Jeongmin Kim

Comparative proton transfer efficiencies of hydronium and hydroxide in aqueous solution: proton transfer vs Brownian motion.

With the help of QM/EFP-MD with modern correlated quantum theories, distinctly different proton transport dynamics for hydronium and hydroxide ions was revealed. The efficiency of proton transfer for hydronium was found to be significantly higher than that for hydroxide, and the difference in efficiency increased as the temperature was lowered. This difference in dynamics suggests that molecular Brownian diffusion may play an important role in hydroxide transport. Our theoretical findings are consistent with recent experimental observations of proton transfer in amorphous solid water.

Swing motion as a diffusion mechanism of lipid bilayers in a gel phase.

Lipid bilayers are a model system for studying the properties of cell membranes. For lipid bilayers of a single lipid component, there is a phase transition from a fluid phase to a gel phase as the temperature is decreased. The dynamic behavior of lipids in the gel phase is interesting: some models show dynamic heterogeneity with a large disparity in timescales between fast and slow molecules, and a spatial segregation of the slow molecules. In this paper we study the dynamics of coarse-grained models of lipid bilayers using the dry Martini, Lennard-Jones Martini, polarizable Martini, and BMW models. All four models show similar dynamical behaviors in the gel phase although the transition temperature is model-dependent. We find that the primary mode of transport in the gel phase is a hopping of the lipid molecules. Hopping is seen in both the translational and rotational dynamics, which are correlated, i.e., the lipid molecules display a swing-like motion in the gel phase.

Conductive network formation of carbon nanotubes in elastic polymer microfibers and its effect on the electrical conductance: Experiment and simulation

We investigate how the electrical conductance of microfibers (made of polymers and conductive nanofillers) decreases upon uniaxial deformation by performing both experiments and simulations. Even though various elastic conductors have been developed due to promising applications for deformable electronic devices, the mechanism at a molecular level for electrical conductance change has remained elusive. Previous studies proposed that the decrease in electrical conductance would result from changes in either distances or contact numbers between conductive fillers. In this work, we prepare microfibers of single walled carbon nanotubes (SWCNTs)/polyvinyl alcohol composites and investigate the electrical conductance and the orientation of SWCNTs upon uniaxial deformation. We also perform extensive Monte Carlo simulations, which reproduce experimental results for the relative decrease in conductance and the SWCNTs orientation. We investigate the electrical networks of SWCNTs in microfibers and find that the decrease in the electrical conductance upon uniaxial deformation should be attributed to a subtle change in the topological structure of the electrical network.

Translational and rotational diffusion of a single nanorod in unentangled polymer melts.

Polymer nanocomposites have been an issue of both academic and industrial interest due to promising electrical, mechanical, optical, and magnetic properties. The dynamics of nanoparticles in polymer nanocomposites is a key to understanding those properties of polymer nanocomposites and is important for applications such as self-healing nanocomposites. In this article we investigate the translational and the rotational dynamics of a single nanorod in unentangled polymer melts by employing extensive molecular dynamics simulations. A nanorod and polymers are modeled as semiflexible tangent chains of spherical beads. The stiffness of a nanorod is tuned by changing the bending potential between chemical bonds. When polymers are sufficiently long and the nanorod is stiff, the nanorod translates in an anisotropic fashion along the nanorod axis within time scales of translational relaxation times even in unentangled polymer melts. The rotational diffusion is suppressed more significantly than the translational diffusion as the polymer chain length is increased, thus the translational and rotational diffusion of the nanorod are decoupled. We also estimate the winding numbers of polymers, i.e., how many times a polymer winds the nanorod. The winding number increases with longer polymers but is relatively insensitive to the nanorod stiffness.

Dynamics and spatial correlation of voids in dense two dimensional colloids

Two dimensional (2D) colloids show interesting phase and dynamic behaviors. In 2D, there is another intermediate phase, called hexatic, between isotropic liquid and solid phases. 2D colloids also show strongly correlated dynamic behaviors in hexatic and solid phases. We perform molecular dynamics simulations for 2D colloids and illustrate how the local structure and dynamics of colloids near phase transitions are reflected in the spatial correlations and dynamics of voids. Colloids are modeled as hard discs and a void is defined as a tangent circle (a pore) to three nearest hard discs. The variation in pore diameters represents the degree of disorder in voids and decreases sharply with the area fraction (ϕ) of colloids after a hexagonal structural motif of colloids becomes significant and the freezing transition begins at ϕ ≈ 0.7. The growth of ordered domains of colloids near the phase transition is captured in the spatial correlation functions of pores. We also investigate the topological hopping probability and the topological lifetime of colloids in different topological states, and find that the stability of different topological states should be related to the size variation of local pores: colloids in six-fold states are surrounded by the most ordered and smallest pores with the longest topological lifetime. The topological lifetime of six-fold states increases by about 50 times as ϕ increases from liquid to hexatic to solid phases. We also compare four characteristic times in order to understand the slow and unique dynamics of two dimensional colloids: a caging time (τ(c)), a topological lifetime (τ(top)), a pore lifetime (τ(p)), and a translational relaxation time (τ(α)).

Fractional Viscosity Dependence of Reaction Kinetics in Glass-Forming Liquids

The diffusion of molecules in complex systems such as glasses and cell cytoplasm is slow, heterogeneous, and sometimes nonergodic. The effects of such intriguing diffusion on the kinetics of chemical and biological reactions remain elusive. In this Letter, we report that the kinetics of the polymer loop formation reaction in a Kob-Andersen (KA) glass forming liquid is influenced significantly by the dynamic heterogeneity. The diffusion coefficient D of a KA liquid deviates from the Stokes-Einstein relation at low temperatures and D shows a fractional dependence on the solvent viscosity η_{s}, i.e., D∼η_{s}^{-ξ_{D}} with ξ_{D}=0.85. The dynamic heterogeneity of a KA liquid affects the rate constant k_{rxn} of the loop formation and leads to the identical fractional dependence of k_{rxn} on η_{s} with k_{rxn}∼η_{s}^{-ξ} and ξ=ξ_{D}, contrary to reactions in dynamically homogeneous solutions where k_{rxn}∼η_{s}^{-1}.

Dynamics of highly polydisperse colloidal suspensions as a model system for bacterial cytoplasm

There are various kinds of macromolecules in bacterial cell cytoplasm. The size polydispersity of the macromolecules is so significant that the crystallization and the phase separation could be suppressed, thus stabilizing the liquid state of bacterial cytoplasm. On the other hand, recent experiments suggested that the macromolecules in bacterial cytoplasm should exhibit glassy dynamics, which should be also affected significantly by the size polydispersity of the macromolecules. In this work, we investigate the anomalous and slow dynamics of highly polydisperse colloidal suspensions, of which size distribution is chosen to mimic Escherichia coli cytoplasm. We find from our Langevin dynamics simulations that the diffusion coefficient (D_{tot}) and the displacement distribution functions (P(r,t)) averaged over all colloids of different sizes do not show anomalous and glassy dynamic behaviors until the system volume fraction ϕ is increased up to 0.82. This indicates that the intrinsic polydispersity of bacterial cytoplasm should suppress the glass transition and help maintain the liquid state of the cytoplasm. On the other hand, colloids of each kind show totally different dynamic behaviors depending on their size. The dynamics of colloids of different size becomes non-Gaussian at a different range of ϕ, which suggests that a multistep glass transition should occur. The largest colloids undergo the glass transition at ϕ=0.65, while the glass transition does not occur for smaller colloids in our simulations even at the highest value of ϕ. We also investigate the distribution (P(θ,t)) of the relative angles of displacement for macromolecules and find that macromolecules undergo directionally correlated motions in a sufficiently dense system.

Tracer Shape and Local Media Structure Determine the Trend of Translation-Rotation Decoupling in Two-Dimensional Colloids.

The translational diffusion of tracers in glass-forming materials often violates the Stokes-Einstein relation while their rotation follows the Debye-Stokes-Einstein relation faithfully, thus decoupling translational and rotational diffusion. In this Letter, we show by performing molecular dynamics simulations for two-dimensional (2D) colloids that the tracer shape and the local media structure are critical such that rotational diffusion is either suppressed or enhanced depending on the tracer shape. For square tracers dissimilar in structure to the local media structure of 2D colloids, the translation-rotation decoupling occurs and the rotational diffusion is enhanced relative to the translation. For sufficiently large diamond tracers similar in structure to the local media structure, tracers undergo rotational hopping motions and their rotation is suppressed relative to the translation. For distorted-diamond tracers, the decoupling is marginal. Translational diffusion does not change significantly with the tracer shape and obeys the Stokes-Einstein relation.

Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former

The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

Translation-rotation decoupling of tracers of locally favorable structures in glass-forming liquids

Particles in glass-forming liquids may form domains of locally favorable structures (LFSs) upon supercooling. Whether and how the LFS domains would relate to the slow relaxation of the glass-forming liquids have been issues of interest. In this study, we employ tracers of which structures resemble the LFS domains in Wahnström and Kob-Andersen (KA) glass-forming liquids and investigate the translation-rotation decoupling of the tracers. We find that the tracer structure affects how the translation and the rotation of tracers decouple and that information on the local mobility around the LFS domains may be gleaned from the tracer dynamics. According to the Stokes-Einstein relation and the Debye-Stokes-Einstein relation, the ratio of the translational (DT) and rotational (DR) diffusion coefficients is expected to be a constant over a range of T/η, where η and T denote the medium viscosity and temperature, respectively. In supercooled liquids and glasses, however, DT and DR decouple due to dynamic heterogeneity, thus DT/DR not being constant any more. In Wahnström glass-forming liquids, icosahedron LFS domains are the most long-lived ones and the mobility of neighbor particles around the icosahedron LFS domain is suppressed. We find from our simulations that the icosahedron tracers, similar in size and shape to the icosahedron LFS domains, experience drastic translation-rotation decoupling upon cooling. The local mobility of liquid particles around the icosahedron tracers is also suppressed significantly. On the other hand, tracers of FCC and HCP structures do not show translation-rotation decoupling in the Wahnström liquid. In KA glass-forming liquids, bicapped square antiprism LFS domains are the most long-lived LFS domains but are not correlated significantly with the local mobility. We find from our simulations that DT and DR of bicapped square antiprism tracers, also similar in size and shape to the bicapped square antiprism LFS domains, do not decouple significantly similarly to tracers of other structures, thus reflecting that the local mobility would not be associated strongly with LFS domains in the KA liquid.