The Experts below are selected from a list of 64491 Experts worldwide ranked by ideXlab platform
Juinndar Huang - One of the best experts on this subject based on the ideXlab platform.
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sample preparation for many reactant bioassay on dmfbs using common dilution operation sharing
International Conference on Computer Aided Design, 2013Co-Authors: Haohan Chang, Tungche Liang, Juinndar HuangAbstract:Sample preparation is an essential processing step in most biochemical applications. Various Reactants are mixed together to produce a solution with the target concentration. Since Reactants generally take a notable part of the cost in a bioassay, their usage should be minimized whenever possible. In this paper, we propose an algorithm, CoDOS, to prepare the target solution with many Reactants using common dilution operation sharing on digital microfluidic biochips (DMFBs). CoDOS first represents the given target concentration as a recipe matrix, and then identifies rectangles in the matrix, where each rectangle indicates an opportunity of dilution operation sharing for reactant minimization. Experimental results demonstrate that CoDOS can achieve up to 27% of reactant saving as compared with the bit-scanning method in single-target sample preparation. Moreover, even if CoDOS is not developed for multi-target sample preparation, it still outperforms the recent state-of-the-art algorithm, RSMA. Hence, it is convincing that CoDOS is a better alternative for many-reactant sample preparation.
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reactant and waste minimization in multitarget sample preparation on digital microfluidic biochips
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 2013Co-Authors: Juinndar HuangAbstract:Sample preparation is one of essential processes in biochemical reactions. Raw Reactants are diluted in this process to achieve given target concentrations. A bioassay may require several different target concentrations of a reactant. Both the dilution operation count and the reactant usage can be minimized if multiple target concentrations are considered simultaneously during sample preparation. Hence, in this paper, we propose a multitarget sample preparation algorithm that extensively exploits the ideas of waste recycling and intermediate droplet sharing to reduce both reactant usage and waste amount for digital microfluidic biochips. Experimental results show that our waste recycling algorithm can reduce the waste and operation count by 48% and 37%, respectively, as compared to an existing state-of-the-art multitarget sample preparation method if the number of target concentrations is ten. The reduction can be up to 97% and 73% when the number of target concentrations goes even higher.
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reactant and waste minimization in multitarget sample preparation on digital microfluidic biochips
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 2013Co-Authors: Juinndar HuangAbstract:Sample preparation is one of essential processes in biochemical reactions. Raw Reactants are diluted in this process to achieve given target concentrations. A bioassay may require several different target concentrations of a reactant. Both the dilution operation count and the reactant usage can be minimized if multiple target concentrations are considered simultaneously during sample preparation. Hence, in this paper, we propose a multitarget sample preparation algorithm that extensively exploits the ideas of waste recycling and intermediate droplet sharing to reduce both reactant usage and waste amount for digital microfluidic biochips. Experimental results show that our waste recycling algorithm can reduce the waste and operation count by 48% and 37%, respectively, as compared to an existing state-of-the-art multitarget sample preparation method if the number of target concentrations is ten. The reduction can be up to 97% and 73% when the number of target concentrations goes even higher.
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graph based optimal reactant minimization for sample preparation on digital microfluidic biochips
International Symposium on VLSI Design Automation and Test, 2013Co-Authors: Tingwei Chiang, Juinndar HuangAbstract:Sample preparation is an essential step in biochemical reactions. Reactants must be diluted to achieve given target concentrations in sample preparation. Since some Reactants like costly reagents and infant's blood are valuable, their usage should be minimized during dilution. In this paper, we propose an optimal reactant minimization algorithm, GORMA, for sample preparation on digital microfluidic biochips. GORMA adopts a systematic method to exhaustively check all possible dilution solutions and then identifies the one with minimal reactant usage and waste through maximal droplet sharing. Experimental results show that GORMA outperforms all the existing methods in reactant usage. Meanwhile, the waste amount is reduced up to 30% as compared with existing waste minimization methods. Moreover, GORMA requires only 0.6% more operations on average when compared with an operation-minimal dilution method.
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graph based optimal reactant minimization for sample preparation on digital microfluidic biochips
International Symposium on VLSI Design Automation and Test, 2013Co-Authors: Tingwei Chiang, Juinndar HuangAbstract:Sample preparation is an essential step in biochemical reactions. Reactants must be diluted to achieve given target concentrations in sample preparation. Since some Reactants like costly reagents and infant's blood are valuable, their usage should be minimized during dilution. In this paper, we propose an optimal reactant minimization algorithm, GORMA, for sample preparation on digital microfluidic biochips. GORMA adopts a systematic method to exhaustively check all possible dilution solutions and then identifies the one with minimal reactant usage and waste through maximal droplet sharing. Experimental results show that GORMA outperforms all the existing methods in reactant usage. Meanwhile, the waste amount is reduced up to 30% as compared with existing waste minimization methods. Moreover, GORMA requires only 0.6% more operations on average when compared with an operation-minimal dilution method.
Bin Jiang - One of the best experts on this subject based on the ideXlab platform.
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effects of reactant rotational excitation on reactivity perspectives from the sudden limit
Journal of Chemical Physics, 2014Co-Authors: Bin JiangAbstract:Excitation of reactant rotational degrees of freedom is known to influence reactivity in bimolecular reactions. In this work, this effect is examined for several prototypical activated atom-diatom and atom-triatom reactions through exact quantum scattering calculations on accurate ab initio potential energy surfaces. To rationalize these mode-specific effects, the recently proposed sudden vector overlap model is extended to include rotational motions of Reactants. Specifically, the enhancement of reactivity is attributed to their coupling with the reaction coordinate at the transition state, as quantified by the alignment between the corresponding normal mode vectors. In addition, a Franck-Condon model is introduced to predict the effect of reactant rotational excitation for reactions in which the reactant rotations are decoupled from the reaction coordinate.
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effects of reactant rotational excitation on reactivity perspectives from the sudden limit
Journal of Chemical Physics, 2014Co-Authors: Bin Jiang, Jun LiAbstract:Excitation of reactant rotational degrees of freedom is known to influence reactivity in bimolecular reactions. In this work, this effect is examined for several prototypical activated atom-diatom and atom-triatom reactions through exact quantum scattering calculations on accurate ab initio potential energy surfaces. To rationalize these mode-specific effects, the recently proposed sudden vector overlap model is extended to include rotational motions of Reactants. Specifically, the enhancement of reactivity is attributed to their coupling with the reaction coordinate at the transition state, as quantified by the alignment between the corresponding normal mode vectors. In addition, a Franck-Condon model is introduced to predict the effect of reactant rotational excitation for reactions in which the reactant rotations are decoupled from the reaction coordinate.
Alieh Kazemeini - One of the best experts on this subject based on the ideXlab platform.
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Aldol reactions with kinetic resolution: scope and limitations of ketal- and dithioketal-protected β-ketoaldehydes.
The Journal of organic chemistry, 2012Co-Authors: Dale E. Ward, Alieh KazemeiniAbstract:The multiplicativity rule suggests that aldol coupling of chiral Reactants will proceed with substantial mutual kinetic enantioselection (MKE) (racemic Reactants) or via a highly enantioselective kinetic resolution (KR) (one enantiopure reactant) if the relative topicity is highly selective and the ketone enolate and aldehyde each have high diastereoface selectivity. The scope and limitations of that paradigm were explored by determining the stereoselectivities of aldol reactions of ketone 1a (known to give 3,5-trans aldol adducts with high selectivity) with a series of ketal- and dithioketal-protected β-ketoaldehydes (±)-5 (predicted to have high Felkin diastereoface selectivity). Using racemic Reactants, all reactions of the (c-Hex)(2)B enolates (highly anti-selective relative topicity) were remarkably selective and gave the 3,5-trans-3,1"-anti-1",2"-syn adduct, one of eight possible diastereomers, via a diastereoselective (dr > 20) preferential reaction (MKE > 17) of like reactant enantiomers [i.e., (3R)-1a + (R)-5 and (3S)-1a + (S)-5]. Reactions of the corresponding Ti(IV) "ate" enolates (anticipated syn-selective relative topicity) were much less selective, and only those of MOM-protected 1a with dithiolane-protected (±)-5 (i.e., X = S, n = 1) gave high selectivity in favor of the 3,5-trans-3,1"-syn-1",2"-syn adduct via a diastereoselective (dr > 20) preferential reaction (MKE ≥ 6) of unlike reactant enantiomers [i.e., (3R)-1a + (S)-5 and (3S)-1a + (R)-5]. Analogous reactions of the (c-Hex)(2)B and Ti(IV) "ate" enolates of enantiopure (+)-1a (R = MOM) with (±)-5c (R(2) = Me, X = S, n = 1) occurred with KR to give the corresponding enantiopure adducts with the expected stereoselectivity. The adducts have applications in polyproionate synthesis.
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Aldol Reactions with Kinetic Resolution: Scope and Limitations of Ketal- and Dithioketal-Protected β‑Ketoaldehydes
2012Co-Authors: Dale E. Ward, Alieh KazemeiniAbstract:The multiplicativity rule suggests that aldol coupling of chiral Reactants will proceed with substantial mutual kinetic enantioselection (MKE) (racemic Reactants) or via a highly enantioselective kinetic resolution (KR) (one enantiopure reactant) if the relative topicity is highly selective and the ketone enolate and aldehyde each have high diastereoface selectivity. The scope and limitations of that paradigm were explored by determining the stereoselectivities of aldol reactions of ketone 1a (known to give 3,5-trans aldol adducts with high selectivity) with a series of ketal- and dithioketal-protected β-ketoaldehydes (±)-5 (predicted to have high Felkin diastereoface selectivity). Using racemic Reactants, all reactions of the (c-Hex)2B enolates (highly anti-selective relative topicity) were remarkably selective and gave the 3,5-trans-3,1″-anti-1″,2″-syn adduct, one of eight possible diastereomers, via a diastereoselective (dr > 20) preferential reaction (MKE > 17) of like reactant enantiomers [i.e., (3R)-1a + (R)-5 and (3S)-1a + (S)-5]. Reactions of the corresponding Ti(IV) “ate” enolates (anticipated syn-selective relative topicity) were much less selective, and only those of MOM-protected 1a with dithiolane-protected (±)-5 (i.e., X = S, n = 1) gave high selectivity in favor of the 3,5-trans-3,1″-syn-1″,2″-syn adduct via a diastereoselective (dr > 20) preferential reaction (MKE ≥ 6) of unlike reactant enantiomers [i.e., (3R)-1a + (S)-5 and (3S)-1a + (R)-5]. Analogous reactions of the (c-Hex)2B and Ti(IV) “ate” enolates of enantiopure (+)-1a (R = MOM) with (±)-5c (R2 = Me, X = S, n = 1) occurred with KR to give the corresponding enantiopure adducts with the expected stereoselectivity. The adducts have applications in polyproionate synthesis
Haruhiko Ohya - One of the best experts on this subject based on the ideXlab platform.
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development of porous solid reactant for thermal energy storage and temperature upgrade using carbonation decarbonation reaction
Applied Energy, 2001Co-Authors: Masahiko Aihara, Junro Matsushita, Yoichi Negishi, Toshiyuki Nagai, Haruhiko OhyaAbstract:Cyclic reaction performances of solid Reactants for a CaO-CO2 chemical heat-pump designed for upgrading and storing high-temperature thermal energy were studied. Solid Reactants composed of CaO as the reactant and CaTiO3 as the inert framework were prepared using the conventional powder method or the metal alkoxide method. Upon experiments of cyclic operation between CaO carbonation and CaCO3 decarbonation at 1023K, the reaction reversibility of the solid Reactants with the inert CaTiO3 framework was steady, whereas that of the solid reactant without the inert framework decreased with sintering of the solid particles during cyclic operation. Reaction rates for the first carbonation and the decarbonation of solid reactant prepared using the alkoxide method were about 1.8 and 2.4 times faster, respectively, than for those prepared by the powder method due to the smaller average diameter of reactant particles derived from the alkoxide method.
Seung Soon Jang - One of the best experts on this subject based on the ideXlab platform.
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molecular dynamics simulations of aldol condensation catalyzed by alkylamine functionalized crystalline silica surfaces
Journal of the American Chemical Society, 2016Co-Authors: Eric G Moschetta, Christopher W Jones, Seung Soon JangAbstract:Molecular dynamics simulations are performed to investigate the cooperatively catalyzed aldol condensation between acetone and 4-nitrobenzaldehyde on alkylamine (or alkylenamine)-grafted silica surfaces, focusing on the mechanism of the catalytic activation of the acetone and 4-nitrobenzaldehyde by the acidic surface silanols followed by the nucleophilic attack of the basic amine functional group toward the activated reactant. From the analysis of the correlations between the catalytically active acid–base sites and Reactants, it is concluded that the catalytic cooperativity of the acid–base pair can be affected by two factors: (1) the competition between the silanol and the amine (or enamine) to form a hydrogen bond with a reactant and (2) the flexibility of the alkylamine (or alkylenamine) backbone. Increasing the flexibility of the alkylamine facilitates the nucleophilic attack of the amine on the Reactants. From the molecular dynamics simulations, it is found that C3 propylamine and C4 butylamine link...
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Molecular Dynamics Simulations of Aldol Condensation Catalyzed by Alkylamine-Functionalized Crystalline Silica Surfaces
2016Co-Authors: Ki Chul Kim, Christopher W Jones, Eric G Moschetta, Seung Soon JangAbstract:Molecular dynamics simulations are performed to investigate the cooperatively catalyzed aldol condensation between acetone and 4-nitrobenzaldehyde on alkylamine (or alkylenamine)-grafted silica surfaces, focusing on the mechanism of the catalytic activation of the acetone and 4-nitrobenzaldehyde by the acidic surface silanols followed by the nucleophilic attack of the basic amine functional group toward the activated reactant. From the analysis of the correlations between the catalytically active acid–base sites and Reactants, it is concluded that the catalytic cooperativity of the acid–base pair can be affected by two factors: (1) the competition between the silanol and the amine (or enamine) to form a hydrogen bond with a reactant and (2) the flexibility of the alkylamine (or alkylenamine) backbone. Increasing the flexibility of the alkylamine facilitates the nucleophilic attack of the amine on the Reactants. From the molecular dynamics simulations, it is found that C3 propylamine and C4 butylamine linkers exhibit the highest probability of reaction, which is consistent with the experimental observation that the activity of the aldol reaction on mesoporous silica depends on the length of alkylamine grafted on the silica surface. This simulation work serves as a pioneering study demonstrating how the molecular simulation approach can be successfully employed to investigate the cooperative catalytic activity of such bifunctional acid–base catalysts
