• Macromolecular Research
• /
• v.9 no.3
• /
• pp.164-170
• /
• 2001

Recently in order to describe the complex rheological behavior of polymer melts with long side branches like low density polyethylene, new constitutive equations called the pom-pom equations have been derived by McLeish and Larson on the basis of the reptation dynamics with simplified branch structure taken into account. In this study mathematical stability analysis under short and high frequency wave disturbances has been performed for the simplified differential version of these constitutive equations. It is proved that they are globally Hadamard stable except for the case of maximum constant backbone stretch (λ = q) with arm withdrawal s$\_$c/ neglected, as long as the orientation tensor remains positive definite or the smooth strain history in the now is previously given. However this model is dissipative unstable, since the steady shear How curves exhibit non-monotonic dependence on shear rate. This type of instability corresponds to the nonlinear instability in simple shear flow under finite amplitude disturbances. Additionally in the flow regime of creep shear flow where the applied constant shear stress exceeds the maximum achievable value in the steady now curves, the constitutive equations will possibly violate the positive definiteness of the orientation tensor and thus become Hadamard unstable.

• Genomics & Informatics
• /
• v.13 no.1
• /
• pp.15-24
• /
• 2015

Fatty acid synthase (FASN, EC 2.3.1.85), is a multi-enzyme dimer complex that plays a critical role in lipogenesis. This lipogenic enzyme has gained importance beyond its physiological role due to its implications in several clinical conditions-cancers, obesity, and diabetes. This has made FASN an attractive pharmacological target. Here, we have attempted to predict the theoretical models for the human enoyl reductase (ER) and ${\beta}$-ketoacyl reductase (KR) domains based on the porcine FASN crystal structure, which was the structurally closest template available at the time of this study. Comparative modeling methods were used for studying the structure-function relationships. Different validation studies revealed the predicted structures to be highly plausible. The respective substrates of ER and KR domains-namely, trans-butenoyl and ${\beta}$-ketobutyryl-were computationally docked into active sites using Glide in order to understand the probable binding mode. The molecular dynamics simulations of the apo and holo states of ER and KR showed stable backbone root mean square deviation trajectories with minimal deviation. Ramachandran plot analysis showed 96.0% of residues in the most favorable region for ER and 90.3% for the KR domain, respectively. Thus, the predicted models yielded significant insights into the substrate binding modes of the ER and KR catalytic domains and will aid in identifying novel chemical inhibitors of human FASN that target these domains.

• Korea-Australia Rheology Journal
• /
• v.13 no.4
• /
• pp.205-217
• /
• 2001

This review article summarizes results of recent viscoelastic and dielectric studies for entangled cis-polyisoprene (PI) chains. The PI chains have the so-called type-A dipoles parallel along the chain backbone, and their slow viscoelastic and dielectric relaxation processes reflect the same global chain motion. However, this motion is differently averaged in the viscoelastic and dielectric properties, the former representing the isochronal orientational anisotropy of individual entanglement segments while the latter detecting the orientational correlation of the segments at two separate times (0 and t). On the basis of this difference, the viscoelastic and dielectric data of the entangled PI chains were compared to elucidate detailed features of the chain dynamics. Specifically, the molecular picture of dynamic tube dilation (DTD) incorporated in recent models was tested for linear and star PI chain. The comparison revealed that the DTD picture was valid for linear PI chains but failed for the star PI chains in the dominant part of the terminal relaxation. The failure for the star chains was related to the pre-requisite for the DTD process, rapid equilibration of successive entanglement segments through their constraint release (CR) motion: For the star chains, the dilated tube diameter expected in the terminal regime was considerably large because of a broad distribution of motional modes of the chains, so that the CR-equilibration required for DTD could not occur in time. The terminal relaxation of the star chain appeared to occur through the CR process before the expected DTD process was completed. The situation was different for the linear chain exhibiting narrowly distributed motional modes. The dilated tube expected for the linear chain was rather thin and the required CR-equilibration occurred in time, resulting in the success of the DTD picture. These detailed features of the chain dynamics was revealed only when the viscoelastic and dielectric properties were compared, demonstrating the importance of this comparison.

• Bulletin of the Korean Chemical Society
• /
• v.28 no.12
• /
• pp.2203-2208
• /
• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.

• 한국전산유체공학회:학술대회논문집
• /
• 2010.05a
• /
• pp.551-555
• /
• 2010

Electrowetting is a versatile tool to handle tiny droplets and forms a backbone of digital microfluidics. Numerical analysis is necessary to fully understand the dynamics of electrowetting, especially in designing electrowetting-based devices, such as liquid lenses and reflective displays. We developed a numerical method to analyze the general contact-line problems, incorporating dynamic contact angle models. The method is based on the conservative level set method to capture the interface of two fluids without loss of mass. We applied the method to the analysis of spreading process of a sessile droplet for step input voltages and oscillation of the droplet for alternating input voltages in electrowetting. The result was compared with experimental data. It is shown that contact line friction significantly affects the contact line motion and the oscillation amplitude. The pinning process of contact line was well represented by including the hysteresis effect in the contact angle models. In level set method, in the mean time, material properties are made to change smoothly across an interface of two materials with different properties by introducing an interpolation or smoothing scheme. So far, the weighted arithmetic mean (WAM) method has been exclusively adopted in level set method, without complete assessment for its validity. We viscosity, thermal conductivity, electrical conductivity, and permittivity, can be an alternative. I.e., the WHM gives more accurate results than the WAM method in certain circumstances. The interpolation scheme should be selected considering various characteristics including type of property, ratio of property of two fluids, geometry of interface, and so on.

• Journal of the Korean Magnetic Resonance Society
• /
• v.8 no.2
• /
• pp.77-85
• /
• 2004

$^1$H-detected $^{15}$N NMR was employed to investigated the effect of mutation (Y14F) on the dynamic properties of catalytic residues in ${\Delta}^5$-3- ketosteroid isomerase (KSI) from Conamonas testosteroni. In particular, the backbone dynamics of the catalytic residues have been studied in free enzyme and its complex with a steroid ligand, 19-nortestosterone hemisuccinate, by $^{15}$N relaxation measurements. The relaxation data were analyzed using the model-free formalism to extract the model-free parameters (S$^2$, ${\tau}_e$, and R$_{ex}$). The results show that the mutation causes a significant decrease in the order parameter (S$^2$) for the catalytic residues of free Y14F KSI, presumably due to breakdown of the hydrogen bond network by mutation. In addition, the order parameters of Phe-14 and Asp-99 increased slightly upon ligand binding, indicating a slight restriction of the high-frequency (pico- to nanosecond) internal motions of the residues in the complexed Y14F KSI, while the order parameter of Tyr-55 decreased significantly upon ligand binding.

• BMB Reports
• /
• v.33 no.3
• /
• pp.268-275
• /
• 2000

In contrast to the pyrimidine (6-4)pyrimidone photoproduct [(6-4) adduct], its Dewar valence isomer (Dewar product) is low mutagenic and produces a broad range of mutations with a 42 % replicating error frequency. In order to determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar·lesion DNA decamer duplex, which contains a mismatched base pair between the 3'-T residue and an opposed G residue. The 3'-T of the Dewar lesion forms stable hydrogen bonds with the opposite G residue. The helical bending and unwinding angles of the DW/GA duplex, however, are much higher than those of the DW/AA duplex. The stable hydrogen bonding of the G 15 residue does not increase the thermal stability of the overall helix. It also does not restore the distorted backbone conformation of the DNA helix that is caused by the forming of a Dewar lesion. These structural features implicate that no thermal stability, or conformational benefits of G over A opposite the 3'-T of the Dewar lesion, facilitate the preferential incorporation of an A. This is in accordance with the A rule during translesion replication and leads to the low frequent $3'-T{\rightarrow}C$ mutation at this site.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.5
• /
• pp.1401-1406
• /
• 2013

This study tested the feasibility of observing H/D exchange of intact protein by top-down electron capture dissociation (ECD) mass spectrometry for the investigation of protein structure. Ubiquitin is selected as a model system. Local structural information was obtained from the deuteration levels of c and $z^{\cdot}$ ions generated from ECD. Our results showed that ${\alpha}$-helix region has the lowest deuteration level and the C-terminal fraction containing a highly mobile tail has the highest deuteration level, which correlates well with previous X-Ray and HDX/NMR analyses. We studied site-specific H/D exchange kinetics by monitoring H/D exchange rate of several structural motives of ubiquitin. Two hydrogen bonded ${\beta}$-strands showed similar HDX rates. However, the outer ${\beta}$-strand always has higher deuteration level than the inner ${\beta}$-strand. The HDX rate of the turn structure (residues 8-11) is lower than that of ${\beta}$-strands (residues 1-7 and residues 12-17) it connects. Although isotopic distribution gets broader after H/D exchange which results in a limited number of backbone cleavage sites detected, our results demonstrate that this method can provide valuable detailed structural information of proteins. This approach should also be suitable for the structural investigation of other unknown proteins, protein conformational changes, as well as protein-protein interactions and dynamics.

• Structural Engineering and Mechanics
• /
• v.70 no.5
• /
• pp.601-621
• /
• 2019

This study presents a comprehensive nonlinear dynamic approach to investigate the linear and nonlinear vibration of sandwich plates fabricated from functionally graded materials (FGMs) resting on an elastic foundation. Higher-order shear deformation theory and Hamilton's principle are employed to obtain governing equations. The Runge-Kutta method is employed together with the commercially available mathematical software MAPLE 14 to solve the set of nonlinear dynamic governing equations. Method validity is evaluated by comparing the results of this study and those of previous research. Good agreement is achieved. The effects of temperature change on frequencies are investigated considering various temperatures and various volume fraction index values, N. As the temperature increased, the plate frequency decreased, whereas with increasing N, the plate frequency increased. The effects of the side-to-thickness ratio, c/h, on natural frequencies were investigated. With increasing c/h, the frequencies increased nonlinearly. The effects of foundation stiffness on nonlinear vibration of the sandwich plate were also studied. Backbone curves presenting the variation of maximum displacement with respect to plate frequency are presented to provide insight into the nonlinear vibration and dynamic behavior of FGM sandwich plates.

• Journal of the Korean Magnetic Resonance Society
• /
• v.26 no.1
• /
• pp.1-9
• /
• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.