Sangil Han

High-throughput screening of metal-organic frameworks for CO2 separation.

A parallel high-throughput sorption methodology is described for screening CO(2) and N(2) adsorption and diffusion selectivity in metal organic frameworks, before and after exposure to water vapor and acid gases. We illustrate this approach by simultaneously investigating 8 candidate Metal-Organic Framework (MOF) materials, of which the best material was found to have a CO(2)/N(2) membrane selectivity of 152 and a CO(2) permeability of 60 barrer for Co-NIC. This approach provides a significant increase in efficiency of obtaining the separation properties of MOFs. While we describe here the identification of novel materials for CO(2) capture, the methodology enables exploration of the performance and stability of novel porous materials for a wide range of applications.

A gene clustering method with masking cross-matching fragments using modified suffix tree clustering method

Multiple sequence alignment is a method for comparing two or more DNA or protein sequences. Most multiple sequence alignment methods rely on pairwise alignment and Smith-Waterman algorithm [Needleman and Wunsch, 1970; Smith and Waterman, 1981] to generate an alignment hierarchy. Therefore, as the number of sequences increases, the runtime increases exponentially. To resolve this problem, this paper presents a multiple sequence alignment method using a parallel processing suffix tree algorithm to search for common subsequences at one time without pairwise alignment. The cross-matched subsequences among the searched common subsequences may be generated and those cause inexact-matching. So the procedure of masking cross-matching pairs was suggested in this study. The proposed method, improved STC (Suffix Tree Clustering), is summarized as follows: (1) construction of suffix tree; (2) search and overlap of common subsequences; (3) grouping of subsequence pairs; (4) masking of cross-matching airs; and (5) clustering of gene sequences. The new method was successfully evaluated with 23 genes inMus musculus and 22 genes in three species, clustering nine and eight clusters, respectively.

Effect of molecular packing density and intermolecular interactions on solute transport in supported liquid crystalline membranes

The transport of organic solutes in 4-(trans-4′-4′-n-pentylcyclohexy)-benzonitrile (PCH5) and 4-cyano-4′-octylbiphenyl (8CB) supported liquid crystal (LC) membranes was reported in order to broaden the understanding of mechanisms for solute transport in ordered mesophases. PCH5 was chosen as it exhibits a lower packing density than 8CB but retains a similar molecular structure. Higher sorption and diffusion coefficients were measured in PCH5 compared to 8CB, due primarily to the lower packing density in the PCH5 nematic phase. Solutes capable of forming a single hydrogen bonding with LC molecules exhibited faster diffusion than those with no hydrogen-bonding ability or those capable of multiple hydrogen-bonding interactions. Measurements of relative solubility of pyridine and salicylic acid in 8CB, PCH5 and kerosene confirmed that intermolecular hydrogen bonding plays a stronger role than π−π interactions in solute absorption. Finally, in the absence of differences in hydrogen bonding, higher dipole–dipole interactions resulted in lower diffusivities in LCs.

Gene Sequences Clustering and Identifying Functional Domain Using a Suffix Tree Algorithm

Most multiple gene sequence alignment methods rely on conventions regarding the score of a multiple alignment by pairwise alignment. Therefore, as the number of sequences increases, the runtime of sequencing expands exponentially In order to solve the problem, this paper presents a multiple sequence alignment method using a linear-time suffix tree algorithm to cluster similar sequences at one time without pairwise alignment. After searching for common subsequences, cross-matching common subsequences were generated, and sometimes inexact matching was found. So, a procedure aimed at masking the inexact cross-matching pairs was suggested here. In addition, BLAST was combined with a clustering tool in order to annotate the clusters generated by suffix tree clustering. The performance of the proposed system, CLAGen, was successfully evaluated with 42 gene sequences in a TCA cycle (a citrate cycle) of bacteria, identifying 11 clusters

An automatic synthesis system for start-up operating procedures of boiler plants

As boiler plants which supply steam and heat into chemical plants become larger in scale and more complicated, accidents caused by the wrong understanding and erroneous operations are increasing. In this paper, we present a computer-aided system that should prevent such mistakes and synthesize operating procedures for start-up of steam boiler plants: 1) This system generates a goal tree by generalizing and classifying the operational situations hierarchically, and uses the relationship between an operation and a function to search for primitive operations in the lowest level of the goal tree. 2) It simulates changes in operational situations caused by the action of primitive operations with heuristic knowledge of transition relationships between operational situations. 3) It determines the priority of low-level operational situations and primitive operations by referring to the database on hazardous situations and properties. We have applied the developed system to a large-scale boiler plant to demonstrate its effectiveness.

Effect of Alloying, Heat Treatment and Carbon Content on White Layer Formation in Machining of Steels

This paper describes an experimental investigation of the role of alloying, carbon content, and heat treatment on white layer formation in machining of steels. This is carried out by machining steels that differ in alloying, heat treatment and carbon content, via orthogonal cutting tests performed with low CBN content tools. The thickness of white layer produced in AISI 1045 and AISI 4340 annealed steels are compared to determine the effect of alloying on white layer formation. The effect of heat treatment on white layer formation is investigated by machining annealed and hardened AISI 4340 steels. The effect of carbon content on white layer formation is investigated by cutting AISI 52100 and AISI 4340 steels of the same hardness (53 HRC). Since 52100 steel has almost twice the amount of carbon and less number of alloying elements than AISI 4340 steel, an approximate understanding of the effect of carbon content on white layer formation can be inferred. The results of the study show that alloying, heat treatment, and carbon content influence white layer formation. The possible roles of the maximum workpiece surface temperature, effective plastic strain and stress on white layer formation in the different steels are also analyzed via finite element simulations performed in a commercially available code.Copyright

A Study on Clustering and Identifying Gene Sequences using Suffix Tree Clustering Method and BLAST

The DNA and protein data of diverse species have been daily discovered and deposited in the public archives according to each established format. Database systems in the public archives provide not only an easy-to-use, flexible interface to the public, but also in silico analysis tools of unidentified sequence data. Of such in silico analysis tools, multiple sequence alignment [1] methods relying on pairwise alignment and Smith-Waterman algorithm [2] enable us to identify unknown DNA, protein sequences or phylogenetic relation among several species. However, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST was combined with a clustering tool. Our clustering and annotating tool is summarized as the following steps: (1) construction of suffix tree; (2) masking of cross-matching pairs; (3) clustering of gene sequences and (4) annotating gene clusters by BLAST search. The system was successfully evaluated with 22 gene sequences in the pyrubate pathway of bacteria, clustering 7 clusters and finding out representative common subsequences of each cluster

Modeling of in Silico Microbe System based on the Combination of a Hierarchical Regulatory Network with Metabolic Network

FBA(flux balance analysis) with Boolean rules for representing regulatory events has correctly predicted cellular behaviors, such as optimal flux distribution, maximal growth rate, metabolic by-product, and substrate concentration changes, with various environmental conditions. However, until now, since FBA has not taken into account a hierarchical regulatory network, it has limited the representation of the whole transcriptional regulation mechanism and interactions between specific regulatory proteins and genes. In this paper, in order to solve these problems, we describe the construction of hierarchical regulatory network with defined symbols and the introduction of a weight for representing interactions between symbols. Finally, the whole cellular behaviors with time were simulated through the linkage of a hierarchical regulatory network module and dynamic simulation module including FBA. The central metabolic network of E. coli was chosen as the basic model to identify our suggested modeling method.