• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.828-832
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• 2012

We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (betahairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.347-358
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• 2014

본 논문에서는 양자 역학적 분자 동역학(Quantum Mechanical/Molecular Mechanical-Molecular Dynamics, QM/MM-MD)을 통해 수용액에 녹아 있는 Potassium Thiocyanate의 dynamics를 연구했다. Umbrella sampling technique을 활용하여 association/dissociation에 해당하는 Free energy surface를 구했다. 두 개의 Free energy minimum이 녹아 있는 두 이온의 center of mass 사이의 거리가 $4{\AA}$일 때와 $5{\sim}6{\AA}$ 부근일 때 나타났으며 $4{\AA}$일 때 더 안정 했다. 본 논문에서는 $4{\AA}$일 때를 Contact Ion Pair(CIP) $6{\AA}$일 때를 Dissociation Ion Pair(DlP)라고 칭했다. 이 minimum들이 무엇인 지를 밝혀 내기 위해 추가 연구를 수행하였다. Free energy 상에서 가장 안정 할 때(CIP) solute인 Potassium thiocyanate의 구조를 살펴 봤더니 Potassium ion은 Thiocyanate ion의 Sulfur보다 Nitrogen side를 선호하였다. 그 원인을 알아보기 위해 salvation shell의 구조를 Radial distribution function을 통해 살펴 봤더니 물 분자가 Nitrogen보다 Sulfur와 더 강한 상호작용을 하고 있었다. 그로 인해 Potassium ion이 Nitrogen을 선호한단 결과가 나온 것이다. 한편, 두 번째 minimum은 물 분자가 Potassium 이온과 Thiocyanate 이온 사이에 flexible하게 bridging을 하는 구조였다. 또한 단순 양자 계산을 통해서도 비슷한 구조를 얻을 수 있었다. 그러나 QM 계산은 0K에서 수행하는 것이기 때문에 엔트로피 효과가 없는 계산이지만 본 연구는 온도 300K로 실제 용매와 가깝게 수행함으로써 고정되어 있는 구조가 아니라 엔트로피와 엔탈피가 균형적으로 존재하는 실제 용액 속에서의 구조를 처음으로 보여주는 것이다.

• Korean Journal of Air-Conditioning and Refrigeration Engineering
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• v.19 no.12
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• pp.883-888
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• 2007

As a starting point of investigating what molecular dynamic simulations can reveal about the nature of atomic level of heating and cooling process, argon described by the LJ potential is considered. Stepwise heating and cooling of constant rates are simulated in the NPT (constant number, pressure and temperature) ensemble. Hysteresis is found due to the superheating and supercooling. Drastic change of volume and energy is involved with phase change, but the melting point can not be obtained by simply observing the changes of these quantities. Since liquid and solid phases can co-exist at the same temperature, Gibbs free energy should be calculated to find the temperature where the Gibbs free energy of liquid is equal to that of the solid since the equilibrium state is the state of minimum Gibbs free energy. The obtained melting temperature, $T^*=0.685$, is close to that of the experiment with only 2% error.

• Molecules and Cells
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• v.20 no.1
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• pp.35-42
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• 2005

A novel combined method for locating box H/ACA small nucleolar RNAs (snoRNAs) is described, together with a software tool. The method adopts both a probabilistic hidden Markov model (HMM) and a minimum free energy (MFE) rule, and filters possible candidate box H/ACA snoRNAs obtained from genomic DNA sequences. With our novel method 12 known box H/ACA snoRNAs, and one strong candidate were identified in 30 nucleolar protein genomic sequences.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.287-293
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• 2005

Predicting RNA secondary structure as accurately as possible is very important in functional analysis of RNA molecules. However, different prediction methods and related parameters including terminal GU pair of helices, minimum length of helices, and free energy systems often give different prediction results for the same RNA sequence. Then, which structure is more important than the others? i.e. which combinations of the methods and related parameters are the optimal? In order to investigate above problems, first, three prediction methods, namely, random stacking of helical regions (RS), helical regions distribution (HD), and Zuker's minimum free energy algorithm (ZMFE) were compared by taking 1139 tRNA sequences from Rfam database as the samples with different combinations of parameters. The optimal parameters are derived. Second, Zuker's dynamic programming method for prediction of RNA secondary structure was revised using the above optimal parameters and related software BJRNAFold was developed. Third, the effects of short-range interaction were studied. The results indicated that the prediction accuracy would be improved much if proper short-range factor were introduced. But the optimal short-range factor was difficult to determine. A user-adjustable parameter for short-range factor was introduced in BJRNAFold software.

• Genomics & Informatics
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• v.9 no.1
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• pp.39-43
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• 2011

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

• The Bulletin of The Korean Astronomical Society
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• v.44 no.2
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• pp.71.3-71.3
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• 2019

Previously we developed a method of coronal force-free field construction using vector potentials. In this method, the boundary normal component of the vector potential should be adjusted at every iteration step to implement the boundary normal current density, which is provided by observations. The method was a variational method in the sense that the excessive kinetic energy is removed from the system at every iteration step. The boundary condition imposing the normal current density, however, is not compatible with the variational procedure seeking for the minimum energy state, which is employed by most force-free field solvers currently being used. To resolve this problem, we have developed a totally new method of force-free field construction. Our new method uses a unique magnetic field description using two scalar functions. Our procedure is non-variational and can impose the boundary normal current density exactly. We have tested the new force-free solver for standard Low & Lou fields and Titov-Demoulin flux ropes. Our code excels others in both examples, especially in Titov-Demoulin flux ropes, for which most codes available now yield poor results. Application to a real active region will also be presented.

• Proceedings of the Korea Information Processing Society Conference
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• 2022.05a
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• pp.94-97
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• 2022

The emerging energy harvesting technology, which has been successfully integrated into Wireless Sensor Networks, enables sensor batteries to be charged using renewable energy sources. In the meantime, the problem of Minimum Latency Aggregation Scheduling (MLAS) in battery-powered WSNs has been well studied. However, because sensors have limited energy harvesting capabilities, captured energy is limited and varies greatly between nodes. As a result, all previous MLAS algorithms are incompatible with Battery-Free Wireless Sensor Networks (BF-WSNs). We investigate the MLAS problem in BF-WSNs in this paper. To make the best use of the harvested energy, we build an aggregation tree that leverages the energy harvesting rates of the sensor nodes with an intuitive explanation. The aggregation tree, which determines sender-receiver pairs for data transmission, is one of the two important phases to obtain a low data aggregation latency in the BF-WSNs.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.848-854
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• 2012

We have studied the oligomerization of a fibril-forming segment of ${\alpha}$-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of ${\alpha}$-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel ${\beta}$-sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.

• Transactions of the Korean hydrogen and new energy society
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• v.27 no.1
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• pp.114-120
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• 2016

This paper describes generating efficiency characteristics of the double acting Stirling engine/generator for domestic small-scale CHP (Combined Heat and Power) system. In small distributed generation applications, Stirling engine has competition from fuel cell, microturbine and etc. In order to be economical in the applications, a long life with minimum maintenance is generally required. Free piston Stirling engine (FPSE) has no crank and rotating parts to generate lateral forces and require lubrication. Double acting Stirling engine/generator has one displacer and two power piston which are supported by flexure springs. Two power pistons oscillate with symmetric displacement and are connected with moving magnet type linear generators for power generation from PV work. In experiments, 1 kW class double acting free piston Stirling engine/generator is fabricated and tested. Heat is supplied to hot end of engine by the combustion of natural gas and converted to electric power by linear generators which are assembled with power pistons. The electric parameters such as voltage, current and phase are measured with for variable flow rate of fuel gas. Especially, generating efficiency of FPSE is measured with three different measurement methods. Generating efficiency of the double acting Stirling engine/alternator is about 24%.