An improved hybrid continuum‐atomistic four‐way coupled model for electrokinetics in nanofluidics

In this study, an efficient hybrid continuum‐atomistic method is proposed to study electrokinetic transport of aqueous solutions in nanofluidics. The aqueous phase is considered as a continuous phase containing immersed ion particles. The behavior of the system is then simulated through utilization of an improved hybrid continuum‐atomistic four‐way coupled approach, including the MultiPhase Particle‐In‐Cell method for the short‐ranged interaction between the ion particles, the Brownian force for the collision between the aqueous phase molecules and the ion particles, and a wall force accounting for the short‐ranged interaction of ions and walls. The validation of the proposed model with the results of Molecular Dynamics simulations suggests that this model can be a promising approach for studying the electrokinetic phenomena in more complicated geometries where the Molecular Dynamics approach is computationally prohibitive. Finally, the effects of electrokinetic parameters, such as the height of the channel, the external electric field, and bulk ionic concentration, on the electroosmotic flow in a nanochannel are investigated and discussed.     

Particle trapping in electrically driven insulator-based microfluidics: Dielectrophoresis and induced-charge electrokinetics

Electrokinetically driven insulator-based microfluidic devices represent an attractive option to manipulate particle suspensions. These devices can filtrate, concentrate, separate, or characterize micro and nanoparticles of interest. Two decades ago, inspired by electrode-based dielectrophoresis, the concept of insulator-based dielectrophoresis (iDEP) was born. In these microfluidic devices, insulating structures (i.e., posts, membranes, obstacles, or constrictions) built within the channel are used to deform the spatial distribution of an externally generated electric field. As a result, particles suspended in solution experience dielectrophoresis (DEP). Since then, it has been assumed that DEP is responsible for particle trapping in these devices, regardless of the type of voltage being applied to generate the electric field—direct current (DC) or alternating current. Recent findings challenge this assumption by demonstrating particle trapping and even particle flow reversal in devices that prevent DEP from occurring (i.e., unobstructed long straight channels stimulated with a DC voltage and featuring a uniform electric field). The theory introduced to explain those unexpected observations was then applied to conventional “DC-iDEP” devices, demonstrating better prediction accuracy than that achieved with the conventional DEP-centered theory. This contribution summarizes contributions made during the last two decades, comparing both theories to explain particle trapping and highlighting challenges to address in the near future.     

Hybrid mechanistic approach in the estimation of flow properties in cylindrical membrane modules

A hybrid computational approach was employed for simulation of molecular separation using polymeric membranes. The considered system is a cylindrical membrane module in which the mass transfer equations were solved numerically using CFD (Computational Fluid Dynamics) to obtain the concentration of the species, and then the simulation results were used in machine learning models. Indeed, the CFD simulation results were used as the inputs for several machine learning models to obtain the hybrid model. We have a dataset with more than 2000 data points and two input features (r and z). Also, the only output is C which is the concentration of the species in the feed channel of membrane module. KNN (K nearest neighbor), PLSR (Partial Least Square Regression), and SGD (Stochastic Gradient Descent) are the models employed in this research to analyze the mentioned data set. Models were optimized with their hyper-parameters and finally evaluated with different statistical metrics. MAE error metric is 3.4, 5.1, and 5.5 for KNN, SGD, and PLSR. Also, they have 0.998, 0.997, 0.896 coefficient of determination (R²) respectively. Finally, based on the overall results, KNN with K = 8 is selected as the best model in this study for simulation of the membrane system. The final maximum error is also 1.35E+02.     

The Inject-Mix-React-Separate-and-Quantitate (IMReSQ) approach to studying reactions in capillaries

A capillary or a narrow channel is an attractive medium for studying reactions. A capillary can serve as (i) a microreactor for carrying out a reaction in a nanoliter volume and (ii) a separation column to separate the reaction products prior to their quantitation. The term “Inject-Mix-React-Separate-and-Quantitate” (IMReSQ) includes all analyses of reactions in capillaries that involve these five steps. We analyze these steps in detail and formulate the requirements for them to be generic and quantitative.     

Unbound exciton–phonon states in oligothiophene crystals – A model approach for spectroscopic purposes

A simple model of exciton–phonon interaction in a crystal with one molecule in the unit cell is used to simulate some peculiar features of the oligothiophene absorption spectra. The model is treated in the limit of weak vibronic coupling, and the configuration interaction between the intense zero-phonon Frenkel state and the one-phonon continuum is described in terms of the Fano formalism. The good agreement between the calculated curve and a part of the experimental absorption profile allows one to discriminate some features that are physically relevant but are not accounted for in the model.     

A new approach to control the dispersion of platinum nanoparticles in a metal oxide coating

The present work shows the feasibility of preparing transparent titania coatings being doped with platinum nanoparticles by sol–gel processing. The used platinum nanoparticles are modified by two different functional thiol ligands, mercaptoethanol and mercaptopropionic acid. The functional ligands are used to create a nanoparticle network and they can also promote anchorage of titanium alkoxides as sol–gel precursors, ensuring a regular distribution of the metal nanoparticles within the coating as well as a good stability to the film.     

Hybrid Monte Carlo — Fluid model for studying the effects of nitrogen addition to argon glow discharges

A computer model is developed for describing argon/nitrogen glow discharges. The species taken into account in the model include electrons, Ar atoms in the ground state and in the 4s metastable levels, N₂ molecules in the ground state and in six different electronically excited levels, N atoms, Ar⁺ ions, N⁺, N₂⁺, N₃⁺ and N₄⁺ ions. The fast electrons are simulated with a Monte Carlo model, whereas all other species are treated in a fluid model. 74 different chemical reactions are considered in the model. The calculation results include the densities of all the different plasma species, as well as information on their production and loss processes. The effect of different N₂ additions, in the range between 0.1 and 10%, is investigated.     

A generalized Langevin dynamics approach to model solvent dynamics effects on proteins via a solvent-accessible surface. The carboxypeptidase A inhibitor protein as a model

A generalized Langevin dynamics (GLD) scheme is derived for (bio)macromolecules having internal structure, arbitrary shapes and a size larger than solvent molecules (i.e. proteins). The concept of solvent-accessible surface area (SASA) is used to incorporate solvent effects via external forces thereby avoiding its explicit molecular representation. A simulation algorithm is implemented in the GROMOS molecular dynamics (MD) program including random forces and memory effects, while solvation effects enter via derivatives of the surface area. The potato carboxypeptidase inhibitor (PCI), a small protein, is used to numerically test the approach. This molecule has N- and C-terminal tails whose structure and fluctuations are solvent dependent. A 1-ns MD trajectory was analyzed in depth. X-ray and NMR structures are used in conjunction with MD simulations with and without explicit solvent to gauge the quality of the results. All the analyses showed that the GLD simulation approached the results obtained for the MD simulation with explicit simple-point-charge-model water molecules. The SASAs of the polar atoms show a natural exposure towards the solvent direction. A FLS solvent simulation was completed in order to sense memory effects. The approach and results presented here could be of great value for developing alternatives to the use of explicit solvent molecules in the MD simulation of proteins, expanding its use and the time-scale explored. Received: 2 February 2000 / Revised: 12 March 2000 / Accepted: 26 May 2000 / Published online: 2 November 2000     

Chemical approach to neutral–ionic valence instability,quantum phase transition,and relaxor ferroelectricity in organic charge-transfer complexes

Neutral–ionic (NI) phase transition is a reversible switching of organic charge-transfer complexes between distinct valence states by external stimuli. This phase transformation in the low-dimensional system is demonstrated to provide a variety of novel dielectric, structural, and electronic properties. Importantly, ionization of the electron donor–acceptor pairs is usually accompanied by a ferroelectric or antiferroelectric order of the molecular lattice, leading to huge dielectric response near the transition point. Although these characteristics are potentially useful for future electronic and optical applications, the thermally accessible NI transition (TINIT) is still an extremely rare case. The TINIT compounds including some new materials are overviewed in order to provide convenient guides to their design and experimental identifications. The phase transition and dielectric properties can be closely controlled in various ways depending on chemical and physical modifications of the crystals. Among them, a quantum phase transition and relaxor ferroelectricity, both of which are currently attracting subjects from both scientific and practical perspectives, are highlighted as the first achievements in organic charge-transfer complexes.     

A novel approach to measure all rate constants in the simplest enzyme kinetics model

Enzymes play vital roles in life processes. Almost all biochemical reactions are mediated by enzymes. The rate constants of enzyme kinetics are the most important parameters for the reactions catalyzed by enzymes. In 1902, Adrian Brown proposed a simple single-substrate-single-product model which contains only three rate constants k ₁, k ₋₁ and k ₂. So far, biologists can measure the Michaelis constant K _M and the catalytic constant k _cat , which actually is equal to k ₂, according to Michaelis–Menten equation. Using temperature jump method or transient state kinetics, k ₁, k ₋₁ and k ₂ can be determined. However, these methods are complicated. In this article, we design a novel simple method that could determine the rate constants k ₁ and k ₋₁ based on knowing k _cat and K _M . Our numerical experiments show that the three rate constants can be calculated rather precisely. Hence, we believe that biochemists could design experiments to measure the rate constants based on our method. This work was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 10771206 and partially by 973 project (2004CB318000) of P. R. China.     

Simple and commercial readily-available approach for the direct use of ionic liquid-based single-drop microextraction prior to gas chromatography: Determination of chlorobenzenes in real water samples as model analytical application

A simple and commercial readily-available approach that enables the direct use of ionic liquid (IL)-based single-drop microextraction (SDME) prior to gas chromatography (GC) is presented. The approach is based on thermal desorption (TD) of the analytes from the IL droplet to the GC system, by using a robust and commercially-available thermodesorption system. For this purpose, a two-glass-tube concentrically disposed system was designed. The inner tube is a laboratory-cut Pyrex tube (20 mm length) that houses the ionic liquid droplet from the SDME process, and the outer tube is a commercially-available TD glass tube (187 mm length) commonly employed for stir-bar sorptive extractions (SBSE). In this way, the proposed device prevents IL from entering the GC system, as this could dirty the inlet or even block the column. The determination of 10 chlorobenzenes in water samples by GC coupled with mass spectrometric (MS) detection has been chosen as model analytical application, showing the feasibility of the proposed approach. The SDME process consists of a 5 μL droplet of 1-hexyl-3-methylimidazolium hexafluorophosphate ([C₆MIM][PF₆]) suspended in the headspace (HS) of a 10 mL stirred sample. After extracting for 37 min at room temperature, the IL droplet is directly placed into the small inner tube, which is placed into the TD tube. The whole device is placed inside the TD unit, where desorption of the analytes is performed at 240 °C for 5 min with a helium flow rate of 100 mL min⁻¹. The analytical figures of merit of the proposed IL-(HS)-SDME-TD-GC–MS approach are very suitable for the determination of chlorobenzenes at ultratrace levels, with relative standard deviation values ranging between 2% and 17%, and limits of detection ranging between 1 and 4 ng L⁻¹, showing the potential offered by the IL-based SDME process with GC.     

A holomorphic representation approach to the regularization of model field theories in coupled cluster form

Summary We explain in detail the so-called Bargmann or holomorphic representation, and apply it to the general class of single-mode bosonic field theories. Since these model field theories have no attribute of separability and are, in some sense, maximally nonlocal, they are an especially severe test of the capability of coupled cluster methods to parametrize them satisfactorily. They include the cases of anharmonic oscillators of order 2K (K=2, 3,...), for which ordinary perturbation theory is known to diverge, and we therefore make a special study of such systems. We demonstrate for the first time for any quantum-mechanical problem with infinite Hilbert space that both the normal and extended coupled cluster methods (NCCM and ECCM) have phase spaces which rigorously exist. We analyze completely the asymptotic properties of the complete sets of the NCCM and ECCM amplitudes, either of which fully characterizes the system. It is thereby shown how the holomorphic representation can be used to regularize completely all otherwise formally divergent series that appear. We demonstrate in detail how the entire NCCM and ECCM programmes can be carried through for these systems, including the diagonalization of the classically mapped Hamilitonians in the respective classical NCCM and ECCM phase spaces.     

Layer model approach to background correction in r.f.‐GDOES

Two methods are presented for dealing with variable background signals in radiofrequency glow discharge optical emission spectroscopy (r.f.‐GDOES). Their aim is to improve elemental analysis at trace levels, in bulk analysis or in compositional depth profiling, without having to measure background signals during the analysis. Each method uses background signals measured away from the analytical emission lines of interest during calibration only. The background signal is first determined during calibration for each material type of interest. During analysis in the first method the estimated background signal is varied according to the material type being analysed. In depth profiles this means identifying the various layers present as different material types, hence the name ‘layer model’. The second method is a more conventional approach, where part of the background signal is estimated as a spectral interference. Results are presented for the bulk analysis of a tool steel and for two depth profiles: TiO₂ coating on silicon and TiN‐coated tool steel. The two methods give similar results in the depth profiles, both significantly better than with a constant background. Copyright © 2004 John Wiley & Sons, Ltd.     

The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents

A simple strategy to compose a new all-atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (E(TOTAL)) is divided into three components; a single amino acid potential term (E(SAAP)), an interamino acid nonbonded interaction term (E(INTER)), and a miscellaneous term (E(OTHERS)), which is ignored (or considered to be constant) at the current version of the force field. The E(INTER) term consists of electrostatic interactions (E(ES')) and van der Waals interactions (E(LJ')). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of For-Ala(2)-NH(2) in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for For-Gly(10)-NH(2) and For-Ala(10)-NH(2) showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (E(TOTAL)) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the E(SAAP) term) may play definitive roles on the topologies of protein secondary structures.     

Development of a systematic approach to rapid classification and identification of notoginsenosides and metabolites in rat feces based on liquid chromatography coupled triple time-of-flight mass spectrometry

The present work contributes to the development of a powerful technical platform to rapidly identify and classify complicated components and metabolites for traditional Chinese medicines. In this process, notoginsenosides, the main active ingredients in Panaxnotoginseng, were chosen as model compounds. Firstly, the fragmental patterns, diagnostic product ions and neutral loss of each subfamily of notoginsenosides were summarized by collision-induced dissociation analysis of representative authentic standards. Next, in order to maximally cover low-concentration components which could otherwise be omitted from previous diagnostic fragment-ion method using only single product ion of notoginsenosides, a multiple product ions filtering strategy was proposed and utilized to identify and classify both non-target and target notoginsenosides of P.notoginseng extract (in vitro). With this strategy, 13 protopanaxadiol-type notoginsenosides and 30 protopanaxatriol-type notoginsenosides were efficiently extracted. Then, a neutral loss filtering technique was employed to trace prototype components and metabolites in rats (in vivo) since diagnostic product ions might shift therefore become unpredictable when metabolic reactions occurred on the mother skeleton of notoginsenosides. After comparing the constitute profiles in vitro with in vivo, 62 drug-related components were identified from rat feces, and these components were classified into 27 prototype compounds and 35 metabolites. Lastly, all the metabolites were successfully correlated to their parent compounds based on chemicalome–metabolome matching approach which was previously built by our group. This study provided a generally applicable approach to global metabolite identification for the complicated components in complex matrices.     

An anisotropic coarse‐grained model based on Gay–Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model

In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay–Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay–Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness (), area per lipid ( ) and volume per lipid ( ). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model. © 2015 Wiley Periodicals, Inc.     

A symmetry-based approach to the heterobicyclic core of the zaragozic acids—model studies in the C2-symmetric series

A conceptually novel access to models for the title structures has been achieved by rapid enantioselective construction of polyhydroxy diketones in a two-directional or convergent fashion and group-selective intramolecular acetalization.     

New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).     

Another approach to the interpretation of various macrophenomena simulated in terms of the properties of the model bodies involved in them and their elementary interactions. I. Gaseous media

In this study attention has been focused on the physical nature of molecular interactions regarded as the function of various properties of the involved molecules and giving rise both to individual pressure impulses () and to variations of their frequency at a constant gas concentration and temperature. The corresponding elementary thermal interactions () have also been taken into account. The quantities and are considered to be of the same physical nature but of different magnitudes. The empirical Van der Waals equation of state for the real gases has been reinterpreted in terms of the elementary interactions. The theoretical predictions following from the developed approach have been compared with and satisfactorily confirmed by the corresponding experimental data available in the relevant literature.