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ABSTRACT: Molecular dynamics (MD) calculations for the plasma membranes of normal murine thymocytes and thymus-derived leukemic GRSL cells in water have been performed under physiological isothermal-isobaric conditions (310.15K and 1atm) to investigate changes in membrane properties induced by canceration. The model membranes used in our calculations for normal and leukemic thymocytes comprised 23 and 25 kinds of lipids, respectively, including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, lysophospholipids, and cholesterol. The mole fractions of the lipids adopted here were based on previously published experimental values. Our calculations clearly showed that the membrane area was increased in leukemic cells, and that the isothermal area compressibility of the leukemic plasma membranes was double that of normal cells. The calculated membranes of leukemic cells were thus considerably bulkier and softer in the lateral direction compared with those of normal cells. The tilt angle of the cholesterol and the conformation of the phospholipid fatty acid tails both showed a lower level of order in leukemic cell membranes compared with normal cell membranes. The lateral radial distribution function of the lipids also showed a more disordered structure in leukemic cell membranes than in normal cell membranes. These observations all show that, for the present thymocytes, the lateral structure of the membrane is considerably disordered by canceration. Furthermore, the calculated lateral self-diffusion coefficient of the lipid molecules in leukemic cell membranes was almost double that in normal cell membranes. The calculated rotational and wobbling autocorrelation functions also indicated that the molecular motion of the lipids was enhanced in leukemic cell membranes. Thus, here we have demonstrated that the membranes of thymocyte leukemic cells are more disordered and more fluid than normal cell membranes.
Biochimica et Biophysica Acta 01/2013; · 4.66 Impact Factor
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ABSTRACT: Free energy profile of a pair of cholesterol molecules in a leaflet of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayers in the liquid-crystalline phase has been calculated as a function of their lateral distance using a combination of NPT-constant atomistic molecular dynamics calculations (P = 1 atm and T = 310.15 K) and the thermodynamic integration method. The calculated free energy clearly shows that the two cholesterol molecules form a dimer separated by a distance of 1.0-1.5 nm in POPC bilayers. Well depth of the free energy profile is about 3.5 kJ/mol, which is comparable to the thermal energy k(B)T at 310.15 K. This indicates that the aggregation of cholesterol molecules in the bilayers depends on the temperature as well as the concentration of the system. The free energy function obtained here may be used as a reference when coarse grained potential model is investigated for this two-component system. Local structure of POPC molecules around two cholesterol molecules has also been investigated.
The Journal of chemical physics 04/2012; 136(15):155104. · 3.09 Impact Factor
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ABSTRACT: An all-atom molecular dynamics simulation of a spherical micelle composed of amphiphilic N-acetylated poly(ethylene glycol)-poly(gamma-benzyl L-glutamate) (PEG-PBLG-Ac) block copolymers was performed in aqueous solution at 298.15 K and 1 atm. Such copolymers have received considerable attention as carriers in drug delivery systems. In this study, we used copolymers consisting of 11 EG units and 9 BLG units as models. Starting from the copolymers arranged spherically, the calculation predicted an equilibrium state consisting of a slightly elliptical micelle structure with a hydrophobic PBLG inner core and a hydrophilic PEG outer shell. The micelle structure was dynamically stable during the simulation, with the PEG blocks showing a compact helical conformation and the PBLG blocks an alpha-helix form. Multiple hydrogen bonds with solvent water molecules stabilized the helical conformation of the PEG blocks, leading to their hydration as shown by longer residence times of water molecules near the PEG ether oxygen atoms compared with that of bulk water. Some water molecules have also been found distributed within the hydrophobic core; they showed continuous exchange with bulk water during the simulation. Those molecules existed mostly as a cluster in spaces between the copolymers, forming hydrogen bonds among themselves as well as with the hydrophobic core through hydrophilic groups such as esters and amides. The water molecules forming hydrogen bonds with the micelle may play an important role in the stabilization of the micelle structure.
The Journal of Physical Chemistry B 11/2009; 113(46):15181-8. · 3.70 Impact Factor
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ABSTRACT: The structures of continuous and truncated AgO chains on Ag(110) surfaces are studied by using density functional theory (DFT) calculations and the thermal fluctuations of truncated chains are simulated by using the Monte Carlo method. Although it is known that oxygen elimination by CO from one-dimensional AgO chains takes place exclusively at chain ends when the chains keep a linear structure at low temperatures, the structure of chain ends has been unexplored. The DFT calculations reveal that oxygen-terminated chains are more stable than silver-terminated ones and have an enhanced density of states near the Fermi level at the terminal oxygen, which is consistent with scanning tunneling microscope (STM) observations. The Monte Carlo simulations with pairwise interactions between AgO units reproduce characteristic features observed in STM studies, including the existence of an onset temperature for the chain fluctuations and the oxygen-coverage dependence of average chain length. The onset temperature, on one hand, is largely controlled by attractive interactions in the direction parallel to chain growth. On the other hand, the spatial distribution of fragmented AgO chains depends strongly on repulsive interactions in the direction perpendicular to chains. In particular, the repulsive interactions ranging ten units of the lattice constant in the direction perpendicular to the AgO chains are essential to mimic STM observations, where fragmented chains almost keep the mutual distance inherent to the (nx1)-O phase even under thermal fluctuations.
The Journal of chemical physics 11/2008; 129(15):154709. · 3.09 Impact Factor
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ABSTRACT: We present a quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution in the framework of mixed quantum-classical molecular dynamics, where the reactant and product states are explicitly defined by dividing the double-well potential into the reactant and product wells. The equation can describe quantum reaction processes such as tunneling and thermal excitation and relaxation assisted by the solvent. Fluctuations of the zero-point energy level, the height of the barrier, and the curvature of the well are all included in the equation. Here, the equation was combined with the surface hopping technique in order to describe the motion of the classical solvent. Applying the present method to model systems, we show two numerical examples in order to demonstrate the potential power of the present method. The first example is a proton transfer by tunneling where the high-energy product state was stabilized very rapidly by solvation. The second example shows a thermal activation mechanism, i.e., the initial vibrational excitation in the reactant well followed by the reacting transition above the barrier and the final vibrational relaxation in the product well.
The Journal of Chemical Physics 02/2008; 128(4):044507. · 3.33 Impact Factor
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The Journal of Chemical Physics 04/2007; 126(9):096101. · 3.33 Impact Factor
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Chemical Physics Letters 01/2007; 448(1-3):70. · 2.34 Impact Factor
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ABSTRACT: Free energy of micelle formation has been evaluated for spherical sodium dodecyl sulfate (SDS) in water by a thermodynamic integration method combined with a series of large-scale molecular dynamics calculations following the chemical species model. In particular, free energy change delta mu(n+1)0 with respect to the addition of one surfactant molecule to the spherical micelle of size n was obtained as a function of n. The free energy profile showed a minimum followed by a maximum, which corresponds to a peak in the size distribution. The calculated peak size n = 57 near its critical micelle concentration is in good agreement with the experimental averaged aggregation number n = 55-75 of the SDS micelle. The distribution showed a rather sharp peak, indicating that the size is almost a monodisperse one. The size is likely to be insensitive to the total concentration of the surfactant.
The Journal of Chemical Physics 06/2006; 124(18):184901. · 3.33 Impact Factor
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ABSTRACT: We present a surface hopping method for chemical reaction in solution based on diabatic representation, where quantum mechanical time evolution of the vibrational state of the reacting nuclei as well as the reaction-related electronic state of the system are traced simultaneously together with the classical motion of the solvent. The method is effective in describing the system where decoherence between reactant and product states is rapid. The diabatic representation can also give a clear picture for the reaction mechanism, e.g., thermal activation mechanism and a tunneling one. An idea of molecular orbital theory has been applied to evaluate the solvent contribution to the electronic coupling which determines the rate of reactive transition between the reactant and product potential surfaces. We applied the method to a model system which can describe complex chemical reaction of the real system. Two numerical examples are presented in order to demonstrate the applicability of the present method, where the first example traces a chemical reaction proceeded by thermal activation mechanism and the second examines tunneling mechanism mimicking a proton transfer reaction.
The Journal of Chemical Physics 04/2006; 124(9):94110. · 3.33 Impact Factor
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ABSTRACT: Mixed quantum-classical molecular dynamics method has been applied to vibrational relaxation of a hydrophilic model NO in supercritical water at various densities along an isotherm above the critical temperature. The relaxation rate was determined based on Fermi's golden rule at each state point and showed an inverse S-shaped curve as a function of bulk density. The hydration number was also calculated as a function of bulk density based on the calculated radial distribution function, which showed a good correlation with the relaxation rate. Change of the survival probability of the solute vibrational state was analyzed as a function of time together with the trajectory of the solvent water and the interaction with it. We will show that the solvent molecule resides near the solute molecule for a while and the solvent contributes to the relaxation by the random-noiselike Coulombic interaction only when it stays near the solute. After the solvent leaves the solute, it shows no contribution to the relaxation. The relaxation mechanism for this system is significantly different from the collisional one found for a nonpolar solute in nonpolar solvent in Paper I. Then, the relaxation rate is determined, on average, by the hydration number or local density of the solvent. Thus, the density dependence of the relaxation rate for the polar solute in supercritical water is apparently similar to that found for the nonpolar solute in nonpolar solvent, although the molecular process is quite different from each other.
The Journal of Chemical Physics 10/2005; 123(12):124509. · 3.33 Impact Factor
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ABSTRACT: In order to investigate vibrational relaxation mechanism in condensed phase, a series of mixed quantum-classical molecular dynamics calculations have been executed for nonpolar solute in nonpolar solvent and polar solute in polar solvent. In the first paper (Paper I), relaxation mechanism of I2 in Ar, where Lennard-Jones force is predominant in the interaction, is investigated as a function of density and temperature, focusing our attention on the isolated binary collision (IBC) model. The model was originally established for the relaxation in gas phase. A key question, here, is "can we apply the IBC model to the relaxation in the high-density fluid?" Analyzing the trajectory of solvent molecule as well as its interaction with the solute, we found that collisions between them may be defined clearly even in the high-density fluid. Change of the survival probability of the vibrationally first excited state on collision was traced. The change caused by collisions with a particular solvent molecule was also traced together with the interaction between them. Each collision makes a contribution to the relaxation by a stepwise change in the probability. The analysis clearly shows that the relaxation is caused by collisions even in the high-density fluid. The difference between stepwise relaxation and the continuous one found for the total relaxation in the low-density fluid and in the high-density one, respectively, was clarified to come from just the difference in frequency of the collision. The stronger the intensity of the collision is, the greater the relaxation caused by the collision is. Further, the shorter the collision time is, the greater the resultant relaxation is. The discussion is followed by the succeeding paper (Paper II), where we report that molecular mechanism of the relaxation of a polar molecule in supercritical water is significantly different from that assumed in the IBC model despite that the density dependence of the relaxation rate showed a linear correlation with the local density of water around the solute, the linear correlation being apparently in good accordance with the IBC model. The puzzle will be solved in Paper II.
The Journal of Chemical Physics 10/2005; 123(12):124508. · 3.33 Impact Factor
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ABSTRACT: Path integral influence functional theory has been applied to the dynamics of coherence between vibrational states of solute in condensed phase. First, time evolution of the off-diagonal term of the reduced density matrix rho(mn)(t) was algebraically described by the cumulant expansion of the perturbative influence functional. Then, the theory is compared with the Redfield theory, rearranging the present description in a familiar way to that found in the Redfield theory. A numerical example of the theory is presented for the vibrational dynamics of cyanide ion in water assuming a coherent state (1/radical2)(|0> + |1>) at t = 0. We find that Re rho(10)(t) oscillates with high frequency and shows a fast damping. Relaxation time of the oscillation amplitude is estimated to be 5.1 ps for a certain configuration of the solution. Then, secular approximation often used in the Redfield theory is found to work well, at least, in the present system. Population relaxation time for the first excited state and pure dephasing time may also be calculated from the component of Re rho(10)(t) to be 7.9 and 7.5 ps, respectively. Further, the many-particle measurement for Re rho(10)(t) gives the relaxation rate about three times faster than the single-measurement above. This comes from the inhomogeneity of the solute environment. We also found the fast oscillation in the diagonal part of the calculated density matrix, Re rho(11)(t). This oscillation is generated only when the initial density matrix includes the coherence.
The Journal of Chemical Physics 11/2004; 121(20):10052-64. · 3.33 Impact Factor
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ABSTRACT: Mixed quantum-classical molecular dynamics method has been applied to vibrational relaxation of CN − in water. The calculated relaxation time was compared with those based upon Fermi's golden rule with classical interaction and influence functional theory with classical bath. They are in good agreement with each other. Flexible water model adopted here enhanced the relaxation rate by a factor of about 5 compared with the rigid rotor model. This supports our previous result of path integral influence functional theory that intramolecular bending of water plays an essential role in the relaxation.
Molecular Simulation 10/2004; 30(13-15):835-839. · 1.33 Impact Factor
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ABSTRACT: Hydration structure and dynamics of sodium chenodeoxycholate (CDC) in water are studied by a long-time molecular dynamics calculation. Strong hydration shell around the hydrophobic region of this large solute and strong hydrogen bonds of water with both hydroxyl and carboxyl oxygen atoms have been identified. The rotation of CDC around its longitudinal axis is found to be particularly active in comparison with that around other axes of the molecule. The diffusion coefficient of CDC calculated from the slope of the mean-square displacement, 0.95 × 10−9 m2/s, is only 1/6 of that for water in the solution, 5.4 × 10−9 m2/s.
Chemical Physics Letters 420:489-492. · 2.34 Impact Factor
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ABSTRACT: Mixed quantum-classical molecular dynamics method has been applied to vibrational relaxation of CN− in water, where coulombic force is predominant in the interaction. The calculation demonstrated that time-dependent interaction between the solute vibrational degree of freedom and the solvent water shows random-noise-like behavior, no collisional or stationary coupling observed in gas or solid, respectively, being found. This is in contrast to the short-ranged-force system where the collision plays a dominant role in the relaxation. The interaction has been analyzed in detail as a function of time defining the effective coupling for the relaxation.
Journal of Molecular Liquids.
