Electrophoresis simulations using Chebyshev pseudo-spectral method on a moving mesh

We present the implementation and demonstration of the Chebyshev pseudo-spectral method coupled with an adaptive mesh method for performing fast and highly accurate electrophoresis simulations. The Chebyshev pseudo-spectral method offers higher numerical accuracy than all other finite difference methods and is applicable for simulating all electrophoresis techniques in channels with open or closed boundaries. To improve the computational efficiency, we use a novel moving mesh scheme that clusters the grid points in the regions with poor numerical resolution. We demonstrate the application of the Chebyshev pseudo-spectral method on a moving mesh for simulating nonlinear electrophoretic processes through examples of isotachophoresis (ITP), isoelectric focusing (IEF), and electromigration-dispersion in capillary zone electrophoresis (CZE) at current densities as high as 1000 A/m. We also show the efficacy of our moving mesh method over existing methods that cluster the grid points in the regions with large concentration gradients. We have integrated the adaptive Chebyshev pseudo-spectral method in the open-source SPYCE simulator and verified its implementation with other electrophoresis simulators.     

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.     

Design strategies for controlling the molecular weight and rate using reversible addition–fragmentation chain transfer mediated living radical polymerization

Living radical polymerization has allowed complex polymer architectures to be synthesized in bulk, solution, and water. The most versatile of these techniques is reversible addition–fragmentation chain transfer (RAFT), which allows a wide range of functional and nonfunctional polymers to be made with predictable molecular weight distributions (MWDs), ranging from very narrow to quite broad. The great complexity of the RAFT mechanism and how the kinetic parameters affect the rate of polymerization and MWD are not obvious. Therefore, the aim of this article is to provide useful insights into the important kinetic parameters that control the rate of polymerization and the evolution of the MWD with conversion. We discuss how a change in the chain‐transfer constant can affect the evolution of the MWD. It is shown how we can, in principle, use only one RAFT agent to obtain a polymer with any MWD. Retardation and inhibition are discussed in terms of (1) the leaving R group reactivity and (2) the intermediate radical termination model versus the slow fragmentation model. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3189–3204, 2005     

Tight‐binding molecular dynamics simulation of Si?H bond dissociation in silicon clusters

New model of Si? H bond dissociation is proposed and tested in the cluster Si₁₀H₁₆ by the simulation approach that combines classic molecular dynamics method and the self‐consistent tight‐binding electronic and total energy calculation one. It is shown that the monohydride Si? H bond is unstable with respect to silicon dangling bond and bend‐bridge Si? H? Si bond formation when this cluster traps the single positive charge and that hydrogen migrates through a path involving rather rotation around the Si? Si bond than the center of this bond (the bond‐centered position). These results can be useful for understanding hydrogen‐related phenomena at surfaces, interfaces, and internal voids of various hydrogenated silicon systems: electronic devices, silicon solar cells, and nanocrystalline and porous silicon. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 351–359, 2003     

Kinetics and equilibrium of multicomponent adsorption on chiraly templated surfaces

In this contribution we propose a simple model of adsorption of a binary (racemic) mixture on a chiraly templated surface. As an example, the adsorption of a liquid mixture of enantiomers on a chiral stationary phase (CSP) is considered. In particular, we study the effect of the lateral interactions in the adsorbed phase on the kinetic and equilibrium isotherms of the enantiomers. Additionally, we investigate the influence of the composition of the surface on the performance of the CSP in the presence of the lateral interactions. To that end, the adsorption of the mixture is modeled by using Monte Carlo simulations as well as by applying an analytical approach involving rate equations coupled with the Mean Field Approximation (MFA). The predictions of the theory are found to be in good agreement with the results of the simulations.     

Size and pH effect on electrical and conformational behavior of poly(acrylic acid): Simulation and experiment

Monte Carlo simulations, experimental titrations and fluorescence correlation spectroscopy experiments were used to investigate the conformational and electrical properties of polyacrylic acids (PAA). On the one hand, titration curves were calculated to get an insight into the role of pH on the degree of ionization and conformation of PAA chains. On the other hand, experimental potentiometric titrations of PAA were also achieved for different PAA molecular weights and compared to the calculated titration curves obtained by Monte Carlo coarse grained simulations. It was found that for a large range at intermediate PAA ionizations, a good correlation is obtained between experimental and simulations data thanks to the prominence of electrostatic interactions in this domain. The effect of ionic concentration and PAA molecular weight on the titration curves was also investigated. In order to get a better understanding of PAA conformational behavior, we also investigated PAA diffusion properties in aqueous solutions as a function of pH and ionic strength by fluorescence correlation spectroscopy (FCS), thanks to its high sensitivity to measure diffusion coefficients of tracer solutes. Good qualitative agreements were observed between experimental diffusivities and polymer properties calculated from MC simulations. It was shown that the high molecular weight PAA chains display more significant changes in diffusivity in agreement with the ionization degrees and conformational changes observed in the simulations.     

Simulations of the active transport of a neutral solute based on a kinase-channel-phosphatase topology

Simulations of coupled interactions involving two opposite enzymatic reactions, solute diffusions, and electrostatic interactions between membrane charges and charged solutes were conducted under a fixed kinase-channel-phosphatase (KCP) topology oriented from the outside to the inside of a porous membrane structure. Depending on the kinase and phosphatase locations, we recently demonstrated that an active transport of a phosphorylated substrate may occur via the opposite topology, that is, a PCK topology. The present analysis demonstrates that, under a KCP membrane topology, which also behaves as a specific ATP-dependent transporter, the active transport of a neutral substrate may occur. This analogous active transport appears to be dependent on the phosphatase location and on the membrane surface potentials. A broad analysis of the role played by the main parameters taken into account in the model was conducted in order to define precisely the physico-chemical conditions and the membrane topology needed for the highest active transports within the shortest time.     

Monte carlo calculations of the conformal charge

The conformal charge is an important quantity which characterizes the nature of the two-dimensional phase transition. We report a first attempt to use a new numerical method to calculate the conformal charge. In this paper, we apply our method to the 2-dimensional, ⁴, continuous-spin Ising model. By varying the parameters in the Hamiltonian, one can change continuously from the known Gaussian limit to the Ising limit. It is well known that the critical points for these two systems are not in the same universality class. We study this behavior for the Gaussian model, the single-well ⁴ model, the border model, and the double-well ⁴ model for a large lattice. Our results, while giving a good general picture, are not so far sufficient to differentiate whether the non-Gaussian cases studied belong to the Ising model universality class or not. Further studies of other lattice sizes should serve to improve greatly our conclusions.     

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.