• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.438-444
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• 2008

A self-assembled monolayer of 2,2'-bipyridine (22BPY) molecules on Au(111) underwent a structural phase transition when the polarity of a bias voltage was switched in scanning tunneling microscopy (STM) experiments. The nature of two bright spots representing each 22BPY molecule on Au(111) in the high-resolution STM images was identified by calculating the partial density plots for a monolayer of 22BPY molecules adsorbed on Au(111) using tight-binding electronic structure calculations. The stacking pattern of the chains of 22BPY molecules on Au(111) was explained by examining the intermolecular interactions between the 22BPY molecules based on first principles electronic structure calculations for a 22BPY dimer, (22BPY)2. The structural instability of the 22BPY molecule arrangement caused by a change in the bias voltage switch was investigated by estimating the adsorbate-surface interaction energy using a point-charge approximation for Au(111).

• Korean Chemical Engineering Research
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• v.56 no.5
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• pp.607-624
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• 2018

We review SAFT equation of state (EOS) which is based on TPT theory and statistical-mechanical principles, and confirm that it can be used as a useful tool to predict vapor-liquid phase equilibria of associating fluid mixtures. We examine theoretical structure of PC-SAFT EOS in great detail, and then assess the applicability and performance of the EOS while applying it to various mixtures containing nonpolar components, polar components and associating components in a stage-wise manner. In contrast to the conventional engineering EOS, PC-SAFT EOS can accurately predict nonideal behaviors of those mixtures without using semi-empirical binary interaction parameter. This is because the SAFT theory is based on a rigorous theoretical framework at molecular level which effectively accounts for various intermolecular interactions, and it thus provides substantial benefits in applying the SAFT EOS to complex thermodynamic phenomena of multi-component mixtures.

• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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• pp.149-155
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• 1987

Growth and development of a higher plant, or any living organism for that matter, could be defined as an orderly expression of the genome in time and space in close interaction with the environment. During differentiation and development of a tissue or organ a group of genes must be selectively turned on or turned off mainly by trans-acting regulators. In this general concept of regulation of regulation of gene expression, a DNA molecule is recognized at a specific nucleotide sequence by DNA-binding factors. Molecular biology of the regulatory factors such as hormones, and their receptors, target DNA sequences and DNA-binding proteins are well advanced. What is not clearly understood is the molecular basis of the interactions between DNA and binding factors, expecially of the usages of the dyad symmetry of the target DNA sequences and the dimeric nature of the DNA-binding proteins. A unique 3-dimensional structure of DNA has been proposed that may play an important role in the orderly expression of the gene. A foldback intercoil (FBI) DNA configuration which was originally found by electron microscopy among mtDNA molecules from pearl millet has some unique features. The FBI configuration of DNA is believed to be formed when a flexible double helix folds back and interwines in the widened major grooves resulting in a four stranded, intercoil DNA whose thickness is the same as that of double stranded DNA. More recently, the FBI structure of DNA has been also induced in vitro by a novel enzyme which was purified from pearl millet mitochondria. It has been proposed that the FBI DNA could be utillized in intramolecular recombination which leads to inversion or deletion, and in intermolecular recombination which can lead to either site-specific recombination, genetic recombination via single strand invasion, or cross strand recombination. The structure and function of DNA in 3-dimensional aspect is emphasized for better understanding orderly expression of genes during growth and development.

• Polymer(Korea)
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• v.33 no.4
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• pp.384-388
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• 2009

The rheological properties of poly (acrylonitrile) (PAN) and cellulose acetate (CA) blend solutions in N,N-dimethyl formamide (DMF) were investigated in terms of temperature and blend composition. The solutions exhibited a very characteristic rheological behavior with variation of temperature. 8 wt% solution showed an increase of viscosity and a decrease of loss tangent as temperature was increased over the temperature range of 20 and $60^{\circ}C$. At $20^{\circ}C$ the physical properties of the solutions exhibited dependence on the blend composition. At 40 and $60^{\circ}C$, however, the effects of blend ratio on the physical properties notably diminished. The longer relaxation time at higher temperature indicated that the formation of physical structures resulting from intermolecular interactions was promoted with increasing temperature. The odd rheological responses were further elucidated by measuring of the physical properties of dilute solutions. The intrinsic viscosity of the solutions suggested that the coiled chain dimension was reduced with increasing temperature.

• Molecules and Cells
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• v.43 no.3
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• pp.286-297
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• 2020

Mammalian patatin-like phospholipase domain containing proteins (PNPLAs) play critical roles in triglyceride hydrolysis, phospholipids metabolism, and lipid droplet (LD) homeostasis. PNPLA7 is a lysophosphatidylcholine hydrolase anchored on the endoplasmic reticulum which associates with LDs through its catalytic region (PNPLA7-C) in response to increased cyclic nucleotide levels. However, the interaction of PNPLA7 with LDs through its catalytic region is unknown. Herein, we demonstrate that PNPLA7-C localizes to the mature LDs ex vivo and also colocalizes with pre-existing LDs. Localization of PNPLA7-C with LDs induces LDs clustering via non-enzymatic intermolecular associations, while PNPLA7 alone does not induce LD clustering. Residues 742-1016 contains four putative transmembrane domains which act as a LD targeting motif and are required for the localization of PNPLA7-C to LDs. Furthermore, the N-terminal flanking region of the LD targeting motif, residues 681-741, contributes to the LD targeting, whereas the C-terminal flanking region (1169-1326) has an anti-LD targeting effect. Interestingly, the LD targeting motif does not exhibit lysophosphatidylcholine hydrolase activity even though it associates with LDs phospholipid membranes. These findings characterize the specific functional domains of PNPLA7 mediating subcellular positioning and interactions with LDs, as wells as providing critical insights into the structure of this evolutionarily conserved phospholipid-metabolizing enzyme family.

• Membrane Journal
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• v.5 no.2
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• pp.89-96
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• 1995

The monolayer characteristics of phosphate amphiphiles with azobenzene at air/water interface were studied by the measurment of $\pi-A$ curves and absorption spectra. Immediately after being spread on the water surface, these amphiphiles having strong intermolecular hydrogen bonding interactions showed the typical absorption spectra which resulted from domain formation. But the aggregated domains could be controlled by changing the subphase conditions (adding bulky salt and rasing pH). Addition of metal ions in subphase changes the molecular orientation of monolayer. As the metal ion charge increases ($1\leq2$ < 3 < 4 valence), the absorption maximum (310nm) of the amphiphile with azobenzene shifts to a longer wavelength (350nm) which means that the orientation of the amphiphile is tilted. These results suggest that the molecular orientation, and furthermore the aggregation state of monolayer can be possibly controlled by the interaction of metal ions with different charge types.

• Genomics & Informatics
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• v.14 no.2
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• pp.53-61
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• 2016

Toxoplasma gondii is an intracellular Apicomplexan parasite and a causative agent of toxoplasmosis in human. It causes encephalitis, uveitis, chorioretinitis, and congenital infection. T. gondii invades the host cell by forming a moving junction (MJ) complex. This complex formation is initiated by intermolecular interactions between the two secretory parasitic proteins-namely, apical membrane antigen 1 (AMA1) and rhoptry neck protein 2 (RON2) and is critically essential for the host invasion process. By this study, we propose two potential leads, NSC95522 and NSC179676 that can efficiently target the AMA1 hydrophobic cleft, which is a hotspot for targeting MJ complex formation. The proposed leads are the result of an exhaustive conformational search-based virtual screen with multilevel precision scoring of the docking affinities. These two compounds surpassed all the precision levels of docking and also the stringent post docking and cumulative molecular dynamics evaluations. Moreover, the backbone flexibility of hotspot residues in the hydrophobic cleft, which has been previously reported to be essential for accommodative binding of RON2 to AMA1, was also highly perturbed by these compounds. Furthermore, binding free energy calculations of these two compounds also revealed a significant affinity to AMA1. Machine learning approaches also predicted these two compounds to possess more relevant activities. Hence, these two leads, NSC95522 and NSC179676, may prove to be potential inhibitors targeting AMA1-RON2 complex formation towards combating toxoplasmosis.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.358-358
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• 2010

Ion beam bombardment at low energy forms nanosize patterns such as ripples, dots or wrinkles on the surface of polymers in ambient temperature and pressure. It has been known that the ion beam can alter the polymer surface that induces skins stiffer or the density higher by higher compressive stress or strain energies associated with chain scissions and crosslinks of the polymer. Atomic scale structure evolution in polymers is essential to understand a stress generation mechanism during the ion beam bombardment, which governs the nanoscale surface structure evolution. In this work, Molecular Dynamics (MD) simulations are employed to characterize the phenomenon occurred in bombardment between the ion beam and polymers that forms nanosize patterns. We investigate the structure evolution of Low Density Polyethylene (LDPE) at 300 K as the polymer is bombarded with Argon ions having various kinetic energies ranging from 100 eV to 1 KeV with 50 eV intervals having the fluence of $1.45\;{\times}\;1014 #/cm2$. These simulations use the Reactive Force Field (ReaxFF), which can mimic chemical covalent bonds and includes van der Waals potentials for describing the intermolecular interactions. The results show the details of the structural evolution of LDPE by the low energy Ar ion bombardment. Analyses through kinetic and potential energy, number of crosslinks and chain scissions, level of local densification and motions of atoms support that the residual strain energies on the surface is strongly associated with the number of crosslinks or scissored chains. Also, we could find an optimal Ar ion beam energy to make crosslinks well.

• Steel and Composite Structures
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• v.34 no.2
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• pp.261-277
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• 2020

The main objective of this research paper is to consider vibration analysis of vacancy defected graphene sheet as a nonisotropic structure via molecular dynamic and continuum approaches. The influence of structural defects on the vibration of graphene sheets is considered by applying the mechanical properties of defected graphene sheets. Molecular dynamic simulations have been performed to estimate the mechanical properties of graphene as a nonisotropic structure with single- and double- vacancy defects using open source well-known software i.e., large-scale atomic/molecular massively parallel simulator (LAMMPS). The interactions between the carbon atoms are modelled using Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential. An isogeometric analysis (IGA) based upon non-uniform rational B-spline (NURBS) is employed for approximation of single-layered graphene sheets deflection field and the governing equations are derived using nonlocal elasticity theory. The dependence of small-scale effects, chirality and different defect types on vibrational characteristic of graphene sheets is investigated in this comprehensive research work. In addition, numerical results are validated and compared with those achieved using other analysis, where an excellent agreement is found. The interesting results indicate that increasing the number of missing atoms can lead to decrease the natural frequencies of graphene sheets. It is seen that the degree of the detrimental effects differ with defect type. The Young's and shear modulus of the graphene with SV defects are much smaller than graphene with DV defects. It is also observed that Single Vacancy (SV) clusters cause more reduction in the natural frequencies of SLGS than Double Vacancy (DV) clusters. The effectiveness and the accuracy of the present IGA approach have been demonstrated and it is shown that the IGA is efficient, robust and accurate in terms of nanoplate problems.

• The Korean Journal of Pain
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• v.34 no.3
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• pp.262-270
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• 2021

Background: Transient receptor potential vanilloid 1 (TRPV1) is a non-selective cation channel implicated in pain sensation in response to heat, protons, and capsaicin (CAPS). It is well established that TRPV1 is involved in mechanical allodynia. This study investigates the effect of Ononis spinosa (Fabaceae) in CAPS-induced mechanical allodynia and its mechanism of action. Methods: Mechanical allodynia was induced by the intraplantar (ipl) injection of 40 ㎍ CAPS into the left hind paw of male Wistar rats. Animals received an ipl injection of 100 ㎍ O. spinosa methanolic leaf extract or 2.5% diclofenac sodium 20 minutes before CAPS injection. Paw withdrawal threshold (PWT) was measured using von Frey filament 30, 90, and 150 minutes after CAPS injection. A molecular docking tool, AutoDock 4.2, was used to study the binding energies and intermolecular interactions between O. spinosa constituents and TRPV1 receptor. Results: The ipsilateral ipl injection of O. spinosa before CAPS injection increased PWT in rats at all time points. O. spinosa decreased mechanical allodynia by 5.35-fold compared to a 3.59-fold decrease produced by diclofenac sodium. The ipsilateral pretreatment with TRPV1 antagonist (300 ㎍ 4-[3-Chloro-2-pyridinyl]-N-[4-[1,1-dimethylethyl] phenyl]-1-piperazinecarboxamide [BCTC]) as well as the β2-adrenoreceptor antagonist (150 ㎍ butoxamine) attenuated the action of O. spinosa. Depending on molecular docking results, the activity of the extract could be attributed to the bindings of campesterol, stigmasterol, and ononin compounds to TRPV1. Conclusions: O. spinosa alleviated CAPS-induced mechanical allodynia through 2 mechanisms: the direct modulation of TRPV1 and the involvement of β2 adrenoreceptor signaling.