scholarly journals QiBAM: Approximate Sub-String Index Search on Quantum Accelerators Applied to DNA Read Alignment

Electronics ◽  
2021 ◽  
Vol 10 (19) ◽  
pp. 2433
Author(s):  
Aritra Sarkar ◽  
Zaid Al-Ars ◽  
Carmen G. Almudever ◽  
Koen L. M. Bertels
Keyword(s):  
Dna Sequences ◽  
Search Algorithm ◽  
Scale Up ◽  
Quantum Algorithm ◽  
Small Scale ◽  
Distributed Search ◽  
Sequence Reconstruction ◽  
Grover’S Search Algorithm ◽  
Physics Labs ◽  
Pipeline Design

With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors in a few years are expected to scale up and be more robust for efficiently computing important algorithms in various fields. In this paper, we propose a quantum algorithm to address the challenging field of data processing for genome sequence reconstruction. This research describes an architecture-aware implementation of a quantum algorithm for sub-sequence alignment. A new algorithm named QiBAM (quantum indexed bidirectional associative memory) is proposed, which uses approximate pattern-matching based on Hamming distances. QiBAM extends the Grover’s search algorithm in two ways, allowing: (1) approximate matches needed for read errors in genomics, and (2) a distributed search for multiple solutions over the quantum encoding of DNA sequences. This approach gives a quadratic speedup over the classical algorithm. A full implementation of the algorithm is provided and verified using the OpenQL compiler and QX Simulator framework. Our implementation represents a first exploration towards a full-stack quantum accelerated genome sequencing pipeline design.

QUANTUM COMPUTING, GROVER'S SEARCH ALGORITHM AND ITS APPLICATIONS IN BIOINFORMATICS

COSMOS ◽  
2006 ◽  
Vol 02 (01) ◽  
pp. 71-80
Author(s):  
K. W. CHOO
Keyword(s):  
Quantum Computing ◽  
Mass Spectra ◽  
Search Algorithm ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Protein Mass ◽  
Quantum Counting ◽  
Grover’S Search Algorithm ◽  
Counting Algorithm

This article reviews quantum computing and quantum algorithms. Some insights into its potential in speeding up computations are covered, with emphasis on the use of Grover's Search. In the last section, we discuss applications of quantum algorithm to bioinformatics. In particular, the extension of quantum counting algorithm to protein mass spectra counting is proposed.

scholarly journals Solid Form and Phase Transformation Properties of Fexofenadine Hydrochloride during Wet Granulation Process

Pharmaceutics ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 802
Author(s):  
Suye Li ◽  
Hengqian Wu ◽  
Yanna Zhao ◽  
Ruiyan Zhang ◽  
Zhengping Wang ◽  
...  
Keyword(s):  
Phase Transition ◽  
Phase Transformation ◽  
Water Content ◽  
Scale Up ◽  
Small Scale ◽  
Dissolution Behavior ◽  
Wet Granulation ◽  
Water Addition ◽  
Granulation Process ◽  
And Performance

The quality control of drug products during manufacturing processes is important, particularly the presence of different polymorphic forms in active pharmaceutical ingredients (APIs) during production, which could affect the performance of the formulated products. The objective of this study was to investigate the phase transformation of fexofenadine hydrochloride (FXD) and its influence on the quality and performance of the drug. Water addition was key controlling factor for the polymorphic conversion from Form I to Form II (hydrate) during the wet granulation process of FXD. Water-induced phase transformation of FXD was studied and quantified with XRD and thermal analysis. When FXD was mixed with water, it rapidly converted to Form II, while the conversion is retarded when FXD is formulated with excipients. In addition, the conversion was totally inhibited when the water content was <15% w/w. The relationship between phase transformation and water content was studied at the small scale, and it was also applicable for the scale-up during wet granulation. The effect of phase transition on the FXD tablet performance was investigated by evaluating granule characterization and dissolution behavior. It was shown that, during the transition, the dissolved FXD acted as a binder to improve the properties of granules, such as density and flowability. However, if the water was over added, it can lead to the incomplete release of the FXD during dissolution. In order to balance the quality attributes and the dissolution of granules, the phase transition of FXD and the water amount added should be controlled during wet granulation.

SUBMERGED CITRIC ACID FERMENTATION OF SUGAR BEET MOLASSES: INCREASE IN SCALE

1955 ◽  
Vol 1 (5) ◽  
pp. 299-311 ◽  
Author(s):  
R. Steel ◽  
C. P. Lentz ◽  
S. M. Martin
Keyword(s):  
Citric Acid ◽  
Scale Up ◽  
Aeration Rate ◽  
Small Scale ◽  
Acid Fermentation ◽  
Inoculum Level ◽  
Cross Sectional ◽  
Factors Affecting ◽  
Beet Molasses ◽  
Initial Ph

Factors affecting the production of citric acid in the submerged fermentation of ferrocyanide-treated beet molasses by Aspergillus niger were studied in 2.5 and 36 liter fermenters. The small fermenters were used to determine the effects of changes in sterilization technique, phosphate supplement, ferrocyanide treatment, inoculum level, initial pH, fermentation temperature, and aeration rate. The relation between ferrocyanide concentration and inoculum level was also studied. Four different samples of molasses were fermented successfully. An average yield of 8.2% citric acid (64% conversion) was obtained from 51 small-scale fermentations. Comparable yields were obtained in the large fermenters under comparable conditions. Most of the information obtained with the small fermenters was applicable to the larger-scale fermenters, but in the latter the fermentation was significantly more stable. Aeration was the main problem in the scale-up and aeration rates approximately double those calculated on a fermenter cross-sectional area basis were required for comparable results in the large fermenters.

scholarly journals Quantifying computational advantage of Grover’s algorithm with the trace speed

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Valentin Gebhart ◽  
Luca Pezzè ◽  
Augusto Smerzi
Keyword(s):  
Quantum Coherence ◽  
Search Algorithm ◽  
Quantum Algorithms ◽  
Physical Origin ◽  
Computational Advantage ◽  
Speed Up ◽  
Quantum Speed Up ◽  
Quantum Statistical ◽  
Grover’S Search Algorithm ◽  
General Physical

AbstractDespite intensive research, the physical origin of the speed-up offered by quantum algorithms remains mysterious. No general physical quantity, like, for instance, entanglement, can be singled out as the essential useful resource. Here we report a close connection between the trace speed and the quantum speed-up in Grover’s search algorithm implemented with pure and pseudo-pure states. For a noiseless algorithm, we find a one-to-one correspondence between the quantum speed-up and the polarization of the pseudo-pure state, which can be connected to a wide class of quantum statistical speeds. For time-dependent partial depolarization and for interrupted Grover searches, the speed-up is specifically bounded by the maximal trace speed that occurs during the algorithm operations. Our results quantify the quantum speed-up with a physical resource that is experimentally measurable and related to multipartite entanglement and quantum coherence.

scholarly journals Sustainable Second-Generation Bioethanol Production from Enzymatically Hydrolyzed Domestic Food Waste Using Pichia anomala as Biocatalyst

2020 ◽  
Vol 13 (1) ◽  
pp. 259
Author(s):  
Ioanna Ntaikou ◽  
Georgia Antonopoulou ◽  
Gerasimos Lyberatos
Keyword(s):  
Food Waste ◽  
Second Generation ◽  
Scale Up ◽  
Pichia Anomala ◽  
Small Scale ◽  
Amylolytic Enzymes ◽  
Second Generation Bioethanol ◽  
Saccharification Efficiency ◽  
Ethanol Yields ◽  
Domestic Food

In the current study, a domestic food waste containing more than 50% of carbohydrates was assessed as feedstock to produce second-generation bioethanol. Aiming to the maximum exploitation of the carbohydrate fraction of the waste, its hydrolysis via cellulolytic and amylolytic enzymatic blends was investigated and the saccharification efficiency was assessed in each case. Fermentation experiments were performed using the non-conventional yeast Pichia anomala (Wickerhamomyces anomalus) under both separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) modes to evaluate the conversion efficiencies and ethanol yields for different enzymatic loadings. It was shown that the fermentation efficiency of the yeast was not affected by the fermentation mode and was high for all handlings, reaching 83%, whereas the enzymatic blend containing the highest amount of both cellulolytic and amylolytic enzymes led to almost complete liquefaction of the waste, resulting also in ethanol yields reaching 141.06 ± 6.81 g ethanol/kg waste (0.40 ± 0.03 g ethanol/g consumed carbohydrates). In the sequel, a scale-up fermentation experiment was performed with the highest loading of enzymes in SHF mode, from which the maximum specific growth rate, μmax, and the biomass yield, Yx/s, of the yeast from the hydrolyzed waste were estimated. The ethanol yields that were achieved were similar to those of the respective small scale experiments reaching 138.67 ± 5.69 g ethanol/kg waste (0.40 ± 0.01 g ethanol/g consumed carbohydrates).

scholarly journals Assessing market-based conservation governance approaches: a socio-economic profile of Indonesian markets for wild birds

Oryx ◽  
2011 ◽  
Vol 45 (4) ◽  
pp. 482-491 ◽  
Author(s):  
Paul Jepson ◽  
Richard J. Ladle ◽  
Sujatnika
Keyword(s):  
Native Species ◽  
Wildlife Conservation ◽  
Scale Up ◽  
Policy Instrument ◽  
Wild Birds ◽  
Small Scale ◽  
Poor Growth ◽  
Cultural Aspects ◽  
Depth Analysis ◽  
Conservation Governance

AbstractOne of the most difficult situations for conservation is where state capacity to regulate is weak, major corporate organizations are absent, and the population does not have a strong culture of wildlife conservation. All these apply to the hugely popular urban Indonesian pastime of keeping wild songbirds, thought to be responsible for rolling local extinctions of several native species. In such situations the introduction of a voluntary, market-based approach could interact with regulation to create new and more effective approaches to reducing the negative conservation impacts of the associated trade. Here we assess the potential of such an approach through an in-depth analysis of the socio-economic and cultural aspects of bird keeping. We project that overall the pastime contributes USD 78.8 million to the economies of the six cities surveyed, supporting a range of associated small-scale rural and urban livelihoods relating to the production of cages and collection of live bird food. Finally, we describe five general bird-breeding models with the capacity to scale up the production of captive-bred birds that may substitute for wild-caught conspecifics. Based on this information we argue that a market-based policy instrument that is capable of shifting bird-keeping trends from wild-caught birds to captive-bred alternatives would align easily with macro-policy agendas in Indonesia relating to pro-poor growth and the creation of more and better jobs. Such a policy instrument could provide exciting opportunities for conservationists to engage the interest and support of non-conservation sectors in Indonesia in efforts to conserve diminishing populations of wild birds.

scholarly journals Energy Production from Biogas: Competitiveness and Support Instruments in Latvia

2016 ◽  
Vol 53 (5) ◽  
pp. 43-53
Author(s):  
G. Klāvs ◽  
A. Kundziņa ◽  
I. Kudrenickis
Keyword(s):  
New Technologies ◽  
Local Economic Development ◽  
Renewable Energy Sources ◽  
Distribution Network ◽  
Scale Up ◽  
Electricity Production ◽  
Small Scale ◽  
Gas Distribution ◽  
Ex Post ◽  
The Impact

Abstract Use of renewable energy sources (RES) might be one of the key factors for the triple win-win: improving energy supply security, promoting local economic development, and reducing greenhouse gas emissions. The authors ex-post evaluate the impact of two main support instruments applied in 2010-2014 – the investment support (IS) and the feed-in tariff (FIT) – on the economic viability of small scale (up to 2MWel) biogas unit. The results indicate that the electricity production cost in biogas utility roughly corresponds to the historical FIT regarding electricity production using RES. However, if in addition to the FIT the IS is provided, the analysis shows that the practice of combining both the above-mentioned instruments is not optimal because too high total support (overcompensation) is provided for a biogas utility developer. In a long-term perspective, the latter gives wrong signals for investments in new technologies and also creates unequal competition in the RES electricity market. To provide optimal biogas utilisation, it is necessary to consider several options. Both on-site production of electricity and upgrading to biomethane for use in a low pressure gas distribution network are simulated by the cost estimation model. The authors’ estimates show that upgrading for use in a gas distribution network should be particularly considered taking into account the already existing infrastructure and technologies. This option requires lower support compared to support for electricity production in small-scale biogas utilities.

scholarly journals TERENO: German network of terrestrial environmental observatories

2016 ◽  
Vol 2 ◽  
Author(s):  
Heye Reemt Bogena
Keyword(s):  
Regional Scale ◽  
Scale Up ◽  
Climate Change Impacts ◽  
Integrated Modelling ◽  
Small Scale ◽  
Catchment Scale ◽  
Terrestrial Environment ◽  
Regional Analyses ◽  
Research Facilities

Central elements of the TERENO network are “terrestrial observatories” at the catchment scale which were selected in climate sensitive regions of Germany for the regional analyses of climate change impacts. Within these observatories small scale research facilities and test areas are placed in order to accomplish energy, water, carbon and nutrient process studies across the different compartments of the terrestrial environment. Following a hierarchical scaling approach (point-plot-field) these detailed information and the gained knowledge will be transferred to the regional scale using integrated modelling approaches. Furthermore, existing research stations are enhanced and embedded within the observatories. In addition, mobile measurement platforms enable monitoring of dynamic processes at the local scale up to the determination of spatial pattern at the regional scale are applied within TERENO.

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