| 1. |
- Abramsson, Mia L, et al.
(author)
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Charge engineering reveals the roles of ionizable side chains in electrospray ionization mass spectrometry
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Other publication (other academic/artistic)abstract
- The role of ionizable side chains in the electrospray ionization mass spectrometry of intact proteins remains hotly debated but has not been conclusively addressed because multiple chargeable sites are present in virtually all proteins. Using engineered soluble proteins, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, whilst co-existing conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. We conclude that the sum of charges is governed solely by Coulombic terms, while their locations affect the stability of the protein in the gas phase.
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| 2. |
- Abramsson, Mia L., et al.
(author)
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Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry
- 2021
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In: JACS Au. - : American Chemical Society (ACS). - 2691-3704. ; 1:12, s. 2385-2393
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Journal article (peer-reviewed)abstract
- In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the ability of native mass spectrometry to inform about protein structure and dynamics. How the behavior of intact proteins in the gas phase depends on the presence and distribution of ionizable surface residues has been difficult to answer because multiple chargeable sites are present in virtually all proteins. Turning to protein engineering, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, while coexisting conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. In fact, moving a single ionizable group can dramatically alter the gas-phase conformation of a protein ion. We conclude that although the sum of the charges is governed solely by Coulombic terms, their locations affect the stability of the protein in the gas phase.
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| 3. |
- Borg, Tessie, et al.
(author)
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Diastereoselective Nucleophilic Addition to Aldehydes with Polar alpha- and alpha,beta-Substituents
- 2011
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In: Advanced Synthesis and Catalysis. - : Wiley. - 1615-4150 .- 1615-4169. ; 353:11-12, s. 2022-2036
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Journal article (peer-reviewed)abstract
- The stereoselectivities obtained in Lewis acid-promoted Mukaiyama aldol additions and Sakurai allylations of mono-, and syn- and anti-disubstituted aldehydes possessing various polar alpha- and beta-substituents under non-chelating conditions are presented. The stereochemical outcome in the nucleophilic addition to alpha-substituted aldehydes containing an alpha-benzyloxy, alpha-fluoro or alpha-sulfonamide substituent are accurately predicted by current stereoinduction models. In contrast, the selectivitites obtained from addition of sterically demanding nucleophiles to alpha-chloro-substituted aldehydes cannot be rationalized by the same models and an alternative is discussed. The stereochemichal outcome in the additions to alpha, beta-disubstituted aldehydes is more complex and cannot be predicted using current models.
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| 4. |
- Borg, Tessie, et al.
(author)
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Mukaiyama aldol addition to α-chloro-substituted aldehydes. Origin of the unexpected syn selectivity.
- 2010
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In: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 46:8, s. 1281-1283
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Journal article (peer-reviewed)abstract
- The addition of sterically demanding enolsilanes to alpha-chloro aldehydes results unexpectedly in preferential formation of the anti-PFA product (1,2-syn), while the addition of the corresponding boron enolate furnishes the expected polar Felkin-Anh product (1,2-anti). A stereoinduction model explaining these observations is proposed.
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| 5. |
- Danielsson, Jakob, et al.
(author)
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1,3-Dipolar Cycloaddition of Azomethine Ylides to Aldehydes : Synthesis of anti alpha-Amino-beta-Hydroxy Esters
- 2011
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In: European Journal of Organic Chemistry. - : Wiley. - 1434-193X .- 1099-0690. ; :3, s. 607-613
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Journal article (peer-reviewed)abstract
- A 1,3-dipolar cycloaddition reaction of azomethine ylides to aldehydes is described. The azomethine ylides, generated by thermal electrocyclic ring opening of aziridines, adds to aldehydes in good yields with moderate to good selectivities to furnish oxazolidines. The oxazolidines were subsequently hydrolyzed to the corresponding amino alcohols, giving the anti diastereomer as the major product.
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| 6. |
- Danielsson, Jakob, et al.
(author)
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A systematic mapping study on real-Time cloud services
- 2018
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In: Proceedings - 11th IEEE/ACM International Conference on Utility and Cloud Computing Companion, UCC Companion 2018. - : Institute of Electrical and Electronics Engineers Inc.. - 9781728103594 ; , s. 245-251
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Conference paper (peer-reviewed)abstract
- Cloud computing is relatively a new technique to host and use the services and applications from the internet. Although it offers a multitude of advantages like scalability, low operating cost, accessibility and maintainability, etc., they are often not utilized to the fullest due to the lack of timeliness property associated with the cloud. Cloud services are mainly designed to maximize throughput and utilization of resources and hence incorporating predictable execution time properties in to the cloud is arduous. Nevertheless, cloud still remains a highly attractive platform for hosting real-Time applications and services owing to features like elasticity, multi-Tenancy, ability to survive hardware failures, virtualization support and abstraction layer support which provides flexibility and portability. In order for real-Time safety-critical applications to exploit the potential of cloud computing, it is essential to ensure the predictable real-Time behavior of cloud services. In this paper, we perform a systematic mapping study on real-Time cloud services to identify the current research directions and potential research gaps. Our study focuses on analyzing the current architectures and software techniques that are available at present to incorporate real-Time property of the cloud services. We also aim at investigating the current challenges involved in realizing a predictable real-Time behavior of cloud services.
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| 7. |
- Danielsson, Jakob
(author)
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Automatic Characterization and Mitigation of Shared-resource Contention in Multi-core Systems
- 2021
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Doctoral thesis (other academic/artistic)abstract
- Multi-core computers are infamous for being hard to use in time-critical systems due to execution-time variations as an effect of shared resource contention. In this thesis, we study the problem of shared resource contention, which occurs when multiple applications executing on different cores do not have exclusive access to of a shared hardware resource. We investigate performance variations of parallel tasks in multi-core systems and present a method to pinpoint the source of the resource contention using hardware performance counters. We investigate mitigation methods for performance variations due to resource contention, including the Jailhouse hypervisor and the cache-partitioning tool PALLOC. We propose a benchmark strategy that quantifies the isolation gained from a specific isolation technique and exemplify this strategy using the Jailhouse hypervisor. We furthermore present and implement solutions for cache-partition allocation during application runtime. Our implementation aims to avoid over-provisioning of cache through pre-runtime estimations of an application's dependency towards the cache and continuous re-partitioning of the cache memory during application runtime.The primary goal of this thesis is to contribute to a process that automates some of the tedious manual testing needed to detect resource contention bottlenecks. The methods we present in this provide a holistic solution for automatic mitigating resource-contention in a multi-core system. First, we evaluate the risk for shared resource contention when several applications execute simultaneously. We then allocate partitions to mitigate resource contention for applications that risk severe performance degradations. We finally present methods that dynamically re-allocate partition space to meet the performance requirements of the running applications.
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| 8. |
- Danielsson, Jakob, et al.
(author)
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Automatic Quality of Service Control in Multi-core Systems using Cache Partitioning
- 2021
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Conference paper (peer-reviewed)abstract
- In this paper, we present a last-level cache partitioning controller for multi-core systems. Our objective is to control the Quality of Service (QoS) of applications in multi-core systems by monitoring run-time performance and continuously re-sizing cache partition sizes according to the applications' needs. We discuss two different use-cases; one that promotes application fairness and another one that prioritizes applications according to the system engineers' desired execution behavior. We display the performance drawbacks of maintaining a fair schedule for all system tasks and its performance implications for system applications. We, therefore, implement a second control algorithm that enforces cache partition assignments according to user-defined priorities rather than system fairness. Our experiments reveal that it is possible, with non-instrusive (0.3-0.7\% CPU utilization) cache controlling measures, to increase performance according to setpoints and maintain the QoS for specific applications in an over-saturated system.
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| 9. |
- Danielsson, Jakob
(author)
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Characterization of Shared Resource Contention in Multi-core Systems
- 2019
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Licentiate thesis (other academic/artistic)abstract
- Multi-core computers are infamous for being hard to use in time-critical systems due to execution-time variations as an effect of shared resource contention. In this thesis we study the problem of shared resource contention which occurs when multiple applications executing on different cores do not have exclusive ownership of a shared resource. We investigate performance variations of parallel tasks in multi-core systems and present a method to pinpoint the source of the resource contention using existing hardware performance counters. Furthermore, we investigate methods to mitigate performance variations using resource isolation techniques. We present a methodology for verifying isolation and tested the achieved isolation using the Jailhouse hypervisor. We further investigate shared cache memory isolation techniques using a page coloring tool called PALLOC. Page-coloring is used for partitioning the cache, assigning specific cache lines to specific processes. Page coloring can however cause system performance degradation since it decreases the total amount of cache memory available for each process. Finally, we propose a dynamic partitioning assignment policy which assigns cache partitions to a process according to an adaptive model based on the process performance. The general conclusion from our investigations is that a large body of applications can suffer from shared resource contention and that techniques for mitigating resource contention are in dire need. Our methods measure and characterise applications, identifies resource contention and finally study isolation techniques.
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| 10. |
- Danielsson, Jakob, et al.
(author)
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Investigating execution-characteristics of feature-detection algorithms
- 2017
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In: IEEE Conference on Emerging Technologies and Factory Automation. - : Institute of Electrical and Electronics Engineers Inc.. - 1946-0740 .- 1946-0759. ; Part F134116, s. 1-4
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Journal article (peer-reviewed)abstract
- We discuss how to obtain information of execution characteristics, such as parallelizability and memory utilization, with the final aim to improve the performance and predictability of feature and corner detection algorithms for use in e.g. robotics and autonomous machines. Our aim is to obtain a better understanding of how computer vision algorithms use hardware resources and how to improve the time predictability and execution time of such algorithms when executing on multi-core CPUs. We evaluate a fork-join model applicable to feature detection algorithms and present a method for measuring how well the algorithm performance correlates with hardware resource usage. We have applied our method to the Featured from Accelerated Segment Test (FAST) algorithm. Our characterization of FAST reveals that it is an algorithm with excellent parallelism opportunities, resulting in an almost linear speed-up per core. Our measurements also reveal that the performance of FAST correlates very little with the number number of misses in the L1 data cache, L1 instruction cache, data translation lookaside buffer and L2 cache. Thus, the FAST algorithm will not have a negative effect on the execution time when the input data fits in the L2 cache.
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