Structural features of sodium silicate glasses from reactive force field-based molecular dynamics simulations

Atomistic computer simulations can provide insights into silicate glass-environment interactions with the recent development of reactive potentials. However, the accuracy of generated glass structures with these potential was usually not fully examined. In this paper, the capability of the reactive force field (ReaxFF) to describe the short and medium range structure features of sodium silicate glasses in molecular dynamics simulations is investigated by comparing a widely used partial charge pairwise potential and available experimental data. Glass structure information such as pair distribution function (PDF), coordination number, Q_n species, neutron broadened structure factor, and X-ray broadened structure factor of the glass structures from ReaxFF simulations were calculated and compared to evaluate the generated glass structure. Advantages and limitations of the potentials and glass forming procedures, as well as areas of further improvement, were discussed. The results show that the recently refined ReaxFF parameters through the proposed procedure enable the simulations of sodium silicate glass structures with minimal defects, which paves the way to investigate water-glass interaction mechanisms with the reactive enabled potentials.     

Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases

We present results obtained for anisotropic potentials for protein simulations extracted from the continually growing databases of protein structures. This work is based on the assumption that the detailed information on molecular conformations can be used to derive statistical (a.k.a. ‘knowledge-based’) potentials that can describe on a coarse-grained level the side chain-side chain interactions in peptides and proteins. The complexity of inter-residue interactions is reflected in a high degree of orientational anisotropy for the twenty amino acids. By including in this coarse-grained interaction model the possibility of quantifying the backbone-backbone and backbone-side chain interactions, important improvements are obtained in characterizing the native protein states. Results obtained from tests that involve the identification of native-like conformations from large sets of decoy structures are presented. The method for deriving orientation-dependent statistical potentials is also applied to obtain water-water interactions. Monte Carlo simulations using the new coarse-grained water model show that the locations of the minima and maxima of the oxygen-oxygen radial distribution function correspond well with experimental measurements.     

Molecular electronics: insight from first-principles transport simulations

Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.     

Multiscale molecular modeling in nanostructured material design and process system engineering

Atomistic-based simulations such as molecular mechanics, molecular dynamics, and Monte Carlo-based methods have come into wide use for material design. Using these atomistic simulation tools, we can analyze molecular structure on the scale of 0.1–10 nm. However, difficulty arises concerning limitations of the time and length scale involved in the simulation. Although a possible molecular structure can be simulated by the atom-based simulations, it is less realistic to predict the mesoscopic structure defined on the scale of 100–1000 nm, for example the morphology of polymer blends and composites, which often dominates actual material properties. For the morphology on these scales, mesoscopic simulations such as the dynamic mean field density functional theory and dissipative particle dynamics are available as alternatives to atomistic simulations. It is therefore inevitable to adopt a mesoscopic simulation technique and bridge the gap between atomistic and mesoscopic simulations for an effective material design. Furthermore, it is possible to transfer the simulated mesoscopic structure to finite elements modeling tools for calculating macroscopic properties for the systems of interest.In this contribution, a hierarchical procedure for bridging the gap between atomistic and macroscopic modeling passing through mesoscopic simulations will be presented and discussed. The concept of multiscale (or many scale) modeling will be outlined, and examples of applications of single scale and multiscale procedures for nanostructured systems of industrial interest will be presented. In particular the following industrial applications will be considered: (i) polymer-organoclay nanocomposites of a montmorillonite–polymer–surface modifier system; (ii) mesoscale simulation for diblock copolymers with dispersion of nanoparticels; (iii) polymer–carbon nanotubes system and (iv) applications of multiscale modeling for process systems engineering.     

Size-dependent melting of polycyclic aromatic hydrocarbon nano-clusters: A molecular dynamics study

The size-dependent melting behaviour of clusters of polycyclic aromatic hydrocarbon (PAH) molecules is studied computationally using the isotropic PAHAP potential (Totton et al., 2012, Phys Chem Chem Phys, 14, 4081–4094). The investigation aims to shed light on the understanding of the liquid-like behaviour of PAH clusters. Detailed molecular dynamic (MD) simulations are performed to investigate the size-dependent melting of two representative homogeneous PAH clusters composed of either pyrene (C₁₆H₁₀) or coronene (C₂₄H₁₂) molecules. The evolution of the intermolecular energy and the Lindemann index are used to estimate the melting points of individual nano-clusters. The results from the MD simulations show that individual PAH molecules within nano-clusters are highly mobile below typical flame temperatures. A detailed morphological investigation of coronene₅₀₀ further reveals that the coronene clusters evolve from a columnar particle in the solid phase to an irregular spherical particle in the liquid phase. In contrast, no such evolution is observed for pyrene₃₀₀ which remains in a spherical configuration. The nano-cluster reduced melting temperature decreases with decreasing particle size following a linear relation with reciprocal size. The melting process of these clusters starts from the surface and the liquid layer grows inwards with increasing temperature.     

Scaling properties in the molecular structure of three-dimensional, nanosized phenylene-based dendrimers as studied by atomistic molecular dynamics simulations

Three-dimensional polyphenylene dendrimers (PDs) can be prepared in ways that enable control of their shape. Their structures may be used as scaffolds with a wide variety of functionality, enabling them to be used as functional nanoparticles with a large range of possible applications, ranging from light emitting devices to biological sensors or drug delivery tools. As PDs have been synthesized only recently, their structural and chemico-physical characterization is still in its infancy. Accordingly, in this paper the shape and internal organization of three PD families based on three different cores were probed by accurate, atomistic molecular dynamics simulations (MD). Particular care was taken to ensure complete structural equilibration by implementing an MD simulated annealing protocol prior to evaluation of the molecular structure and dynamics. All dendrimer families were found to be characterized by molecular dimensions in the nano-range, and by a shape-persistent, non-spherical structure, of molecular fractal dimension around 2.5-2.6, and of surface fractal dimension practically constant and almost equal to 2 with increasing generations in all cases. The MD analysis revealed also that, for this type of dendrimers, the starburst limited generation is presumably located in correspondence of the third generation.     

Numerical simulation of the fire behaviour of façade equipped with aluminium composite material‐based claddings—Model validation at intermediate scale

Increasing the energy performance of buildings is a crucial sustainable development objective. However, building features, products, mounting, and fixing of façade components have a large impact on fire safety. Authors in previous study performed façade fire propagation tests according to ISO13785‐1 on different combinations of ACM claddings and insulants. In this paper, simulations are performed to reproduce three of these tests. The model is validated with the aforementioned experimental results, including details in terms of thermal conditions in the system. This allows better understanding of the fire propagation on the overall system. Additional information, such as the relative contribution of the cladding and the insulant, are investigated numerically. The fire behaviour of each component of the overall system is thus validated. Simulations and tests performed show that the ACM cladding is the most important element driving the global fire behaviour of façade types considered. In particular, ACM‐PE–based cladding systems show large fire propagation whatever the insulant. This series of simulations is a part of a larger study including several steps of increasing complexity. Once the model for the fire behaviour of façade system is validated at intermediate scale, larger façade systems will be investigated numerically to evaluate the influence of scaling.     

Long time dynamics of complex systems

Molecular dynamics trajectories of large biological molecules are restricted to nanoseconds. We describe a computational method, based on optimization of a functional, to extend the time of molecular simulations by orders of magnitude. Variants of our technique have already produced microsecond and millisecond trajectories. The large steps enable feasible computations of atomically detailed approximate trajectories. Numerical examples are provided: (i) a conformational change in blocked glycine peptide and (ii) helix formation of an alanine-rich peptide.     

Surface structures of sodium borosilicate glasses from molecular dynamics simulations

Surface plays an important role in the physical and chemical properties of oxide glasses and controls the interactions of these glasses with the environment, thus dominating properties such as the chemical durability and bioactivity. The surface atomic structures of a series of sodium borosilicate glasses were studied using classical molecular dynamics simulations with recently developed compositional dependent partial charge potentials. The surface structural features and defect speciation were characterized and compared with the bulk glasses with the same composition. Our simulation results show that the borosilicate glass surfaces have significantly different chemical compositions and structures as compared to the bulk. The glass surfaces are found to be sodium enriched and behave like borosilicate glasses with higher R (Na₂O/B₂O₃) values. As a result of this composition and associated structure changes, the amount of fourfold boron decreases at the surface and the network connectivity on the surface decreases. In addition to composition variation and local structure environment change, defects such as two‐membered rings and three‐coordinated silicon were also observed on the surface. These unusual surface composition and structure features are expected to significantly impact the chemical and physical properties and the interactions with the environments of sodium borosilicate glasses.     

Surface Characteristics of Kaolinite and Other Selected Two Layer Silicate Minerals

The electrokinetic features and interfacial water structure, as revealed from molecular dynamics simulations (MDS) are considered with respect to the anisotropic features of selected two layer silicate minerals. Planar structures of kaolinite and antigorite are compared to the, compositionally equivalent, tubular structures of halloysite and chrysotile with respect to the pH dependency of zeta potential as determined from the electrophoretic mobility measurements. The importance of the atomic mismatch between the tetrahedral and octahedral sheets in a particular bilayer is discussed in order to explain the electrokinetic behaviour of these two layer silicate minerals. Interfacial water structure from MDS suggests that the silica tetrahedral surface is not wetted by water. In the case of planar silicates structural imperfections are considered to explain wetting characteristics. The possibility of polarity reversal (domain inversion) within a tetrahedral/octahedral layer and an out‐of‐order layer (inserted layer) within the tetrahedral/octahedral stack are considered in order to explain electrokinetic behaviour and wetting characteristics.     

The electrochemical oxidation of aqueous sulfur dioxide: A critical review of work with respect to the hybrid sulfur cycle

Literature regarding the mechanism of the electrochemical oxidation of aqueous sulfur dioxide to sulfuric acid has been critically evaluated to provide a detailed understanding of the reaction under various applied conditions. This reaction is of high relevance to the hybrid sulfur cycle for large scale hydrogen production, as well as other industrial applications such as flue gas desulfurisation. Widespread disagreement in the literature and non-reproducible behaviour of the electrochemical oxidation reaction has been found in this review to often be a result of poorly defined electrode preconditioning procedures. It has also been found that the mechanistic pathway of the oxidation reaction is heavily influenced by the electrode material, solution pH and the applied anodic potential. These factors are thought to influence adsorption and the reductive formation of sulfur species at low potentials.     

Development of boron oxide potentials for computer simulations of multicomponent oxide glasses

Molecular dynamics and related atomistic computer simulations are effective ways in studying the structures and structure–property relations of glass materials. However, simulations of boron oxide (B₂O₃)-containing oxide glasses pose a challenge due to the lack of reliable empirical potentials. This paper reports development of a set of partial charge pairwise composition-dependent potentials for boron-related interactions that enable simulations of multicomponent borosilicate glasses, together with some of the existing parameters. This set of potentials was tested in sodium borate glasses and sodium borosilicate glasses and it is shown capable to describe boron coordination change with glass composition in wide composition ranges. Structure features such as boron N₄ value, density, Q_n species distribution, fraction of non-bridging oxygen around boron and silicon, total correlation function, and bond angle distribution function were calculated and compared with available experimental data. Mechanical properties of the simulated glasses calculated with the new potential also show good agreement with experiments. Therefore, this new set of potential can be used to simulate boron oxide-containing multicomponent glasses including those with wide industrial and technology applications.     

The effect of large particles on the flow properties of powders

This paper is presented to fill a gap in the knowledge of the effect of larger particles on the flow behaviour of finer powders. Very little has appeared in the literature on the matter and the study is justified in that it is common practice to remove coarse particles before testing on a shear tester. The assumption is made in removing larger particles that they do not affect behaviour and that it is the fines which cause the binding and hence the flowability problems.Four different dry fine powders, a fine white sand, an electrostatic precipitator dust, a mixture of zircon and pyrophyllite (ZAP75) and a local steaming coal were investigated. No generalisation can be made about the addition of various volumetric percentages of spheres of varying sizes or of irregular particles. Thus, with fine sand, balls had little effect on the shear strength whereas irregular coal particles produced marked effect increasing consistently with the relative amount added. On the other hand, with the ZAP75, an increase in strength at low normal loads was exhibited but a decrease (over strength of powder alone) was found at higher normal loads.Experiments were conducted on a whole coal with varying limits of upper size (and also with varying limits of lower size) and the shear strength was found to be strongly dependent on those size limits. It is concluded that whereas much more experimental work is necessary before generalisation can be made of the effect of the presence (or absence, depending on the viewpoint) of large particles on the flowability of a powder, such an effect cannot be ignored.     

Quantum Computing for Molecular Biology**

Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these interactions are well established, the computational solution of the relevant quantum mechanical equations is very hard. However, much of molecular function in biology can be understood in terms of classical mechanics, where the interactions of electrons and nuclei have been mapped onto effective classical surrogate potentials that model the interaction of atoms or even larger entities. The simple mathematical structure of these potentials offers huge computational advantages; however, this comes at the cost that all quantum correlations and the rigorous many-particle nature of the interactions are omitted. In this work, we discuss how quantum computation may advance the practical usefulness of the quantum foundations of molecular biology by offering computational advantages for simulations of biomolecules. We not only discuss typical quantum mechanical problems of the electronic structure of biomolecules in this context, but also consider the dominating classical problems (such as protein folding and drug design) as well as data-driven approaches of bioinformatics and the degree to which they might become amenable to quantum simulation and quantum computation.     

Charge transport with single molecules--an electrochemical approach

After an introduction and brief review of charge transport in nanoscale molecular systems we report on experimental studies in gold / (single) molecule / gold junctions at solid / liquid interfaces employing a scanning tunneling microscopy (STM)-based 'break junction' technique. We demonstrate attempts in developing basic relationships between molecular structure, conductance properties and nanoscale electrochemical concepts based on four case studies from our own work. In experiments with alpha, omega-alkanedithiol and biphenyldithiol molecular junctions we address the role of sulfur-gold couplings and molecular conformation, such as gauche defects in the alkyl chains and the torsion angle between two phenyl rings. Combination with quantum chemistry calculations enabled a detailed molecular-level understanding of the electronic structure and transport characteristics of both systems. Employing the concept of 'electrolyte gating' with redox-active molecules, such as thiol-terminated derivatives of viologens (HS-6V6-SH or (HS-6V6)) we demonstrate the construction of symmetric and asymmetric active molecular junctions with transistor- or diode-like behavior upon polarization in an electrochemical environment. The experimental data could be represented quantitatively by the Kutznetsov/Ulstrup model assuming a two-step electron transfer with partial vibration relaxation. Finally, we show that surface-immobilized gold nanoparticles with a diameter of (2.4 +/- 0.5) nm exhibit features of locally addressable multi-state electronic switching upon electrolyte gating, which appears to be reminiscent of a sequential charging through several 'oxidation/reduction states'.     

Folding and Unfolding of Two Mixed α/β Peptides

We present a molecular dynamics simulation study of two peptides containing α‐ and β‐amino acid residues. According to experiment, the two peptides differ in the dominant fold when solvated in methanol: one shows a helical fold, the other a β hairpin. The simulations at 300 and 340 K were done by starting from a NMR spectroscopic model structure and from an extended (denatured) structure. The typical structural features of the two peptides are reproduced and a folding/unfolding equilibrium is observed on the nanosecond timescale at 300 K. Analysis of proton–proton NOE distance bounds and backbone ³J coupling constants gives results consistent with the experimental data. We conclude that our simulations are complementary to the experiments by providing detailed information on the conformational distributions.     

Large area flexible SERS active substrates using engineered nanostructures

Surface enhanced Raman scattering (SERS) is an analytical sensing method that provides label-free detection, molecularly specific information, and extremely high sensitivity. The Raman enhancement that makes this method attractive is mainly attributed to the local amplification of the incident electromagnetic field that occurs when a surface plasmon mode is excited at a metallic nanostructure. Here, we present a simple, cost effective method for creating flexible, large area SERS-active substrates using a new technique we call shadow mask assisted evaporation (SMAE). The advantage of large, flexible SERS substrates such as these is they have more area for multiplexing and can be incorporated into irregular surfaces such as clothing. We demonstrate the formation of four different types of nanostructure arrays (pillar, nib, ellipsoidal cylinder, and triangular tip) by controlling the evaporation angle, substrate rotation, and deposition rate of metals onto anodized alumina nanoporous membranes as large as 27 mm. In addition, we present experimental results showing how a hybrid structure comprising of gold nanospheres embedded in a silver nano-pillar structure can be used to obtain a 50× SERS enhancement over the raw nanoparticles themselves.     

The Use of Simulation Techniques in Developing Kinetic Models for Polymerization

The demands on simulations of polymerization reactions grow continuously, as do their capabilities. Using two examples it will be demonstrated how the use of detailed kinetic models in such simulations can contribute to the development of experimental strategies for determining rate coefficients, assist in mechanistic analysis and enable feasibility studies about operational strategies. Using the high‐temperature butyl acrylate polymerization as an example, it will be illustrated, based on detailed analytical information, how the kinetic scheme of the butyl acrylate polymerization expands to a complex network of elementary reactions. Based on this model an experimental strategy will be developed for the selective determination of the individual rate coefficients. A comparison of the results from these simulations with experimental data shows that a realization of the developed concept appears to be within reach. The second example is based on a kinetic scheme of the, high‐temperature high‐pressure, polymerization of ethene. In addition, using this kinetic scheme, the capability of nitroxyl species in establishing a controlled radical polymerization mechanism in polymerizations that show high polymerization rates and significant quantities of intra‐ and inter‐molecular branching reactions will be tested. This feasibility study will examine the potential effect a nitroxyl species has on the kinetic mechanism with respect to its stability and the structural characteristics of a polymer that results from such a polymerization.     

Numerical study on the turbulent reacting flow in the vicinity of the injector of an LDPE tubular reactor

Three-dimensional (3-D), transient numerical simulations of the turbulent reacting flow in the vicinity of the initiator injection point of a low-density polyethylene (LDPE) tubular reactor using a large eddy simulation (LES) approach combined with a filtered density function (FDF) technique are presented. The numerical approach allows for detailed predictions of the turbulent flow field and the associated (passive and reactive) scalar mixing. The aim is to study the influence of the injector geometry and initiator injection temperature on the LDPE process in terms of product quality (average polymer chain length, and polydispersity) and process efficiency (such as initiator consumption).