Towards a force field based on density fitting

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.     

Self-assembly mechanism based on charge density topological interaction energies

The packing interactions have been evaluated in the context of the self-assembly mechanism of crystal growth and also for its impacts on the aromaticity of the trimesate anion. The structure of ethylammonium trimesate hydrate (1) measured at 100 K and a charge density model, derived in part from theoretical structures, is reported. Theoretical structure factors were obtained from the geometry-optimized periodic wave function. The trimesic acid portion of 1 is fully deprotonated and participates in a variety hydrogen bonding motifs. Topological analysis of the charge density model reveals the most significant packing interactions and is then compared to a complementary analysis performed by the Hirshfeld surface method. The results presented herein demonstrate that in organic salt crystals the small structural motifs are most stable and once formed as stand-alone structures, may direct the self-assembly process. Moreover, when intermolecular interactions supported by the electrostatic forces are analyzed, the care must be taken with interpretation of the results of Hirshfeld surface analysis for organic salts crystals.     

Multiscale modeling of biological functions

Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed.     

Impact of surface charge density and motor force upon polyelectrolyte packaging in viral capsids

By means of Langevin molecular dynamics simulations, we study the packaging dynamics of flexible and semiflexible polyelectrolytes in spherical cavities that resemble viral capsids. We employ a coarse‐grained model of the polymer–capsid complex that allows us to perform simulations of a 900mer and investigate the influence of surface charges inside the capsid and an additional motor force, acting on the polymer in the portal region of the cavity, on the packaging process. Our results indicate that it is most efficient if surface charges are present that initially promote the formation of an ordered surface layer inside the capsid. Once these charges are screened, the motor force pulls in the remaining part of the chain. Additionally, the simulations also demonstrate that the packaging dynamics depends on the counterion valence. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1054–1065     

The relation of harmonic force constant and charge density in bonding region for diatomic molecules

The perfectly following density (PFD) model of Anderson and Parr is used to formulate semiempirical model relatings electron density at the saddle point to the harmonic force constant of the diatomic molecule. The most importants of the model are shortly discussed.     

Comparison of direct and flow integration based charge density population analyses

Different exhaustive and fuzzy partitions of the molecular electron density (rho) into atomic densities (rho(A)) are used to compute the atomic charges (Q(A)) of a representative set of molecules. The Q(A)'s derived from a direct integration of rho(A) are compared to those obtained from integrating the deformation density rho(def) = rho - rho(0) within each atomic domain. Our analysis shows that the latter methods tend to give Q(A)'s similar to those of the (arbitrary) reference atomic densities rho(A)(0) used in the definition of the promolecular density, rho(0) = SigmaArho(A)(0). Moreover, we show that the basis set independence of these charges is a sign not of their intrinsic quality, as commonly stated, but of the practical insensitivity on the basis set of the atomic domains that are employed in this type of methods.     

Multiscale description of polymeric foam behavior: A new approach based on discrete element modeling

The mechanical behavior of polymeric foams depends on several parameters, such as temperature, material density, and strain rate. The studied foams are multiscale materials; agglomerated beads (bead scale is millimetric) are composed of microscopic closed cells (a few tens of microns). The response of the material to dynamic loading consists of three regions: an elastic phase, a plastic phase, and densification. The first part of this work has been the identification of the behavior of these multiscale foams in terms of density and strain rate. Some results are presented in this paper. From these first dynamic results, the second step has been the observation and the analysis of the physical phenomena initiated during the yield plateau. Buckling of the bead and cell wall and strong damage localization were studied with several devices and techniques such as high-speed camera, SEM, and microtomography. The final objective is the development of a model adapted to the multiscale structure of the foam. The first step of this numerical approach consists in the modeling of the microstructure. Due to the microscopic discrete aspect of the foam, a Discrete Element Model has been developed to study the relationship between microscopic properties and the macroscopic behavior of foam. Published in Russian in Vysokomolekulyarnye Soedineniya, Ser. A, 2008, Vol. 50, No. 6, pp. 1037–1050. This article was submitted by the authors in English.     

Influence of mechanical properties of pectin films on charge density and charge density distribution in pectin macromolecule

The hydration and mechanical properties of citrus pectin films were examined in conditions relevant to those in the plant cell wall. The pectins used for this study varied in the degree of esterification (DE) (high or low) and charge distribution on the backbone (random or block). The hydration of the films was controlled in an osmotic pressure experiment using polyethylene glycol solutions (PEG 20000). Hysteresis tests at constant deformation rate (stress vs deformation) were used for investigating the mechanical behaviour of films. Mechanical and hydration properties of pectin films were examined as a function of charge density, charge density distribution and counterion environment—K⁺, Ca²⁺, Mg²⁺. Swelling decreased with increasing counterion concentration. The effect is stronger in the case of Ca²⁺ and Mg²⁺ for low esterified pectins and therefore crosslinks from divalent ions could be assumed. The crosslink effect is confirmed in mechanical experiments where an increase in the film tensile modulus is observed with increasing counterion concentration. It is shown for the first time that in case of highly concentrated pectin solutions Mg²⁺ cations also act as a crosslinker for pectin macromolecules.     

Multiscale modeling of cellular systems in biology

Here we review eight different multiscale modeling efforts dealing with cellular systems in biology. The first two models focus on collagen based tissue, one dealing with the biomechanical properties of the tissue and the other focusing on how the dermis is remodeled in scar tissue formation. The next two models deal with first avascular tumor growth and then the role of the vasculature in tumor growth. We then consider two models which use the Immersed Boundary method to model tissue properties and cell–cell adhesion. Finally we conclude with two models with treatments of the Cellular Potts Model. The first models somitogenisis in the chick and the second links the Cellular Potts Model with the Keller–Segel model.     

Problems and the progress made in modeling devices based on ionic materials

Computational simulation techniques have been extensively used to investigate physical phenomena in semiconductor devices with similar techniques utilized for the study of their competitors, ionic devices [1]. This paper is focusing on models based on the physics of carrier transport referring also shortly to equivalent circuit models, a much celebrated tool in the area of ionics. Published in Russian in Elektrokhimiya, 2009, Vol. 45, No. 6, pp. 693–698. The article is published in the original. Published by report at IX Conference “Fundamental Problems of Solid State Ionics”, Chernogolovka, 2008.     

Multiscale modeling of viscoelastic properties of polymer nanocomposites

A methodology for simple multiscale modeling of mechanical properties of polymer nanocomposites has been developed. This methodology consists of three steps: (1) obtaining from molecular dynamics simulations the viscoelastic properties of the bulklike polymer and approximating the position-dependent shear modulus of the interfacial polymer on the basis of the polymer-bead mean-square displacements as a function of the distance from the nanoparticle surface, (2) using bulk- and interfacial-polymer properties obtained from molecular dynamics simulations and performing stress–relaxation simulations of the nanocomposites with material-point-method simulations to extract the nanocomposite viscoelastic properties, and (3) performing direct validation of the average composite viscoelastic properties obtained from material-point-method simulations with those obtained from the molecular dynamics simulations of the nanocomposites. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1005-1013, 2005     

Surface charge density determination of single conical nanopores based on normalized ion current rectification

Current rectification is well known in ion transport through nanoscale pores and channel devices. The measured current is affected by both the geometry and fixed interfacial charges of the nanodevices. In this article, an interesting trend is observed in steady-state current-potential measurements using single conical nanopores. A threshold low-conductivity state is observed upon the dilution of electrolyte concentration. Correspondingly, the normalized current at positive bias potentials drastically increases and contributes to different degrees of rectification. This novel trend at opposite bias polarities is employed to differentiate the ion flux affected by the fixed charges at the substrate-solution interface (surface effect), with respect to the constant asymmetric geometry (volume effect). The surface charge density (SCD) of individual nanopores, an important physical parameter that is challenging to measure experimentally and is known to vary from one nanopore to another, is directly quantified by solving Poisson and Nernst-Planck equations in the simulation of the experimental results. The flux distribution inside the nanopore and the SCD of individual nanopores are reported. The respective diffusion and migration translocations are found to vary at different positions inside the nanopore. This knowledge is believed to be important for resistive pulse sensing applications because the detection signal is determined by the perturbation of the ion current by the analytes.     

Multiscale modeling of proteins interaction with functionalized nanoparticles

Understanding protein interactions with inorganic nanoparticle is central to the rational design of new tools in biomaterial sciences, nanobiotechnology, and nanomedicine. Theoretical modeling and simulations provide complementary approaches for experimental studies and are applied for exploring protein–particle surface-binding mechanisms, the determinants of binding specificity toward different surfaces, and the thermodynamics and kinetics of adsorption. The use of multiscale approaches is inevitable because the adsorption events extend over a wide range of time and length scales, which require the system to be addressed at different resolution levels. Here, we review the latest advances in coarse-grained treatment of these systems, usually addressed using residue-level resolution for proteins and mesoscale for the nanoparticle. We illustrate the parameterization strategies, focusing on those combining experimental and atomistic simulation data, within the theoretical framework of multiscale approaches.     

Multiscale modeling of self-assembled monolayers of thiophenes on electronic material surfaces

Computer simulation programs, spanning different time and length scales, are used to describe the fundamentals of thin film growth morphology in organic self-assembled monolayers using thiophenes on gold as representative systems. Ab initio calculations created a catalog of the energetics between two N-[4-(thien-2ylethynyl)phenyl] hydroxyl ("1P" molecules) in vacuum and interactions in three orthogonal orientations (parallel, perpendicular, and gamma-phase) to a Au (111) surface. This energetic dataset was supplied as the input for kinetic Monte Carlo simulations of dimer and trimer representations of small organic molecules to describe both sub-monolayer and multilayer growth on a series of hypothetical model substrates. On strongly binding metallic-like substrates, sub-monolayers of the model organic molecules formed ordered phases in the x and y directions at high temperatures and a disordered polycrystalline structure at low temperatures with the molecules lying down. Only at high temperatures was a "phase inversion" observed from a completely flat to an upright structure, suggesting the upright phase to be kinetically limited. Results for multilayer deposition of 1P molecules on three substrates which differ in their binding energy to the molecule (from non-interacting to strongly binding substrates) provided a rich view of the polymorphism that can result from differing choices of temperature and flux conditions. Irrespective of the binding energy of the molecule to the substrate, on highly corrugated surfaces we always observed 3D-island growth of multiple layers of the thiophenes, in contrast to Stranski-Krastanov or Frank-van der Merwe growth on more uniform substrates. The qualitative picture we obtained agrees with the growth habits of other small organic molecule systems like the acene series. Finally, molecular dynamics studies were used to understand the packing structures of stable polymorphs of thiophene SAMs. Different deposition conditions and substrate-molecule binding captured different regimes of growth morphology, some of which have already been observed experimentally.     

Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations

With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, in our hands those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for small molecules, proteins, lipids, and lipid bilayers and recently have begun work on carbohydrate force fields. The latter area has been relatively untouched by force field developers with particular focus on polarizable, non-additive interaction potential models. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration method for phase-dependent polarizable force fields, lipid molecules, and small-molecule carbohydrates. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields.     

Fmoc-protected amino acids as luminescent and circularly polarized luminescence materials based on charge transfer interaction

Fluorenylmethyloxycarbonyl (Fmoc)-protected amino acids are effective building blocks in self-assembled architectures at hierarchical levels, which however show limited luminescent properties and chiroptical activities. Here we introduce a charge-transfer strategy to build two-component luminescent materials with emerged circularly polarized luminescence properties. A library of Fmoc-amino acids was built, which selectively form charge-transfer complexes with the electron-deficient acceptor. Embedding in amorphous polymer matrix or physical grinding could trigger the charge-transfer luminescence with adjusted wavelengths in a general manner. X-ray diffraction results suggest the multiple binding modes between donor and acceptor. And, the solution-processed coassembly could selectively exhibit circularly polarized luminescence with high dissymmetry g-factors. This work illustrates a noncovalent charge-transfer strategy to construct luminescent and chiroptical organic composites based on the easy-accessible and economic chiral N-terminal aromatic amino acids.     

Multiscale modeling of the elastic properties of natural fibers based on a generalized method of cells and laminate analogy approach

In this article, a new method based on a generalized method of cells and laminate analogy approach was used to predict the elastic properties of natural fibers. The elastic properties of cellulose crystals and amorphous cellulose were adopted to calculate the effective properties of microfibrils. A ten-layer antisymmetrical laminated structure was used to predict the effective properties of cell walls. The effects of the aspect ratio and volume fraction of cellulose crystal, the microfibril angle in the S2 layer and the lumen ratio of fiber on the axial Young’s moduli of natural fibers were analyzed in detail. The results show that the predicted properties of fibers are those of the cell fibers, and the final elastic properties of natural fibers can be obtained with the volume fractions of cell fibers as the corresponding conversion coefficients. The multiscale method is very effective in the predictions of the axial Young’s moduli of natural fibers.