Simon Lin - Academia.edu (original) (raw)

Papers by Simon Lin

The discovery of potent therapeutic compounds against dengue virus is urgently needed. The NS2B-N... more The discovery of potent therapeutic compounds against dengue virus is urgently needed. The NS2B-NS3 protease (NS2B-NS3 pro) of dengue fever virus carries out all enzymatic activities needed for polyprotein processing and is considered to be amenable to antiviral inhibition by analogy. Virtual screening of 300,000 compounds using Autodock 3 on the GVSS platform was conducted to identify novel inhibitors against the NS2B-NS3 pro. Thirty-six compounds were selected for in vitro assay against NS2B-NS3 pro expressed in Pichia pastoris. Seven novel compounds were identified as inhibitors with IC 50 values of 3.9 ± 0.6-86.7 ± 3.6 μM. Three strong NS2B-NS3 pro inhibitors were further confirmed as competitive inhibitors with K i values of 4.0 ± 0.4, 4.9 ± 0.3, and 3.4 ± 0.1 μM, respectively. Hydrophobic and hydrogen bond interactions between amino acid residues in the NS3 pro active site with inhibition compounds were also identified.

Proceedings of The International Symposium on Grids and Clouds (ISGC) 2012 — PoS(ISGC 2012), 2012

Water, 2020

This study explores the discrepancies of storm surge predictions driven by the parametric wind mo... more This study explores the discrepancies of storm surge predictions driven by the parametric wind model and the numerical weather prediction model. Serving as a leading-order storm wind predictive tool, the parametric Holland wind model provides the frictional-free, steady-state, and geostrophic-balancing solutions. On the other hand, WRF-ARW (Weather Research and Forecasting-Advanced Research WRF) provides the results solving the 3D time-integrated, compressible, and non-hydrostatic Euler equations, but time-consuming. To shed light on their discrepancies for storm surge predictions, the storm surges of 2013 Typhoon Haiyan in the Leyte Gulf and the San Pedro Bay are selected. The Holland wind model predicts strong southeastern winds in the San Pedro Bay after Haiyan makes landfall at the Leyte Island than WRF-ARW 3 km and WRF-ARW 1 km. The storm surge simulation driven by the Holland wind model finds that the water piles up in the San Pedro Bay and its maximum computed storm surges ar...

Percolation models with multiple percolating clusters have attracted much attention in recent yea... more Percolation models with multiple percolating clusters have attracted much attention in recent years. Here we use Monte Carlo simulations to study bond percolation on L_1× L_2 planar random lattices, duals of random lattices, and square lattices with free and periodic boundary conditions, in vertical and horizontal directions, respectively, and with various aspect ratio L_1/L_2. We calculate the probability for the appearance of n percolating clusters, W_n, the percolating probabilities, P, the average fraction of lattice bonds (sites) in the percolating clusters, <c^b>_n (<c^s>_n), and the probability distribution function for the fraction c of lattice bonds (sites), in percolating clusters of subgraphs with n percolating clusters, f_n(c^b) (f_n(c^s)). Using a small number of nonuniversal metric factors, we find that W_n, P, <c^b>_n (<c^s>_n), and f_n(c^b) (f_n(c^s)) for random lattices, duals of random lattices, and square lattices have the same universal fi...

Water

This study presents a numerical tool for calculating storm surges from offshore, nearshore, and c... more This study presents a numerical tool for calculating storm surges from offshore, nearshore, and coastal regions using the finite-difference method, two-way grid-nesting function in time and space, and a moving boundary scheme without any numerical filter adopted. The validation of the solitary wave runup on a circular island showed the perfect matches between the model results and measurements for the free surface elevations and runup heights. After the benchmark problem validation, the 2013 Super Typhoon Haiyan event was selected to showcase the storm surge calculations with coastal inundation and flood depths in Tacloban. The catastrophic storm surges of about 8 m and wider, storm-induced inundation due to the Super Typhoon Haiyan were found in the Tacloban Airport, corresponding to the findings from the field survey. In addition, the anti-clockwise, storm-induced currents were explored inside of Cancabato Bay. Moreover, the effect of the nonlinear advection terms with the fixed a...

In 1998, the Functional Requirements for Bibliographic Records (FRBR) model which is composed by ... more In 1998, the Functional Requirements for Bibliographic Records (FRBR) model which is composed by four entities (work, expression, manifestation and item) and their associative relationships ( primary, responsibility and subject) , was proposed by the International Federation of Library Associations and Institutions (IFLA). The FRBR model can be deployed as a logical framework for proceeding metadata analysis and developing metadata format. This paper presents a case study of the National Palace Museum (NPM) in Taipei to examine the feasibility of the FRBR model. With the diversified needs from various content communities, an analysis model is introduced at Academia Sinica to refine and enhance the FRBR model, in order to meet metadata requirements across diverse knowledge domains, which is composed of three facets ( function, subject domain, data type and style)and one supportive community layer.

scaling functions for bond percolation on

2018 5th International Conference on Information and Communication Technologies for Disaster Management (ICT-DM)

Hazard risk assessment is essential to coexist with the natural disasters. An open application fr... more Hazard risk assessment is essential to coexist with the natural disasters. An open application framework for knowledge-oriented hazard risk assessment based on deeper understanding of the root cause and drivers of a disaster is developed and verified in this study. Hazard risks estimation by numerical simulation could be effective and reliable only if we have enough knowledge and observation data to the hazards. Insufficient knowledge to the natural hazards is the most critical barrier for efficient disaster risk assessment. To transform the knowledge into valuable simulations on hazard risks is still a challenge. To overcome the challenges, we proposed and implemented the application framework for hazard risk evaluation based on deeper understanding approach. For each case study, scientists achieved the accurate simulation processes with best knowledge to the root cause and physical mechanism of the target hazard. Simulation portal was then developed for easier access to the most updated analysis facility. All the data, services, methods and knowledge were compiled into a knowledge base. Those shared data, analysis and simulation facility, knowledge base and value-added services, and the distributed could infrastructure constitute the open application framework. This is a practical framework verified by case studies and will be evolved progressively with more cases of various types of disasters in different places. In this paper, design details of the application framework based on deeper understanding approach and the verification by a case study are explained. The application framework would be a facilitator for capacity building on hazard risk assessment and will be a solid ground for open science development of this domain in the future.

As the first part of the treatise on A General Theory of Concept Lattice (I-V), this work develop... more As the first part of the treatise on A General Theory of Concept Lattice (I-V), this work develops the general concept lattice for the problem concerning categorization of objects according to their properties. Unlike the conventional approaches, such as the formal concept lattice and the rough set lattice, the general concept lattice is designed to adhere to the general principle that the information content should be invariant regardless how the variables/parameters are presented. Here, one will explicitly demonstrate the existence of such a construction by a sequence of fulfillment compatible with the conventional lattice structure. The general concept lattice promises to be a comprehensive categorization for all the distinctive object classes according to whatever properties they are equipped with. It will be shown that one can always regain the formal concept lattice and rough set lattice from the general concept lattice.

As the second part of the treatise 'A General Theory of Concept Lattice', this paper spea... more As the second part of the treatise 'A General Theory of Concept Lattice', this paper speaks of the tractability of the general concept lattice for both its lattice structure and logic content. The general concept lattice permits a feasible construction that can be completed in a single scan of the formal context, though the conventional formal-concept lattice and rough-set lattice can be regained from the general concept lattice. The logic implication deducible from the general concept lattice takes the form of {\mu}_1 {\rightarrow} {\mu}_2 where {\mu}_1,{\mu}_2 {\in} M^{\ast} are composite attributes out of the concerned formal attributes M. Remarkable is that with a single formula based on the contextual truth 1_{\eta} one can deduce all the implication relations extractable from the formal context. For concreteness, it can be shown that any implication A {\rightarrow} B (A, B being subsets of the formal attributes M) discussed in the formal-concept lattice corresponds to ...

Frontiers in Earth Science

Proceedings of The International Symposium on Grids and Clouds (ISGC) 2012 — PoS(ISGC 2012)

Eprint Arxiv Cond Mat 0408393, Aug 18, 2004

Physical Review E, 2008

The conventional periodic boundary conditions in two dimensions are extended to general boundary ... more The conventional periodic boundary conditions in two dimensions are extended to general boundary conditions, prescribed by primitive vector pairs that may not coincide with the coordinate axes. This extension is shown to be unambiguously specified by the twisting scheme. Equivalent relations between different twist settings are constructed explicitly. The classification of finite-size scaling functions is discussed based on the equivalent relations. A self-similar pattern for distinct classes of finite-size scaling functions is shown to appear on the plane that parametrizes the toroidal geometry.

International Journal of Humanities and Arts Computing, 2013

Theoretical Computer Science

Proceedings of The International Symposium on Grids and Clouds and the Open Grid Forum — PoS(ISGC 2011 & OGF 31)

The discovery of potent therapeutic compounds against dengue virus is urgently needed. The NS2B-N... more The discovery of potent therapeutic compounds against dengue virus is urgently needed. The NS2B-NS3 protease (NS2B-NS3 pro) of dengue fever virus carries out all enzymatic activities needed for polyprotein processing and is considered to be amenable to antiviral inhibition by analogy. Virtual screening of 300,000 compounds using Autodock 3 on the GVSS platform was conducted to identify novel inhibitors against the NS2B-NS3 pro. Thirty-six compounds were selected for in vitro assay against NS2B-NS3 pro expressed in Pichia pastoris. Seven novel compounds were identified as inhibitors with IC 50 values of 3.9 ± 0.6-86.7 ± 3.6 μM. Three strong NS2B-NS3 pro inhibitors were further confirmed as competitive inhibitors with K i values of 4.0 ± 0.4, 4.9 ± 0.3, and 3.4 ± 0.1 μM, respectively. Hydrophobic and hydrogen bond interactions between amino acid residues in the NS3 pro active site with inhibition compounds were also identified.

Proceedings of The International Symposium on Grids and Clouds (ISGC) 2012 — PoS(ISGC 2012), 2012

Water, 2020

This study explores the discrepancies of storm surge predictions driven by the parametric wind mo... more This study explores the discrepancies of storm surge predictions driven by the parametric wind model and the numerical weather prediction model. Serving as a leading-order storm wind predictive tool, the parametric Holland wind model provides the frictional-free, steady-state, and geostrophic-balancing solutions. On the other hand, WRF-ARW (Weather Research and Forecasting-Advanced Research WRF) provides the results solving the 3D time-integrated, compressible, and non-hydrostatic Euler equations, but time-consuming. To shed light on their discrepancies for storm surge predictions, the storm surges of 2013 Typhoon Haiyan in the Leyte Gulf and the San Pedro Bay are selected. The Holland wind model predicts strong southeastern winds in the San Pedro Bay after Haiyan makes landfall at the Leyte Island than WRF-ARW 3 km and WRF-ARW 1 km. The storm surge simulation driven by the Holland wind model finds that the water piles up in the San Pedro Bay and its maximum computed storm surges ar...

Percolation models with multiple percolating clusters have attracted much attention in recent yea... more Percolation models with multiple percolating clusters have attracted much attention in recent years. Here we use Monte Carlo simulations to study bond percolation on L_1× L_2 planar random lattices, duals of random lattices, and square lattices with free and periodic boundary conditions, in vertical and horizontal directions, respectively, and with various aspect ratio L_1/L_2. We calculate the probability for the appearance of n percolating clusters, W_n, the percolating probabilities, P, the average fraction of lattice bonds (sites) in the percolating clusters, <c^b>_n (<c^s>_n), and the probability distribution function for the fraction c of lattice bonds (sites), in percolating clusters of subgraphs with n percolating clusters, f_n(c^b) (f_n(c^s)). Using a small number of nonuniversal metric factors, we find that W_n, P, <c^b>_n (<c^s>_n), and f_n(c^b) (f_n(c^s)) for random lattices, duals of random lattices, and square lattices have the same universal fi...

Water

This study presents a numerical tool for calculating storm surges from offshore, nearshore, and c... more This study presents a numerical tool for calculating storm surges from offshore, nearshore, and coastal regions using the finite-difference method, two-way grid-nesting function in time and space, and a moving boundary scheme without any numerical filter adopted. The validation of the solitary wave runup on a circular island showed the perfect matches between the model results and measurements for the free surface elevations and runup heights. After the benchmark problem validation, the 2013 Super Typhoon Haiyan event was selected to showcase the storm surge calculations with coastal inundation and flood depths in Tacloban. The catastrophic storm surges of about 8 m and wider, storm-induced inundation due to the Super Typhoon Haiyan were found in the Tacloban Airport, corresponding to the findings from the field survey. In addition, the anti-clockwise, storm-induced currents were explored inside of Cancabato Bay. Moreover, the effect of the nonlinear advection terms with the fixed a...

In 1998, the Functional Requirements for Bibliographic Records (FRBR) model which is composed by ... more In 1998, the Functional Requirements for Bibliographic Records (FRBR) model which is composed by four entities (work, expression, manifestation and item) and their associative relationships ( primary, responsibility and subject) , was proposed by the International Federation of Library Associations and Institutions (IFLA). The FRBR model can be deployed as a logical framework for proceeding metadata analysis and developing metadata format. This paper presents a case study of the National Palace Museum (NPM) in Taipei to examine the feasibility of the FRBR model. With the diversified needs from various content communities, an analysis model is introduced at Academia Sinica to refine and enhance the FRBR model, in order to meet metadata requirements across diverse knowledge domains, which is composed of three facets ( function, subject domain, data type and style)and one supportive community layer.

scaling functions for bond percolation on

2018 5th International Conference on Information and Communication Technologies for Disaster Management (ICT-DM)

Hazard risk assessment is essential to coexist with the natural disasters. An open application fr... more Hazard risk assessment is essential to coexist with the natural disasters. An open application framework for knowledge-oriented hazard risk assessment based on deeper understanding of the root cause and drivers of a disaster is developed and verified in this study. Hazard risks estimation by numerical simulation could be effective and reliable only if we have enough knowledge and observation data to the hazards. Insufficient knowledge to the natural hazards is the most critical barrier for efficient disaster risk assessment. To transform the knowledge into valuable simulations on hazard risks is still a challenge. To overcome the challenges, we proposed and implemented the application framework for hazard risk evaluation based on deeper understanding approach. For each case study, scientists achieved the accurate simulation processes with best knowledge to the root cause and physical mechanism of the target hazard. Simulation portal was then developed for easier access to the most updated analysis facility. All the data, services, methods and knowledge were compiled into a knowledge base. Those shared data, analysis and simulation facility, knowledge base and value-added services, and the distributed could infrastructure constitute the open application framework. This is a practical framework verified by case studies and will be evolved progressively with more cases of various types of disasters in different places. In this paper, design details of the application framework based on deeper understanding approach and the verification by a case study are explained. The application framework would be a facilitator for capacity building on hazard risk assessment and will be a solid ground for open science development of this domain in the future.

As the first part of the treatise on A General Theory of Concept Lattice (I-V), this work develop... more As the first part of the treatise on A General Theory of Concept Lattice (I-V), this work develops the general concept lattice for the problem concerning categorization of objects according to their properties. Unlike the conventional approaches, such as the formal concept lattice and the rough set lattice, the general concept lattice is designed to adhere to the general principle that the information content should be invariant regardless how the variables/parameters are presented. Here, one will explicitly demonstrate the existence of such a construction by a sequence of fulfillment compatible with the conventional lattice structure. The general concept lattice promises to be a comprehensive categorization for all the distinctive object classes according to whatever properties they are equipped with. It will be shown that one can always regain the formal concept lattice and rough set lattice from the general concept lattice.

As the second part of the treatise 'A General Theory of Concept Lattice', this paper spea... more As the second part of the treatise 'A General Theory of Concept Lattice', this paper speaks of the tractability of the general concept lattice for both its lattice structure and logic content. The general concept lattice permits a feasible construction that can be completed in a single scan of the formal context, though the conventional formal-concept lattice and rough-set lattice can be regained from the general concept lattice. The logic implication deducible from the general concept lattice takes the form of {\mu}_1 {\rightarrow} {\mu}_2 where {\mu}_1,{\mu}_2 {\in} M^{\ast} are composite attributes out of the concerned formal attributes M. Remarkable is that with a single formula based on the contextual truth 1_{\eta} one can deduce all the implication relations extractable from the formal context. For concreteness, it can be shown that any implication A {\rightarrow} B (A, B being subsets of the formal attributes M) discussed in the formal-concept lattice corresponds to ...

Frontiers in Earth Science

Proceedings of The International Symposium on Grids and Clouds (ISGC) 2012 — PoS(ISGC 2012)

Eprint Arxiv Cond Mat 0408393, Aug 18, 2004

Physical Review E, 2008

The conventional periodic boundary conditions in two dimensions are extended to general boundary ... more The conventional periodic boundary conditions in two dimensions are extended to general boundary conditions, prescribed by primitive vector pairs that may not coincide with the coordinate axes. This extension is shown to be unambiguously specified by the twisting scheme. Equivalent relations between different twist settings are constructed explicitly. The classification of finite-size scaling functions is discussed based on the equivalent relations. A self-similar pattern for distinct classes of finite-size scaling functions is shown to appear on the plane that parametrizes the toroidal geometry.

International Journal of Humanities and Arts Computing, 2013

Theoretical Computer Science

Proceedings of The International Symposium on Grids and Clouds and the Open Grid Forum — PoS(ISGC 2011 & OGF 31)