ system has been completely rebuilt during the first long shutdown of the LHC in 2013/14. The new DAQ architecture is based on state-ofthe-art network technologies for the event building. For the data concentration, 10/40 Gb/s Ethernet technologies are used together with a reduced TCP/IP protocol implemented in FPGA for a reliable transport between custom electronics and commercial computing hardware. A 56 Gb/s Infiniband FDR CLOS network has been chosen for the event builder. We report on the performance of the event builder system and the steps taken to exploit the full potential of the network technologies. Presented at CHEP 2016 22nd International Conference on Computing in High Energy and Nuclear Physics Performance of the CMS Event Builder J-M Andre5, U Behrens1, J Branson4, P Brummer2, O Chaze2, S Cittolin4, C Contescu5, B G Craigs2, G-L Darlea6, C Deldicque2, Z Demiragli6, M Dobson2, N Doualot5, S Erhan3, J F Fulcher2, D Gigi2, M G ladki2, F Glege2, G Gomez-Ceballos6, J Hegeman2, A Holzner4, M Janulis2a, R Jimenez-Estupiñán2, L Masetti2, F Meijers2, E Meschi2, R K Mommsen5, S Morovic2, V O’Dell5, L Orsini2, C Paus6, P Petrova2, M Pieri4, A Racz2, T Reis2, H Sakulin2, C Schwick2, D Simelevicius2a and P Zejdl5b 1 DESY, Hamburg, Germany 2 CERN, Geneva, Switzerland 3 University of California, Los Angeles, California, USA 4 University of California, San Diego, California, USA 5 FNAL, Chicago, Illinois, USA 6 Massachusetts Institute of Technology, Cambridge, Massachusetts, USA a also at Vilnius University, Vilnius, Lithuania b also at CERN, Geneva, Switzerland E-mail: remigius.mommsen@cern.ch Abstract. The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider assembles events at a rate of 100 kHz, transporting event data at an aggregate throughput of O(100 GB/s) to the high-level trigger farm. The DAQ architecture is based on state-of-the-art network technologies for the event building. For the data concentration, 10/40 Gbit/s Ethernet technologies are used together with a reduced TCP/IP protocol implemented in FPGA for a reliable transport between custom electronics and commercial computing hardware. A 56 Gbit/s Infiniband FDR Clos network has been chosen for the event builder. This paper presents the implementation and performance of the event-building system. The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider assembles events at a rate of 100 kHz, transporting event data at an aggregate throughput of O(100 GB/s) to the high-level trigger farm. The DAQ architecture is based on state-of-the-art network technologies for the event building. For the data concentration, 10/40 Gbit/s Ethernet technologies are used together with a reduced TCP/IP protocol implemented in FPGA for a reliable transport between custom electronics and commercial computing hardware. A 56 Gbit/s Infiniband FDR Clos network has been chosen for the event builder. This paper presents the implementation and performance of the event-building system.

New operator assistance features in the CMS Run Control System

During Run-1 of the LHC, many operational procedures have been automated in the run control system of the Compact Muon Solenoid (CMS) experiment. When detector high voltages are ramped up or down or upon certain beam mode changes of the LHC, the DAQ system is automatically partially reconfigured with new parameters. Certain types of errors such as errors caused by single-event upsets may trigger an automatic recovery procedure. Furthermore, the top-level control node continuously performs cross-checks to detect sub-system actions becoming necessary because of changes in configuration keys, changes in the set of included front-end drivers or because of potential clock instabilities. The operator is guided to perform the necessary actions through graphical indicators displayed next to the relevant command buttons in the user interface. Through these indicators, consistent configuration of CMS is ensured. However, manually following the indicators can still be inefficient at times. A new assistant to the operator has therefore been developed that can automatically perform all the necessary actions in a streamlined order. If additional problems arise, the new assistant tries to automatically recover from these. With the new assistant, a run can be started from any state of the sub-systems with a single click. An ongoing run may be recovered with a single click, once the appropriate recovery action has been selected. We review the automation features of CMS Run Control and discuss the new assistant in detail including first operational experience.