Calvin Chen | Pace University (original) (raw)

Papers by Calvin Chen

Research paper thumbnail of A cautionary case of casual causality

Journal of High Energy Physics, 2022

We distinguish between the notions of asymptotic causality and infrared causality for gravitation... more We distinguish between the notions of asymptotic causality and infrared causality for gravitational effective field theories, and show that the latter gives constraints consistent with gravitational positivity bounds. We re-explore the scattering of gravitational waves in a spherically symmetric background in the EFT of gravity in D ≥ 5, for which the leading-order correction to Einstein gravity is determined by the Gauss-Bonnet operator. We reproduce the known result that the truncated effective theory exhibits apparent time advances relative to the background geometry for specific polarisations, which naively signal a violation of causality. We show that by properly identifying the regime of validity of the effective theory, the apparent time advance can be shown to be unresolvable. To illustrate this, we identify specific higher-dimension operators in the EFT expansion which become large for potentially resolvable time advances, rendering the EFT expansion invalid. Our results de...

Research paper thumbnail of Drug design of cyclin-dependent kinase 2 inhibitor for melanoma from traditional Chinese medicine

BioMed research international, 2014

One has found an important cell cycle controller. This guard can decide the cell cycle toward pro... more One has found an important cell cycle controller. This guard can decide the cell cycle toward proliferation or quiescence. Cyclin-dependent kinase 2 (CDK2) is a unique target among the CDK family in melanoma therapy. We attempted to find out TCM compounds from TCM Database@Taiwan that have the ability to inhibit the activity of CDK2 by systems biology. We selected Tetrahydropalmatine, Reserpiline, and (+)-Corydaline as the candidates by docking and screening results for further survey. We utilized support vector machine (SVM), multiple linear regression (MLR) models and Bayesian network for validation of predicted activity. By overall analysis of docking results, predicted activity, and molecular dynamics (MD) simulation, we could conclude that Tetrahydropalmatine, Reserpiline, and (+)-Corydaline had better binding affinity than the control. All of them had the ability to inhibit the activity of CDK2 and might have the opportunity to be applied in melanoma therapy.

Research paper thumbnail of Quantifying Athermality and Quantum Induced Deviations from Classical Fluctuation Relations

Entropy

In recent years, a quantum information theoretic framework has emerged for incorporating non-clas... more In recent years, a quantum information theoretic framework has emerged for incorporating non-classical phenomena into fluctuation relations. Here, we elucidate this framework by exploring deviations from classical fluctuation relations resulting from the athermality of the initial thermal system and quantum coherence of the system’s energy supply. In particular, we develop Crooks-like equalities for an oscillator system which is prepared either in photon added or photon subtracted thermal states and derive a Jarzynski-like equality for average work extraction. We use these equalities to discuss the extent to which adding or subtracting a photon increases the informational content of a state, thereby amplifying the suppression of free energy increasing process. We go on to derive a Crooks-like equality for an energy supply that is prepared in a pure binomial state, leading to a non-trivial contribution from energy and coherence on the resultant irreversibility. We show how the binomi...

Research paper thumbnail of Coordinating product configuration in the order fulfilment processing: an approach based on the binary tree algorithm

International Journal of Computer Integrated Manufacturing, Feb 19, 2007

Research paper thumbnail of Magnolol Encapsulated by Liposome in Inhibiting Smooth Muscle Cell Proliferation

Journal of the Chinese Chemical Society, 2008

Research paper thumbnail of Insight into molecular dynamics simulation of BRAF(V600E) and potent novel inhibitors for malignant melanoma

International Journal of Nanomedicine, 2015

Research paper thumbnail of Abstract 101: Pilot study of oral microbiome and risk of pancreatic cancer

Research paper thumbnail of Screening from the World's Largest TCM Database Against H1N1 Virus

Journal of Biomolecular Structure and Dynamics, 2011

The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti... more The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.

Research paper thumbnail of How to design a drug for the disordered proteins?

Drug Discovery Today, 2013

Structural disorders of proteins make drug design a difficult task. The gel-like state of intrins... more Structural disorders of proteins make drug design a difficult task. The gel-like state of intrinsically disordered protein (IDP) or intrinsically disordered regions (IDRs) remains a big puzzle for drug designers. Here, we propose a novel concept for drug design by understanding protein disintegration and protein-protein interaction (PPI) using molecular dynamics (MD) simulation and propose a possible approach for overcoming current obstacles in IDP drug design.

Research paper thumbnail of Some fast parallel algorithms for parentheses matching

Lecture Notes in Computer Science, 1991

The parentheses matching problem is to determine the mate of each parenthesis in a balanced strin... more The parentheses matching problem is to determine the mate of each parenthesis in a balanced string of n parentheses. In this paper, we present three novel and elegant parallel algorithms for this problem on parallel random-access machine (PRAM) models. Each of ...

Research paper thumbnail of Efficient EREW PRAM algorithms for parentheses-matching

IEEE Transactions on Parallel and Distributed Systems, 1994

Abstract We present four polylog-time parallel algorithms for matching parentheses on an exclusiv... more Abstract We present four polylog-time parallel algorithms for matching parentheses on an exclusive-read and exclusive-write (EREW) parallel random-access machine (PRAM) model. These algorithms provide new insights into the parentheses-matching problem. ...

Research paper thumbnail of High-frequency Ds remobilization over multiple generations in barley facilitates gene tagging in large genome cereals

Plant Molecular Biology, 2006

Transposable elements have certain advantages over other approaches for identifying and determini... more Transposable elements have certain advantages over other approaches for identifying and determining gene function in large genome cereals. Different strategies have been used to exploit the maize Activator/dissociation (Ac/Ds) transposon system for functional genomics in heterologous species. Either large numbers of independent Ds insertion lines or transposants (TNPs) are generated and screened phenotypically, or smaller numbers of TNPs are produced, Ds locations mapped and remobilized for localized gene targeting. It is imperative to characterize key features of the system in order to utilize the latter strategy, which is more feasible in large genome cereals like barley and wheat. In barley, we generated greater than 100 single-copy Ds TNPs and determined remobilization frequencies of primary, secondary, and tertiary TNPs with intact terminal inverted repeats (TIRs); frequencies ranged from 11.8 to 17.1%. In 16% of TNPs that had damaged TIRs no transposition was detected among progeny of crosses using those TNPs as parental lines. In half of the greater than 100 TNP lines, the nature of flanking sequences and status of the 11 bp TIRs and 8-bp direct repeats were determined. BLAST searches using a gene prediction program revealed that 86% of TNP flanking sequences matched either known or putative genes, indicating preferential Ds insertion into genic regions, critical in large genome species. Observed remobilization frequencies of primary, secondary, tertiary, and quaternary TNPs, coupled with the tendency for localized Ds transposition, validates a saturation mutagenesis approach using Ds to tag and characterize genes linked to Ds in large genome cereals like barley and wheat.

Research paper thumbnail of Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family1(w

The wall-associated kinase (WAK) gene family, one of the receptor-like kinase (RLK) gene families... more The wall-associated kinase (WAK) gene family, one of the receptor-like kinase (RLK) gene families in plants, plays important roles in cell expansion, pathogen resistance, and heavy-metal stress tolerance in Arabidopsis (Arabidopsis thaliana). Through a reiterative database search and manual reannotation, we identified 125 OsWAK gene family members from rice (Oryza sativa) japonica cv Nipponbare; 37 (approximately 30%) OsWAKs were corrected/reannotated from earlier automated annotations. Of the 125 OsWAKs, 67 are receptor-like kinases, 28 receptor-like cytoplasmic kinases, 13 receptor-like proteins, 12 short genes, and five pseudogenes. The two-intron gene structure of the Arabidopsis WAK/WAK-Likes is generally conserved in OsWAKs; however, extra/missed introns were observed in some OsWAKs either in extracellular regions or in protein kinase domains. In addition to the 38 OsWAKs with full-length cDNA sequences and the 11 with rice expressed sequence tag sequences, gene expression analyses, using tiling-microarray analysis of the 20 OsWAKs on chromosome 10 and reverse transcription-PCR analysis for five OsWAKs, indicate that the majority of identified OsWAKs are likely expressed in rice. Phylogenetic analyses of OsWAKs, Arabidopsis WAK/WAK-Likes, and barley (Hordeum vulgare) HvWAKs show that the OsWAK gene family expanded in the rice genome due to lineage-specific expansion of the family in monocots. Localized gene duplications appear to be the primary genetic event in OsWAK gene family expansion and the 125 OsWAKs, present on all 12 chromosomes, are mostly clustered.

Research paper thumbnail of Efficient EREW PRAM Algorithms for Parentheses-Matching

IEEE Transactions on Parallel and Distributed Systems, 1994

We present four polylog-time parallel algorithms for matching parentheses on an exclusive-read an... more We present four polylog-time parallel algorithms for matching parentheses on an exclusive-read and exclusive-write (EREW) parallel random-access machine (PRAM) model. These algorithms provide new insights into the parentheses-matching problem. The first algorithm has a time complexity of O(log2 n ) employing O ( & ) processors for an input string containing n parentheses. Although this algorithm is not cost-optimal, it is extremely simple to implement. The remaining three algorithms, which are based on a different approach, achieve O( log n ) time complexity in each case, and represent successive improvements. The second algorithm requires O ( n ) processors and working space, and it is comparable to the first algorithm in its ease of

Research paper thumbnail of Pharmacoinformatics approach for mPGES-1 in anti-inflammation by 3D-QSAR pharmacophore mapping

Journal of The Taiwan Institute of Chemical Engineers, 2009

Microsomal prostablandin E synthase-1 (mPGES-1) has been recently investigated to be a novel, hot... more Microsomal prostablandin E synthase-1 (mPGES-1) has been recently investigated to be a novel, hot, and promising target for inflammation-related diseases. The quantitative structure–activity relationship (QSAR) study was used to explore the critical pharmacophore features of mPGES-1 by using a set of 35 azaphenanthrenone derivatives. Twenty-four selected pharmacophore models derived from 240 hypotheses were employed to identify the critical features. The best two pharmacophore hypotheses, generated by HypoGen Technique, exhibited the residuals of approximately 150 and the high correlation coefficient of 0.92. The selected four hypotheses all showed a confidence level of 95% in the Fischer's randomization test. The final four pharmacophore model showed that the four dominant features (hydrogen bond donor and three hydrophobic features, occasionally replaced by ring aromatic feature) had significant impact on activity of mPGES-1 inhibitors. The database virtual screening and drug design can be further implement to searching the novel mPGES-1 inhibitors.

Research paper thumbnail of Chemoinformatics and pharmacoinformatics approach for exploring the GABA-A agonist from Chinese herb suanzaoren

Journal of The Taiwan Institute of Chemical Engineers, 2009

Research paper thumbnail of PARAMETRIC PROCESS OPTIMIZATION TO IMPROVE THE ACCURACY OF RAPID PROTOTYPED STEREOLITHOGRAPHY PARTS

The functional requirements of a rapid prototyping system are speed and accuracy, and they both a... more The functional requirements of a rapid prototyping system are speed and accuracy, and they both are functions of vendor defaulted and user selected manufacturing parameters. Accuracy is evaluated by dimensional errors, form errors and surface roughness of manufactured parts. A special designed specimen with twenty dimensional, geometrical, and surface roughness features has been used in the inspection of RP manufacturing processes. In terms of Taguchi experimental design techniques, an orthogonal array of experiments has been developed which has the least number of experimental runs and desired process parameter settings. Using the 3-D coordinate measuring machine and surface profilometer, a series of measurements in evaluating the SLA parts quality has been conducted to find the functional relationships between the output part quality and input manufacturing process parameters. Two analysis tools, response surface methodology and Analysis of Variance (ANOVA) have been used to evaluate the SLA RP process and to perform the product optimization. The optimal setups of SLA manufacturing parameters for both individual features and a general part with various features have been concluded from this study.

Research paper thumbnail of Parametric process optimization to improve the accuracy of rapid prototyped stereolithography parts

International Journal of Machine Tools & Manufacture, 2000

The functional requirements of a rapid prototyping system are speed and accuracy, and they both a... more The functional requirements of a rapid prototyping system are speed and accuracy, and they both are functions of vendor defaulted and user selected manufacturing parameters. Accuracy is evaluated by dimensional errors, form errors and surface roughness of manufactured parts. A special designed specimen with twenty dimensional, geometrical, and surface roughness features has been used in the inspection of RP manufacturing processes. In terms of Taguchi experimental design techniques, an orthogonal array of experiments has been developed which has the least number of experimental runs and desired process parameter settings. Using the 3-D coordinate measuring machine and surface profilometer, a series of measurements in evaluating the SLA parts quality has been conducted to find the functional relationships between the output part quality and input manufacturing process parameters. Two analysis tools, response surface methodology and Analysis of Variance (ANOVA) have been used to evaluate the SLA RP process and to perform the product optimization. The optimal setups of SLA manufacturing parameters for both individual features and a general part with various features have been concluded from this study.

Research paper thumbnail of A cautionary case of casual causality

Journal of High Energy Physics, 2022

We distinguish between the notions of asymptotic causality and infrared causality for gravitation... more We distinguish between the notions of asymptotic causality and infrared causality for gravitational effective field theories, and show that the latter gives constraints consistent with gravitational positivity bounds. We re-explore the scattering of gravitational waves in a spherically symmetric background in the EFT of gravity in D ≥ 5, for which the leading-order correction to Einstein gravity is determined by the Gauss-Bonnet operator. We reproduce the known result that the truncated effective theory exhibits apparent time advances relative to the background geometry for specific polarisations, which naively signal a violation of causality. We show that by properly identifying the regime of validity of the effective theory, the apparent time advance can be shown to be unresolvable. To illustrate this, we identify specific higher-dimension operators in the EFT expansion which become large for potentially resolvable time advances, rendering the EFT expansion invalid. Our results de...

Research paper thumbnail of Drug design of cyclin-dependent kinase 2 inhibitor for melanoma from traditional Chinese medicine

BioMed research international, 2014

One has found an important cell cycle controller. This guard can decide the cell cycle toward pro... more One has found an important cell cycle controller. This guard can decide the cell cycle toward proliferation or quiescence. Cyclin-dependent kinase 2 (CDK2) is a unique target among the CDK family in melanoma therapy. We attempted to find out TCM compounds from TCM Database@Taiwan that have the ability to inhibit the activity of CDK2 by systems biology. We selected Tetrahydropalmatine, Reserpiline, and (+)-Corydaline as the candidates by docking and screening results for further survey. We utilized support vector machine (SVM), multiple linear regression (MLR) models and Bayesian network for validation of predicted activity. By overall analysis of docking results, predicted activity, and molecular dynamics (MD) simulation, we could conclude that Tetrahydropalmatine, Reserpiline, and (+)-Corydaline had better binding affinity than the control. All of them had the ability to inhibit the activity of CDK2 and might have the opportunity to be applied in melanoma therapy.

Research paper thumbnail of Quantifying Athermality and Quantum Induced Deviations from Classical Fluctuation Relations

Entropy

In recent years, a quantum information theoretic framework has emerged for incorporating non-clas... more In recent years, a quantum information theoretic framework has emerged for incorporating non-classical phenomena into fluctuation relations. Here, we elucidate this framework by exploring deviations from classical fluctuation relations resulting from the athermality of the initial thermal system and quantum coherence of the system’s energy supply. In particular, we develop Crooks-like equalities for an oscillator system which is prepared either in photon added or photon subtracted thermal states and derive a Jarzynski-like equality for average work extraction. We use these equalities to discuss the extent to which adding or subtracting a photon increases the informational content of a state, thereby amplifying the suppression of free energy increasing process. We go on to derive a Crooks-like equality for an energy supply that is prepared in a pure binomial state, leading to a non-trivial contribution from energy and coherence on the resultant irreversibility. We show how the binomi...

Research paper thumbnail of Coordinating product configuration in the order fulfilment processing: an approach based on the binary tree algorithm

International Journal of Computer Integrated Manufacturing, Feb 19, 2007

Research paper thumbnail of Magnolol Encapsulated by Liposome in Inhibiting Smooth Muscle Cell Proliferation

Journal of the Chinese Chemical Society, 2008

Research paper thumbnail of Insight into molecular dynamics simulation of BRAF(V600E) and potent novel inhibitors for malignant melanoma

International Journal of Nanomedicine, 2015

Research paper thumbnail of Abstract 101: Pilot study of oral microbiome and risk of pancreatic cancer

Research paper thumbnail of Screening from the World's Largest TCM Database Against H1N1 Virus

Journal of Biomolecular Structure and Dynamics, 2011

The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti... more The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.

Research paper thumbnail of How to design a drug for the disordered proteins?

Drug Discovery Today, 2013

Structural disorders of proteins make drug design a difficult task. The gel-like state of intrins... more Structural disorders of proteins make drug design a difficult task. The gel-like state of intrinsically disordered protein (IDP) or intrinsically disordered regions (IDRs) remains a big puzzle for drug designers. Here, we propose a novel concept for drug design by understanding protein disintegration and protein-protein interaction (PPI) using molecular dynamics (MD) simulation and propose a possible approach for overcoming current obstacles in IDP drug design.

Research paper thumbnail of Some fast parallel algorithms for parentheses matching

Lecture Notes in Computer Science, 1991

The parentheses matching problem is to determine the mate of each parenthesis in a balanced strin... more The parentheses matching problem is to determine the mate of each parenthesis in a balanced string of n parentheses. In this paper, we present three novel and elegant parallel algorithms for this problem on parallel random-access machine (PRAM) models. Each of ...

Research paper thumbnail of Efficient EREW PRAM algorithms for parentheses-matching

IEEE Transactions on Parallel and Distributed Systems, 1994

Abstract We present four polylog-time parallel algorithms for matching parentheses on an exclusiv... more Abstract We present four polylog-time parallel algorithms for matching parentheses on an exclusive-read and exclusive-write (EREW) parallel random-access machine (PRAM) model. These algorithms provide new insights into the parentheses-matching problem. ...

Research paper thumbnail of High-frequency Ds remobilization over multiple generations in barley facilitates gene tagging in large genome cereals

Plant Molecular Biology, 2006

Transposable elements have certain advantages over other approaches for identifying and determini... more Transposable elements have certain advantages over other approaches for identifying and determining gene function in large genome cereals. Different strategies have been used to exploit the maize Activator/dissociation (Ac/Ds) transposon system for functional genomics in heterologous species. Either large numbers of independent Ds insertion lines or transposants (TNPs) are generated and screened phenotypically, or smaller numbers of TNPs are produced, Ds locations mapped and remobilized for localized gene targeting. It is imperative to characterize key features of the system in order to utilize the latter strategy, which is more feasible in large genome cereals like barley and wheat. In barley, we generated greater than 100 single-copy Ds TNPs and determined remobilization frequencies of primary, secondary, and tertiary TNPs with intact terminal inverted repeats (TIRs); frequencies ranged from 11.8 to 17.1%. In 16% of TNPs that had damaged TIRs no transposition was detected among progeny of crosses using those TNPs as parental lines. In half of the greater than 100 TNP lines, the nature of flanking sequences and status of the 11 bp TIRs and 8-bp direct repeats were determined. BLAST searches using a gene prediction program revealed that 86% of TNP flanking sequences matched either known or putative genes, indicating preferential Ds insertion into genic regions, critical in large genome species. Observed remobilization frequencies of primary, secondary, tertiary, and quaternary TNPs, coupled with the tendency for localized Ds transposition, validates a saturation mutagenesis approach using Ds to tag and characterize genes linked to Ds in large genome cereals like barley and wheat.

Research paper thumbnail of Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family1(w

The wall-associated kinase (WAK) gene family, one of the receptor-like kinase (RLK) gene families... more The wall-associated kinase (WAK) gene family, one of the receptor-like kinase (RLK) gene families in plants, plays important roles in cell expansion, pathogen resistance, and heavy-metal stress tolerance in Arabidopsis (Arabidopsis thaliana). Through a reiterative database search and manual reannotation, we identified 125 OsWAK gene family members from rice (Oryza sativa) japonica cv Nipponbare; 37 (approximately 30%) OsWAKs were corrected/reannotated from earlier automated annotations. Of the 125 OsWAKs, 67 are receptor-like kinases, 28 receptor-like cytoplasmic kinases, 13 receptor-like proteins, 12 short genes, and five pseudogenes. The two-intron gene structure of the Arabidopsis WAK/WAK-Likes is generally conserved in OsWAKs; however, extra/missed introns were observed in some OsWAKs either in extracellular regions or in protein kinase domains. In addition to the 38 OsWAKs with full-length cDNA sequences and the 11 with rice expressed sequence tag sequences, gene expression analyses, using tiling-microarray analysis of the 20 OsWAKs on chromosome 10 and reverse transcription-PCR analysis for five OsWAKs, indicate that the majority of identified OsWAKs are likely expressed in rice. Phylogenetic analyses of OsWAKs, Arabidopsis WAK/WAK-Likes, and barley (Hordeum vulgare) HvWAKs show that the OsWAK gene family expanded in the rice genome due to lineage-specific expansion of the family in monocots. Localized gene duplications appear to be the primary genetic event in OsWAK gene family expansion and the 125 OsWAKs, present on all 12 chromosomes, are mostly clustered.

Research paper thumbnail of Efficient EREW PRAM Algorithms for Parentheses-Matching

IEEE Transactions on Parallel and Distributed Systems, 1994

We present four polylog-time parallel algorithms for matching parentheses on an exclusive-read an... more We present four polylog-time parallel algorithms for matching parentheses on an exclusive-read and exclusive-write (EREW) parallel random-access machine (PRAM) model. These algorithms provide new insights into the parentheses-matching problem. The first algorithm has a time complexity of O(log2 n ) employing O ( & ) processors for an input string containing n parentheses. Although this algorithm is not cost-optimal, it is extremely simple to implement. The remaining three algorithms, which are based on a different approach, achieve O( log n ) time complexity in each case, and represent successive improvements. The second algorithm requires O ( n ) processors and working space, and it is comparable to the first algorithm in its ease of

Research paper thumbnail of Pharmacoinformatics approach for mPGES-1 in anti-inflammation by 3D-QSAR pharmacophore mapping

Journal of The Taiwan Institute of Chemical Engineers, 2009

Microsomal prostablandin E synthase-1 (mPGES-1) has been recently investigated to be a novel, hot... more Microsomal prostablandin E synthase-1 (mPGES-1) has been recently investigated to be a novel, hot, and promising target for inflammation-related diseases. The quantitative structure–activity relationship (QSAR) study was used to explore the critical pharmacophore features of mPGES-1 by using a set of 35 azaphenanthrenone derivatives. Twenty-four selected pharmacophore models derived from 240 hypotheses were employed to identify the critical features. The best two pharmacophore hypotheses, generated by HypoGen Technique, exhibited the residuals of approximately 150 and the high correlation coefficient of 0.92. The selected four hypotheses all showed a confidence level of 95% in the Fischer's randomization test. The final four pharmacophore model showed that the four dominant features (hydrogen bond donor and three hydrophobic features, occasionally replaced by ring aromatic feature) had significant impact on activity of mPGES-1 inhibitors. The database virtual screening and drug design can be further implement to searching the novel mPGES-1 inhibitors.

Research paper thumbnail of Chemoinformatics and pharmacoinformatics approach for exploring the GABA-A agonist from Chinese herb suanzaoren

Journal of The Taiwan Institute of Chemical Engineers, 2009

Research paper thumbnail of PARAMETRIC PROCESS OPTIMIZATION TO IMPROVE THE ACCURACY OF RAPID PROTOTYPED STEREOLITHOGRAPHY PARTS

The functional requirements of a rapid prototyping system are speed and accuracy, and they both a... more The functional requirements of a rapid prototyping system are speed and accuracy, and they both are functions of vendor defaulted and user selected manufacturing parameters. Accuracy is evaluated by dimensional errors, form errors and surface roughness of manufactured parts. A special designed specimen with twenty dimensional, geometrical, and surface roughness features has been used in the inspection of RP manufacturing processes. In terms of Taguchi experimental design techniques, an orthogonal array of experiments has been developed which has the least number of experimental runs and desired process parameter settings. Using the 3-D coordinate measuring machine and surface profilometer, a series of measurements in evaluating the SLA parts quality has been conducted to find the functional relationships between the output part quality and input manufacturing process parameters. Two analysis tools, response surface methodology and Analysis of Variance (ANOVA) have been used to evaluate the SLA RP process and to perform the product optimization. The optimal setups of SLA manufacturing parameters for both individual features and a general part with various features have been concluded from this study.

Research paper thumbnail of Parametric process optimization to improve the accuracy of rapid prototyped stereolithography parts

International Journal of Machine Tools & Manufacture, 2000

The functional requirements of a rapid prototyping system are speed and accuracy, and they both a... more The functional requirements of a rapid prototyping system are speed and accuracy, and they both are functions of vendor defaulted and user selected manufacturing parameters. Accuracy is evaluated by dimensional errors, form errors and surface roughness of manufactured parts. A special designed specimen with twenty dimensional, geometrical, and surface roughness features has been used in the inspection of RP manufacturing processes. In terms of Taguchi experimental design techniques, an orthogonal array of experiments has been developed which has the least number of experimental runs and desired process parameter settings. Using the 3-D coordinate measuring machine and surface profilometer, a series of measurements in evaluating the SLA parts quality has been conducted to find the functional relationships between the output part quality and input manufacturing process parameters. Two analysis tools, response surface methodology and Analysis of Variance (ANOVA) have been used to evaluate the SLA RP process and to perform the product optimization. The optimal setups of SLA manufacturing parameters for both individual features and a general part with various features have been concluded from this study.