Kyoto University · Materials Science
Professor Mayank Dixit's research lab specializes in polymer physics and molecular dynamics, focusing on the structure-property relationships in natural and synthetic polymers, particularly cis-1,4-polyisoprene in natural rubber. The lab employs advanced computational techniques such as molecular dynamics simulations, free energy perturbation, and 2D NMR to investigate terminal group effects, hydrophobic interactions, and solvation phenomena in complex systems. Key research directions include understanding the role of end groups in enhancing mechanical properties of natural rubber and probing ion-solvent interactions in mixed solvents. The lab also explores the thermodynamics of hydrophobic association and pore formation in lipid bilayers, contributing to fundamental insights in soft matter and biophysical chemistry.
Figures are computed from collected data and may differ slightly.
The terminal structures of <i>cis</i>-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The <i>cis</i>-1,4-polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(<i>trans</i>-1,4-isoprene)<sub>2
The free energy of pore formation in lipid bilayers has been previously calculated using a variety of reaction coordinates. Here, we use free energy perturbation of a cylindrical lipid exclusion restraint to compute the free energy profile as a function of pore radius in dimyristoylphosphatidylcholine (DMPC) and dioleoylphosphatidylcholine (DOPC) bilayers. Additionally restraining the headgroups to lie on the membrane surface allows us to also calculate the free energy profile of hydrophobic por
Hevea natural rubber (NR) consists of 99% cis-polyisoprene with dimethyl allyl-(trans-1,4-isoprene)2 (ω) and α terminal groups. These terminal groups provide excellent mechanical and physical properties to NR. Oochi et al. (Oouchi, M.; Ukawa, J.; Ishii, Y.; Maeda, H. Biomacromolecules 2019, 20, 1394–1400) have elucidated the structures of six types of α terminals of NR by using a solid -state NMR study. We examine four types of cis-1,4-polyisoprene (PI) melt systems with different combinations o
We have studied the hydrophobic association and solvation of methane molecules in aqueous solutions of urea and glycine betaine (GB). We have calculated the potentials of mean force (PMFs) between methane molecules in water, aqueous GB, aqueous urea and aqueous urea-GB mixtures. The PMFs and equilibrium constants indicate that both urea and GB increase the hydrophobic association of methane. Calculation of thermodynamic parameters shows that the association of methane is stabilized by entropy wh
Natural rubber (NR), containing nonrubber constituents such as proteins, exhibits exceptional characteristics including high toughness, tear resistance, and wet skid resistance. Gaining a thorough understanding of the interplay between proteins and the terminal groups of the <i>cis</i>-1,4-polyisoprene chains in NR is vital for comprehending the superior properties of NR in comparison to synthetic polyisoprene rubber. The terminal ends of the <i>cis</i>-1,4-polyisoprene chains in NR encompass tw
A constrained molecular dynamics technique has been used to study the structures and dynamics of the solvation shells of three sodium halides, namely sodium chloride (Na+–Cl−), sodium bromide (Na+–Br−) and sodium iodide (Na+–I−) in DMSO–MeOH mixtures. In the case of Na+–Cl− and Na+–Br−, Na+ is preferentially solvated by DMSO and Cl− and Br− are preferentially solvated by methanol in the contact ion pair (CIP) state. In the solvent-assisted ion pair (SAIP) configuration, Na+ ions of Na+–Cl− and N
A detailed knowledge of hydrophobic association and solvation is crucial for understanding the con-formational stability of proteins and polymers in osmolyte solutions. Using molecular dynamics simulations, it is found that the hydrophobic association of neopentane molecules is greater in a mixed urea-TMAO-water solution in comparison to that in 8 M urea solution, 4 M TMAO solution and neat water. The neopentane association in urea solution is greater than that in TMAO solution or neat water. We
Ionic liquids (ILs) with dimethyl sulfoxide (DMSO) and water act as a promising solvent medium for the dissolution of cellulose in an efficient manner. To develop a proper solvent system, it is really important to understand the thermodynamics of the molecular solutions consisting of ILs, DMSO, and water. The ion-pairing propensity of the ILs in the presence of DMSO and water plays a crucial role in governing the property of the solvent mixtures. Employing all-atom molecular dynamics simulations
This study elucidates the pivotal role of terminal structures in <i>cis</i>-1,4-polyisoprene (PI) chains, contributing to the exceptional mechanical properties of Hevea natural rubber (NR). NR's unique networking structure, crucial for crack resistance, elasticity, and strain-induced crystallization, involves two terminal groups, ω and α. The proposed ω terminal structure is dimethyl allyl-(<i>trans</i>-1,4-isoprene)<sub>2</sub>, and α terminals exist in various forms, including hydroxy, ester,
The Fourier Grid Hamiltonian (FGH) method is used to compute the vibrational eigenvalues and eigenfunctions of bound states of diatomic molecules. For these computations, the Hulburt and Hirschfelder (HH) potential model for diatomics is used. These potential energy functions are used for constructing and diagonalizing the molecular Hamiltonians. The vibrational wave functions for the ground and the excited states are used to calculate the Franck-Condon factors (FCFs), r-Centroids and average in
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