Combining smart darting with parallel tempering using Eckart space: application to Lennard-Jones clusters

The smart-darting algorithm is a Monte Carlo based simulation method used to overcome quasiergodicity problems associated with disconnected regions of configurations space separated by high energy barriers. As originally implemented, the smart-darting method works well for clusters at low temperatures with the angular momentum restricted to zero and where there are no transitions to permutational isomers. If the rotational motion of the clusters is unrestricted or if permutational isomerization becomes important, the acceptance probability of darting moves in the original implementation of the method becomes vanishingly small. In this work the smart-darting algorithm is combined with the parallel tempering method in a manner where both rotational motion and permutational isomerization events are important. To enable the combination of parallel tempering with smart darting so that the smart-darting moves have a reasonable acceptance probability, the original algorithm is modified by using a restricted space for the smart-darting moves. The restricted space uses a body-fixed coordinate system first introduced by Eckart, and moves in this Eckart space are coupled with local moves in the full 3N-dimensional space. The modified smart-darting method is applied to the calculation of the heat capacity of a seven-atom Lennard-Jones cluster. The smart-darting moves yield significant improvement in the statistical fluctuations of the calculated heat capacity in the region of temperatures where the system isomerizes. When the modified smart-darting algorithm is combined with parallel tempering, the statistical fluctuations of the heat capacity of a seven-atom Lennard-Jones cluster using the combined method are smaller than parallel tempering when used alone.     

Monte Carlo simulations of biomolecules: The MC module in CHARMM

We describe the implementation of a general and flexible Monte Carlo (MC) module for the program CHARMM, which is used widely for modeling biomolecular systems with empirical energy functions. Construction and use of an almost arbitrary move set with only a few commands is made possible by providing several predefined types of moves that can be combined. Sampling can be enhanced by noncanonical acceptance criteria, automatic optimization of step sizes, and energy minimization. A systematic procedure for improving MC move sets is introduced and applied to simulations of two peptides. The resulting move sets allow MC to sample the configuration spaces of these systems much more rapidly than Langevin dynamics. The rate of convergence of the difference in free energy between ethane and methanol in explicit solvent is also examined, and comparable performances are observed for MC and the Nosé-Hoover algorithm. Its ease of use combined with its sampling efficiency make the MC module in CHARMM an attractive alternative for exploring the behavior of biomolecular systems.     

Complexation between a macromolecule and an amphiphile by Monte Carlo technique

Using a simple modified version of Larson's model, we studied the complexation between a macromolecule and an amphiphile in a dilute range of concentrations. The main characteristic of amphiphile molecules, that is, the hydrophobicity of the tails and hydrophilicity of the heads, is used to model the self-assembling process. Contrary to the molecular thermodynamics approaches, no prior shape was considered for the aggregates and the system was allowed to choose the most stable structure. For true ensemble averaging, without any synthetic results, configurational bias Monte Carlo and reptation moves are used to produce a Markov chain of configurations. From the results, it is found that the macromolecule causes the clusters of surfactants to be formed at a concentration much lower than the critical micelle concentration. Furthermore, the shape of the clusters tends to be more spherical, which is in line with theory and experiments. From the results, it is learned how a polymer can change the behavior of an amphiphilic molecule. All of the results are in good qualitative agreement with experimental and molecular thermodynamics results. Furthermore, the model predicts network formation between bound clusters at high concentrations of the surfactant.     

One-dimensional model for water and aqueous solutions. I. Pure liquid water

Two simplified one-dimensional models for waterlike particles are studied. One is referred to as the primitive model which is a simplified version of a model introduced by Ben-Naim in 1992 [Statistical Thermodynamics for Chemists and Biochemists (Plenum, New York, 1992)]. The second, referred to as the primitive cluster model, is a simplified version of the model used by Lovett and Ben-Naim in 1969 [J. Chem. Phys. 51, 3108 (1969)]. The two models are shown to be nearly equivalent and both exhibit some of the most characteristic behavior of liquid water. It is argued that a key feature of the molecular interactions--the correlation between the strong binding energy and low local density--is essential for the manifestation of the anomalous behavior of liquid water. It is also essential for the understanding of the outstanding behavior of liquid water.     

Monte Carlo simulation of freely jointed chains with variable bond lengths

Monte Carlo simulation of freely jointed off-lattice chains with variable bond length is usually done with local random displacements of beads and with reptation moves (displacements of a bead along a chain). In dense systems, the acceptance ratio of reptations decreases strongly with density. We discuss versions of reptation moves, which are effective in dense systems. The idea, which comes from lattice systems, is to use a pseudovacancy (walker), which has the same size as a bead of a chain. The walker is attached to a neighbor chain and then another bead of that chain is cleaved. This is equivalent to a reptation move and a nonlocal displacement of the walker and since no free volume is needed, the move can be used with advantage in dense systems. A related technique are cooperative motions, which were introduced by T. Pakula for lattice models, where several chains change their conformation concomitantly. Such cooperative loops are implemented in the Monte Carlo algorithm by creating a temporary walker by cleaving a bead from a chain, moving it with reptations and finally annihilating the walker by attaching it to the same chain it was cleaved from. These moves and the condition of detailed balance are discussed in detail. As an example, we study the integrated autocorrelation time τ_int for the radius of gyration for a two-dimensional system. For reduced densities larger than 0,4, we find that with standard reptations and local bead displacements τ_int increases strongly with density. If reptations with either a permanent or a temporary walker are used in addition to local moves, the integrated autocorrelation time changes only very little with density and very dense systems can still be simulated efficiently.     

Computerized simulation of aerosol-droplet desolvation in an inductively coupled plasma

A mathematical model for the desolvation of solvent droplets has been used in conjunction with an existing code for simulation of ICP fundamental parameters. The combination has been used for the calculation of droplet histories and desolvation behavior along the central channel of an ICP. Calculations have been performed for droplets of various sizes and under a variety of ICP operating conditions. As central-channel gas flow rate increases, the point of complete desolvation of the droplet shifts upward in the plasma, away from the load coil. This relationship is fairly linear. As forward power increases, the point of complete desolvation moves down in the discharge, closer to the load coil. This is approximately an inverse relationship. Finally, simulation of behavior for a log-normal size distribution of a large number of droplets (10⁸) shows that the number of surviving droplets falls sigmoidally with height above the load coil. For most nebulizer/spray chamber systems, the desolvation process is complete at a well-defined height in the plasma.     

Multiparticle moves in acceptance rate optimized monte carlo

Molecular Dynamics (MD) and Monte Carlo (MC) based simulation methods are widely used to investigate molecular and nanoscale structures and processes. While the investigation of systems in MD simulations is limited by very small time steps, MC methods are often stifled by low acceptance rates for moves that significantly perturb the system. In many Metropolis MC methods with hard potentials, the acceptance rate drops exponentially with the number of uncorrelated, simultaneously proposed moves. In this work, we discuss a multiparticle Acceptance Rate Optimized Monte Carlo approach (AROMoCa) to construct collective moves with near unit acceptance probability, while preserving detailed balance even for large step sizes. After an illustration of the protocol, we demonstrate that AROMoCa significantly accelerates MC simulations in four model systems in comparison to standard MC methods. AROMoCa can be applied to all MC simulations where a gradient of the potential is available and can help to significantly speed up molecular simulations. © 2015 Wiley Periodicals, Inc.     

Reaction and mass transfer effects in a catalytic monolith reactor

Zeolite-based monoliths (Cu/ZSM-5 on cordierite) are prepared and used to catalyze direct decomposition of nitrogen monoxide. Two-dimensional heterogeneous model is applied to describe the behavior of the monolith reactor, with the emphasis on the features introduced due to coupling of flow, mass transfer and chemical reaction. The proposed model has been verified by comparing computer simulation data with laboratory experimental data. It is shown that both inter- and intraphase diffusion limitations have to be considered when modeling complex reactor configuration, such as monolith reactors, especially when monolith with thicker catalytic layer are used at higher temperatures.     

Improvement in molecule exchange efficiency in Gibbs ensemble Monte Carlo: development and implementation of the continuous fractional component move

The continuous fractional component Monte Carlo (CFC MC) move (J Chem Theory Comput, 2007, 3, 1451) is extended to the Gibbs ensemble. The algorithm is validated against conventional simulations for the Lennard Jones fluid and a flexible water model. The method is also used to compute the vapor-liquid coexistence densities of a model for SO(2). The CFC molecule exchange move relies on the gradual insertion and deletion of molecules in conjunction with a self-adapting bias potential. As a result, the method does not require the formation of spontaneous voids in the dense fluid phase to be successful, leading to molecule exchange acceptance probabilities that are nearly independent of temperature. For example, over 1% of the vapor-liquid molecule exchange moves are successful for water at 280 K, whereas advanced rotational and configurational bias methods have success rates of less than 0.03%. The CFC move can be combined with other Monte Carlo moves to enable efficient simulation of dense strongly associating fluids that are to this point infeasible to model with standard methods.     

The Effect of Anomeric Head Groups, Surfactant Hydrophilicity, and Electrolytes onn-Alkyl Monoglucoside Microemulsions

The effects of the variables of head group structure and salt concentration on microemulsions formed in mixtures of water, alkyl ethylene glycol ethers (C_kOC₂OC_k), andn-alkyl β- -glucopyranosides (C_mβG₁) are explored. Phase behavior of mixtures containing an anomer of the surfactant (n-alkyl α- -glucopyranoside, C_mαG₁), or surfactants with long head groups (n-alkyl maltopyranosides, C_mG₂), or NaCl or NaClO₄as electrolyte are systematically reported as a function of temperature and composition. The substitution ofn-alkyl α- -glucopyranosides forn-alkyl β- -glucopyranosides causes precipitation under some conditions in all mixtures studied. These solubility boundaries begin in the water–surfactant binary mixture at the Krafft boundary, then extend to high concentrations of both surfactant and oil. Increasing the effective length of the surfactant head group by adding C_mG₂to water–C_kOC₂OC_k–C_mβG₁mixtures moves the phase behavior dramatically up in temperature when even small amounts of C_mG₂are used. Adding a lyotropic electrolyte, NaCl, to water–C_kOC₂OC_k–C_mβG₁mixtures moves the phase behavior down in temperature, while the hydrotropic electrolyte NaClO₄moves the phase behavior up in temperature.     

pH-zone-refining counter-current chromatography: Origin,mechanism, procedure and applications

Since 1980, high-speed counter-current chromatography (HSCCC) has been used for separation and purification of natural and synthetic products in a standard elution mode. In 1991, a novel elution mode called pH-zone refining CCC was introduced from an incidental discovery that an organic acid in the sample solution formed the sharp peak of an acid analyte. The cause of this sharp peak formation was found to be bromoacetic acid present in the sample solution which formed a sharp trailing border to trap the acidic analyte. Further studies on the separation of DNP-amino acids with three spacer acids in the stationary phase revealed that increased sample size resulted in the formation of fused rectangular peaks, each preserving high purity and zone pH with sharp boundaries. The mechanism of this phenomenon was found to be the formation of a sharp trailing border of an acid (retainer) in the column which moves at a lower rate than that of the mobile phase. In order to facilitate the application of the method, a new method was devised using a set of retainer and eluter to form a sharp retainer rear border which moves through the column at a desired rate regardless of the composition of the two-phase solvent system. This was achieved by adding the retainer in the stationary phase and the eluter in the mobile phase at a given molar ratio. Using this new method the hydrodynamics of pH-zone-refining CCC was diagrammatically illustrated by three acidic samples. In this review paper, typical pH-zone-refining CCC separations were presented, including affinity separations with a ligand and a separation of a racemic mixture using a chiral selector in the stationary phase. Major characteristics of pH-zone-refining CCC over conventional HSCCC are as follows: the sample loading capacity is increased over 10 times; fractions are highly concentrated near saturation level; yield is improved by increasing the sample size; minute charged compounds are concentrated and detected at the peak boundaries; and elution peaks are monitored with a pH flow meter for compounds with no chromophore. Since 1994, over 70 research papers on pH-zone-refining CCC have been published with the trends increasing in the recent years.     

Textural characteristics,surface chemistry and oxidation of activated carbon

Numerous researches were reviewed and interpreted to depict a comprehensive illustration of activated carbon and its behavior towards oxidation.Activated carbon as one of the most important adsorbents is tried to be described in this review paper by terms of its"Textural Characteristics"and"Surface Chemistry".These two terms,coupled with each other,are responsible for behavior of activated carbon in adsorption processes and in catalytic applications.Although as-prepared activated carbons are usually nonselective and their surfaces suffer from lack of enough reactive groups,their different aspects may be improved and developed by diverse types of modifications.Oxidation is one of the most conventional modifications used for activated carbons.It may be used as a final modification or as a pre-modification followed by further treatment.In this paper,methods of oxidation of activated carbon and other graphene-layer carbon materials are introduced and wet oxidation as an extensively-used category of oxidation is discussed in more detail.     

Textural characteristics, surface chemistry and oxidation of activated carbon

Numerous researches were reviewed and interpreted to depict a comprehensive illustration of activated carbon and its behavior towards oxidation. Activated carbon as one of the most important adsorbents is tried to be described in this review paper by terms of its "Textural Characteristics" and "Surface Chemistry". These two terms, coupled with each other, are responsible for behavior of activated carbon in adsorption processes and in catalytic applications. Although as-prepared activated carbons are usually non-selective and their surfaces suffer from lack of enough reactive groups, their different aspects may be improved and developed by diverse types of modifications. Oxidation is one of the most conventional modifications used for activated carbons. It may be used as a final modification or as a pre-modification followed by further treatment. In this paper, methods of oxidation of activated carbon and other graphene-layer carbon materials are introduced and wet oxidation as an extensively-used category of oxidation is discussed in more detail.     

Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: chain breakage/closure algorithm and associated Jacobians

This article describes a method for solving the geometric closure problem for simplified models of nucleic acid structures by using the constant bond lengths approximation. The resulting chain breakage/closure equations, formulated in the space of variable torsion and bond angles, are easy to solve, and have only two solutions. The analytical simplicity is in contrast with the high complexity of the closure problem in the torsion angle space with at most 16 solutions, which has been dealt with by several authors and was solved analytically by Wu and Deem (J. Chem. Phys. 1999, 111, 6625). The discussion on the choice of variables and associated Jacobians is focussed on the question of how conformational equilibration is affected in Monte Carlo simulations of molecular systems. In addition to the closure of the phosphate backbone, it is necessary to also solve the closure problem for the five-membered flexible furanose sugar ring. Explicit closure equations and the resulting Jacobians are given both for the complete four-variable model of the furanose ring and simulations in the phase-amplitude space of the five-membered ring, which are based on the approximate two-variable model of furanose introduced by Gabb et al. (J. Comput. Chem. 1995, 16, 667). The suggested closure algorithm can be combined with collective variables defined by translations and rotations of the monomeric nucleotide units. In comparison with simple internal coordinate moves, the resulting concerted moves describe local structural changes that have high acceptance rates and enable fast conformational equilibration. Appropriate molecular models are put forward for prospective Monte Carlo simulations of nucleic acids, but can be easily adapted to other biomolecular systems, such as proteins and lipid structures in biological membranes.     

Stability analysis and scattering properties of charged crosslinked blends in solution

The phase behavior and scattering properties of crosslinked charged polymer blends in solution are examined. De Gennes' analogy between the effects of crosslinks in a network and electrostatic charges in a dielectric medium on the scattering properties and the phase behavior of crosslinked polymer blends is used. This analogy is extended to include the effects of screening in order to improve its agreement with the experimental data in the small q range. The excluded volume interactions are explicitely introduced through the blob model. The enhancement of compatibility of the mixture and the increase of its rigidity constant are evaluated in certain cases. The limit of neutral polymers is discussed because it corresponds to the case of charged mixtures in the presence of excess salt. The kinetics of the microphase separation transition is briefly discussed. A dynamical model including the long range hydrodynamic interaction is presented. The relaxation frequency of the stable modes and the growth rate of unstable ones are also considered.     

Evolution of defect states in doped polythiophene: A study based on the method of simulated annealing

A modified Su–Schrieffer–Heeger Hamiltonian‐based model is used to compute the electronic and geometric structures of fairly long polythiophene (PT) chains, neutral as well as doped. The geometry optimization is carried out by the simulated annealing method. Both Metropolis and Glauber functions are used for sampling. It is shown that a bipolaron can be structurally represented by a fragment of the PT chain containing 14 thiophene units. As a series of bipolaronic defects are introduced in a long PT chain (50–100 rings), the highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap energy (Δ) becomes vanishingly small, a feature not present in the PT chains of similar sizes containing polaronic defects. The Fermi energy level (E_F) also moves into the valency band and nonzero density of states at ? = E_F are created. Once again, this feature is shown to be missing in PT chains containing polaronic defects. Implications of these findings are analyzed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003