• Fibers and Polymers
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• v.7 no.4
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• pp.333-338
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• 2006

Silk fibroin (SF) fiber from the Antheraea pernyi silkworm was treated with a 1.23 N iodine-potassium iodide ($I_2-KI$) aqueous solution, and the structure and physical properties were investigated to clarify the effects of the iodine treatment. The noticeably high weight gain value of SF fiber, about 25 wt% was attributed to the absorption of polyiodide ions in the form of $I_3{^-}\;and\;I_5{^-}$. Fourier transform infrared spectroscopy and X-ray diffraction measurements suggested that polyiodide ions mainly entered the amorphous region. In addition, a new sharp reflection on the meridional direction, corresponding to a period of $7.0{\AA}$, was observed and indicated the possibility of the formation of mesophase structure of ${\beta}$-conformation chains. Dynamic viscoelastic measurements showed that the damping tan ${\delta}$ peak at $270^{\circ}C$ gradually shifted to lower temperature in the iodinated SF fibers, suggesting an enhancement of the molecular motion of the fibroin chains induced by the presence of polyiodide ions. With heating above $254^{\circ}C$, the iodine component introduced intermolecular cross-linking of SF, and the melt flow of the sample was inhibited. The thermal decomposition stability of fibroin molecules was greatly enhanced by iodine treatment.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.453-456
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• 2010

The structural and energetic preferences of thiacalix[4]biscrown-5 with and without alkali metal ions ($Na^+$, $K^+$, $Rb^+$, and $Cs^+$) have been theoretically investigated for the first time using molecular dynamic (MD) simulations and density functional theory (MPWB1K/6-31G(d)//B3LYP/6-31G(d)) methods. The formation of the metal ion complex by the host is mainly driven by the electrostatic attraction between crown-5 oxygens and a cation together with the minor contribution of the cation-$\pi$ interaction between two facing phenyl rings around the cation. The computed binding energies and the atomic charge distribution analysis for the metal binding complexes indicate the selectivity toward a potassium ion. The theoretical results herein explain the experimentally observed extractability order by this host towards various alkali metal ions. The physical nature and the driving forces for cation recognition by this host are discussed in detail.

• Membrane and Water Treatment
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• v.10 no.3
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• pp.207-212
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• 2019

Non-aqueous solvents (NASs) are generally known to be barely miscible, and reactive with polar compounds, such as water. However, water can interact with some NASs, which can be used as a new means for water recovery from saline water. This study explored the fate of water and salt in NAS, when saline water is mixed with NAS. Three amine solvents were selected as NAS. They had the same molecular formula, but were differentiated by their molecular structures, as follows: 1) NAS 'A' having the hydrophilic group ($NH_2$) at the end of the straight carbon chain, 2) NAS 'B' with symmetrical structure and having the hydrophilic group (NH) at the middle of the straight carbon chain, 3) NAS 'C' having the hydrophilic group ($NH_2$) at the end of the straight carbon chain but possessing a hydrophobic ethyl branch in the middle of the structure. In batch experiments, 0.5 M NaCl water was blended with NASs, and then water and salt content in the NAS were individually measured. Water absorption efficiencies by NAS 'B' and 'C' were 3.8 and 10.7%, respectively. However, salt rejection efficiency was 98.9% and 58.2%, respectively. NAS 'A' exhibited a higher water absorption efficiency of 35.6%, despite a worse salt rejection efficiency of 24.7%. Molecular dynamic (MD) simulation showed the different interactions of water and salts with each NAS. NAS 'A' formed lattice structured clusters, with the hydrophilic group located outside, and captured a large numbers of water molecules, together with salt ions, inside the cluster pockets. NAS 'B' formed a planar-shaped cluster, where only some water molecules, but no salt ions, migrated to the NAS cluster. NAS 'C', with an ethyl group branch, formed a cluster shaped similarly to that of 'B'; however, the boundary surface of the cluster looked higher than that of 'C', due to the branch structure in solvent. The MD simulation was helpful for understanding the experimental results for water absorption and salt rejection, by demonstrating the various interactions between water molecules and the salts, with the different NAS types.

• Applied Chemistry for Engineering
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• v.34 no.3
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• pp.285-290
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• 2023

Poly-lactic acid (PLA) is the most promising polymer in additive manufacturing as an alternative to acrylonitrile butadiene styrene (ABS). Since it is produced from renewable resources such as corn starch and sugar beets, it is also biocompatible and biodegradable. However, PLA has a couple of issues that limit its use. First, it has a comparatively low glass transition temperature of around 60 ℃, such that it exhibits low thermal resistance. Second, PLA has low impact strength because it is brittle. Due to these problems, scientists have found methods to improve the crystallinity and ductility of PLA. Polyethylene glycol (PEG) is one of the most studied plasticizers for PLA to give it chain mobility. However, the blend of PLA and PEG becomes unstable, and phase separation occurs even at room temperature as PEG is self-crystallized. Thus, it is necessary to investigate the optimal mixing ratio of PLA-PEG at the molecular scale. In this study, molecular dynamics will be conducted with various ratios of L-type PLA (PLLA) or DL-type PLA-PEG (PDLA-PEG) systems by using BIOVIA Materials Studio.

• Journal of the Mineralogical Society of Korea
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• v.31 no.1
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• pp.13-22
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• 2018

Aluminum silicates ($Al_2SiO_5$) undergo phase transitions among kyanite, andalusite, and sillimanite depending on temperature and pressure conditions. The minerals are often used as an important indicator of the degree of metamorphism for certain metamorphic rocks. In this study, we have applied classical molecular dynamics (MD) simulations and density functional theory (DFT) to the aluminum silicates. We examined the crystal structures as a function of applied pressure and the corresponding stabilities based on calculated enthalpies at each pressure. In terms of the lattice parameters, both methods showed that the volume decreases as the pressure increases as observed in the experiment. In particular, DFT results differed from experimental results by much less than 1%. As to the relative stability, however, both methods showed different levels of accuracy. In the MD simulations, a transition pressure at which the relative stability between two minerals reverse could not be determined because the enthalpies were insensitive to the applied pressure. On the other hand, in DFT calculations, the relative stability relation among the three minerals was consistent with experiment, although the transition pressure was strongly dependent on the choice of the electronic exchange-correlation functional.

• Journal of Integrative Natural Science
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• v.16 no.3
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• pp.81-95
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• 2023

Colorectal cancer is one of the most common types of cancer worldwide, ranking third after lung and breast cancer in terms of global prevalence. With an expected 1.93 million new cases and 935,000 deaths in 2020, it is more prevalent in males than in women. Evidence has shown that during the later stages of colon cancer, STAT1 promotes tumor progression by promoting cell survival and resistance to chemotherapy. Recent studies have shown that inhibiting STAT1 pathway leads to a reduction in tumor cell proliferation and growth, and can also promote apoptosis in colon cancer cells. One of the recent approaches in the field of drug discovery is drug repurposing. In drug repurposing approach we have virtually screened FDA database against STAT1 protein and their interactions have been studied through Molecular docking. Cross docking was performed with the top 10 compounds to be more specific with STAT1 comparing the affinity with STAT2, STAT3, STAT4, STAT5a, STAT5b and STAT6. The drugs that showed higher affinity were subjected to Conceptual - Density functional theory. Besides, the Molecular dynamic simulation was also carried out for the selected leads. We also validated in-vitro against colon cancer cell lines. The results showed mainly Acetyldigitoxin has shown better binding to the target. From this study, we can predict that the drug Acetyldigitoxin has shown noticeable inhibitory efficiency against STAT1, which in turn can also lead to the reduction of tumor cell growth in colon cancer.

• Bulletin of the Korean Chemical Society
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• v.7 no.5
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• pp.367-371
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• 1986

Dynamic and equilibrium properties of n-alkane chains immersed in solvent molecules have been investigated by a molecular dynamics method. The n-alkane chain is assumed to be a chain of elements (CH$_2$) interconnected by bonds having a fixed bond length and bond angle, but each bond of the chain is allowed to execute hindered internal rotation. We studied the effect of the number of the chain elements (N$_c$ = 10, 15 and 20) on the equilibrium properties of the system, e.g., the pair correlation functions between a chain element and solvent molecules, g$_{cs}$(r), and between the chain elements, g$_{cc}$(r), and the configurational properties such as the mean-square end-to-end distance < R$^2$ >, the mean-square radius of gyration < S$^2$ >, and the eigenvalues of the moment-of-inertia tensor < S$_i^2$ > / < S$^2$ > (i = 1, 2 and 3). We also studied the dynamic properties of the system, e.g., the autocorrelation function C(A;t) where A = R$^2$(t), = S$^2$(t), or = ${\vec{V}}(t)({\vec{V}}$ = velocity of the center of mass), and the diffusion coefficient D. The g$_{cs}$(r)'s are almost equal irrespective of the change of Nc while g$_{cc}$(r) becomes larger as N$_c$ increases; The MD computed configurational properties < R$^2$2 > and < S$^2$ > were found to be a little different from the values calculated from the statistical equations of < R$^2$ > and < S$^2$ >, it may be due to the fact that our model for the MD simulations includes a long-range volume effect. From the < S$_i^2$ > / < S$^2$ >, it is found that the chain molecule has a nearly spherical shape irrespective of the variation of N$_c$. For the dynamic properties we found that the C(R$^2$;t) and C(S$^2$;t) of lower N$_c$ decay faster than those of higher N$_c$, while the C($\vec V$;t) of the center of mass in the chain is weakly dependent on the N$_c$. The center of mass diffusion coefficient D$_c$ decreases as N$_c$ increases while the end point diffusion coefficient D$_e$ is nearly equal irrespective of the change of N$_c$.

• Journal of the Korean GEO-environmental Society
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• v.25 no.4
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• pp.13-20
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• 2024

In this paper, a parallel analysis algorithm for Smoothed Particle Hydrodynamics (SPH), one of the numerical methods for fluidic materials, is introduced. SPH, which is a meshless method, can represent the behavior of a continuum using a particle-based approach, but it demands substantial computational resources. Therefore, parallel analysis algorithms are essential for SPH simulations. The domain decomposition algorithm, which divides the computational domain into partitions to be independently analyzed, is the most representative method among parallel analysis algorithms. In Discrete Element Method (DEM) and Molecular Dynamics (MD), the Cartesian coordinate-based domain decomposition method is popularly used because it offers advantages in quickly and conveniently accessing particle positions. However, in SPH, it is important to share particle information among partitioned domains because SPH particles are defined based on information from nearby particles within the smoothing length. Additionally, maintaining CPU load balance is crucial. In this study, a highly parallel efficient algorithm is proposed to dynamically minimize the size of orthogonal domain partitions to prevent excess CPU utilization. The efficiency of the proposed method was validated through numerical analysis models. The parallel efficiency of the proposed method is evaluated for up to 30 CPUs for fluidic models, achieving 90% parallel efficiency for up to 28 physical cores.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.3
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• pp.95-101
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• 2016

Apolipoprotein B-100 (Apo-B100) is a major component of low density lipoprotein (LDL). Apo B-100 protein has 4,536 amino acid sequence and these amino acids are classified into peptide groups A to G with subsequent 20 amino acids (P1-P302). The peptide groups were act as immunoglobulin (Ig) antigens which oxidized via malondialdehyde (MDA). The mimetic peptide P1 (EEEMLENVSLVCPKDAT RFK) out of D-group peptides carrying the highest value of IgG antigens were selected for structural studies that may provide antigen specificity. Circular Dichroism (CD) spectra were measured for peptide secondary structure in the range of 190-250 nm. Experimental results show that P1 exhibit partial of ${\beta}-sheet$ and random coil structure. Homonuclear (COSY, TOCSY, NOESY) 2D-NMR experiments were carried out for NMR signal assignments and structure determination for P1. On the basis of these completely assigned NMR spectra and distance data, distance geometry (DG) and Molecular dynamics (MD) were carried out to determine the structures of P1. The proposed structure was selected by comparisons between experimental NOE spectra and back calculated 2D NOE results from determined structure showing acceptable agreement. The total Root-Mean-Square-Deviation (RMSD) value of P1 obtained upon superposition of all atoms was in the range $0.33{\AA}$. The solution state P1 has mixed structure of ${\beta}-sheet$ (Glu[1] to Cys[12]) and random coil (Pro[13] to Lys[20]). These NMR results are well consistent with secondary structure from experimental results of circular dichroism. Structural studies based on NMR may contribute to the studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.

• Advances in nano research
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• v.12 no.5
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• pp.529-547
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• 2022

Graphene is one of the strongest, stiffest, and lightest nanoscale materials known to date, making it a potentially viable and attractive candidate for developing lightweight structural composites to prevent high-velocity ballistic impact, as commonly encountered in defense and space sectors. In-plane twist in bilayer graphene has recently revealed unprecedented electronic properties like superconductivity, which has now started attracting the attention for other multi-physical properties of such twisted structures. For example, the latest studies show that twisting can enhance the strength and stiffness of graphene by many folds, which in turn creates a strong rationale for their prospective exploitation in high-velocity impact. The present article investigates the ballistic performance of twisted bilayer graphene (tBLG) nanostructures. We have employed molecular dynamics (MD) simulations, augmented further by coupling gaussian process-based machine learning, for the nanoscale characterization of various tBLG structures with varying relative rotation angle (RRA). Spherical diamond impactors (with a diameter of 25Å) are enforced with high initial velocity (V_i) in the range of 1 km/s to 6.5 km/s to observe the ballistic performance of tBLG nanostructures. The specific penetration energy (E_p^*) of the impacted nanostructures and residual velocity (V_r) of the impactor are considered as the quantities of interest, wherein the effect of stochastic system parameters is computationally captured based on an efficient Gaussian process regression (GPR) based Monte Carlo simulation approach. A data-driven sensitivity analysis is carried out to quantify the relative importance of different critical system parameters. As an integral part of this study, we have deterministically investigated the resonant behaviour of graphene nanostructures, wherein the high-velocity impact is used as the initial actuation mechanism. The comprehensive dynamic investigation of bilayer graphene under the ballistic impact, as presented in this paper including the effect of twisting and random disorder for their prospective exploitation, would lead to the development of improved impact-resistant lightweight materials.