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Mutual diffusion of six hydrocarbons (methane, ethane, isobutane, benzene, toluene or naphthalene) diluted in supercritical carbon dioxide (CO 2) is studied by molecular dynamics simulation near the Widom line, i.e. in the temperature range from 290 to 345 K along the isobar 9 MPa. The CO 2 + aromatics mixtures are additionally sampled at 10 and 12 MPa and an experimental database with Fick diffusion coefficient data for those systems is provided. Taylor dispersion experiments of CO 2 with benzene, toluene, n-dodecane and 1,2,3,4-tetrahydronaphthalene are conducted along the p= 10 MPa isobar. Maxwell–Stefan and Fick diffusion coefficients are analyzed, together with the thermodynamic factor that relates them. It is found that the peculiar behavior of the Fick diffusion coefficient of some CO 2 mixtures in the extended critical region is a consequence of the thermodynamic factor minimum due to pronounced clustering on the molecular scale. Further, the strong dependence of the Fick diffusion coefficient on the molecular mass of the solute as well as the breakdown of the Stokes–Einstein relation near the Widom line are confirmed. Eleven correlations for the prediction of the Fick diffusion coefficient of CO 2 mixtures are assessed. An alternative two-step approach for the prediction of the infinite dilution Fick diffusion coefficient of supercritical CO 2 mixtures is proposed. It requires only the state point in terms of temperature and pressure (or density) as well as the molecular solute mass as input parameters. First, entropy scaling is applied to estimate the self-diffusion coefficient of CO 2 .Subsequently, this coefficient is used to determine the infinite dilution Fick diffusion coefficient of the mixture, based on the finding that these two diffusion coefficients exhibit a linear relationship, where the slope depends only on the molecular solute mass., SCOPUS: ar.j, info:eu-repo/semantics/published

Particle simulations often require the use of HPC architectures for which N-body codes need to be adapted to allow faster executions and bigger simulations, thus decreasing the time to get simulation results or enabling more accurate simulations. I employ algorithm and performance engineering to improve the performance, scalability, and load balancing of the MD code ls1 mardyn. These improvements resulted in speedups of more than 3x for real-world scenarios and up to 130x for benchmark problems., Partikelsimulationen erfordern den Einsatz von HPC-Rechnern, für die N-Körper-Codes angepasst werden müssen, um schnellere und größere Simulationen zu ermöglichen. Dies beschleunigt den Erhalt von Ergebnissen und verbessert deren Genauigkeit. Ich benutze Algorithmus- und Performance-Engineering, um die Leistung, Skalierbarkeit und Lastverteilung des MD-Codes ls1 mardyn zu verbessern. Beschleunigungen von mehr als 3x für reale Szenarien und bis zu 130x für Benchmark-Probleme wurden erreicht.

Two boundary lines are frequently discussed in the literature, separating state regions dominated by repulsion or attraction. The Fisher-Widom line indicates where the longest-range decay of the total pair correlation function crosses from monotonic to exponentially damped oscillatory. In the context of thermodynamic metric geometry, such a transition exists where the Ricci curvature scalar vanishes, R = 0. To establish a possible relation between these two lines, R is worked out for four simple fluids. The truncated and shifted Lennard-Jones, a colloid-like and the square-well potential are analyzed to investigate the influence of the repulsive nature on the location of the R = 0 line. For the longer-ranged Lennard-Jones potential, the influence of the cutoff radius on the R = 0 line is studied. The results are compared with literature data on the Fisher-Widom line. Since such data are rare for the longer-ranged Lennard-Jones potential, dedicated simulations are carried out to determine the number of zeros of the total correlation function, which may provide approximate information about the position of the FisherWidom line. An increase of the repulsive strength toward hard sphere interaction leads to the disappearance of the R = 0 line in the fluid phase. A rising attraction range results in the nonexistence of the Fisher-Widom line, while it has little effect on the R = 0 line as long as it is present in the fluid state.

Particle simulations often require the use of HPC architectures for which N-body codes need to be adapted to allow faster executions and bigger simulations, thus decreasing the time to get simulation results or enabling more accurate simulations. I employ algorithm and performance engineering to improve the performance, scalability, and load balancing of the MD code ls1 mardyn. These improvements resulted in speedups of more than 3x for real-world scenarios and up to 130x for benchmark problems., Partikelsimulationen erfordern den Einsatz von HPC-Rechnern, für die N-Körper-Codes angepasst werden müssen, um schnellere und größere Simulationen zu ermöglichen. Dies beschleunigt den Erhalt von Ergebnissen und verbessert deren Genauigkeit. Ich benutze Algorithmus- und Performance-Engineering, um die Leistung, Skalierbarkeit und Lastverteilung des MD-Codes ls1 mardyn zu verbessern. Beschleunigungen von mehr als 3x für reale Szenarien und bis zu 130x für Benchmark-Probleme wurden erreicht.

The effect of traces of ethanol in supercritical carbon dioxide on the mixture's thermodynamic properties is studied by molecular simulations and Taylor dispersion measurements. This mixture is investigated along the isobarp= 10 MPa in the temperature range betweenT= 304 and 343 K. Along this path, the mixture undergoes two transitions: First, the Widom line is crossed, marking the transition from liquid-like to gas-like conditions. A second transition occurs from the supercritical gas-like domain to a subcritical gas. The Widom line crossover entails inflection points for most of the studied properties,i.e.density, enthalpy, shear viscosity, Maxwell-Stefan and intradiffusion coefficients. On the other hand, the transition between the super- and subcritical regions is found to be generally smooth, an observation that is qualitatively confirmed by experimental Taylor dispersion measurements. Dedicated atomistic simulations show the presence of microheterogeneities due to ethanol self-association along the investigated path, which lead to the mixture's anomalous behavior in its extended critical region., SCOPUS: ar.j, info:eu-repo/semantics/published

The focus of this work lies on implementational improvements and, in particular, node-level performance optimization of the simulation software ls1-mardyn. Through data structure improvements, SIMD vectorization and, especially, OpenMP parallelization, the world’s first simulation of 2*1013 molecules at over 1 PFLOP/sec was enabled. To allow for long-range interactions, the Fast Multipole Method was introduced to ls1-mardyn. The algorithm was optimized for sequential, shared-memory, and distributed-memory execution on up to 32,768 MPI processes., Der Fokus dieser Arbeit liegt auf Code-Optimierungen und insbesondere Leistungsoptimierung auf Knoten-Ebene für die Simulationssoftware ls1-mardyn. Durch verbesserte Datenstrukturen, SIMD-Vektorisierung und vor allem OpenMP-Parallelisierung wurde die weltweit erste Petaflop-Simulation von 2*1013 Molekülen ermöglicht. Zur Simulation von langreichweitigen Wechselwirkungen wurde die Fast-Multipole-Methode in ls1-mardyn eingeführt. Sequenzielle, Shared- und Distributed-Memory-Optimierungen wurden angewandt und erlaubten eine Ausführung auf bis zu 32768 MPI-Prozessen.

The Lennard-Jones potential is taken as a basis to study the structure and dynamics of the face centered cubic (fcc) solid along an isochore from low temperatures up to the solid/fluid transition. The Z method is applied to estimate the melting point. Molecular dynamics simulations are used to calculate the pair distribution function, numbers of nearest neighbors, and the translational order parameter, analyzing the weakening of the fcc-symmetry due to emerging premelting effects. A range of dynamic properties, such as the mean-squared displacement, non-Gaussian parameter, Debye-Waller factor, and vibrational density of states, is considered for the analysis of the solid state. All of these parameters clearly show that bulk mobility is activated at about 2/3 of the melting temperature, known as the Tammann temperature. This indicates that vibrational motion of atoms is not maintained exclusively in the entire stable solid state and that collective atomic motion constitutes a precursor of the melting process.

The Lennard-Jones potential is taken as a basis to study the structure and dynamics of the face centered cubic (fcc) solid along an isochore from low temperatures up to the solid/fluid transition. The Z method is applied to estimate the melting point. Molecular dynamics simulations are used to calculate the pair distribution function, numbers of nearest neighbors, and the translational order parameter, analyzing the weakening of the fcc-symmetry due to emerging premelting effects. A range of dynamic properties, such as the mean-squared displacement, non-Gaussian parameter, Debye-Waller factor, and vibrational density of states, is considered for the analysis of the solid state. All of these parameters clearly show that bulk mobility is activated at about 2/3 of the melting temperature, known as the Tammann temperature. This indicates that vibrational motion of atoms is not maintained exclusively in the entire stable solid state and that collective atomic motion constitutes a precursor of the melting process.

The focus of this work lies on implementational improvements and, in particular, node-level performance optimization of the simulation software ls1-mardyn. Through data structure improvements, SIMD vectorization and, especially, OpenMP parallelization, the world’s first simulation of 2*1013 molecules at over 1 PFLOP/sec was enabled. To allow for long-range interactions, the Fast Multipole Method was introduced to ls1-mardyn. The algorithm was optimized for sequential, shared-memory, and distributed-memory execution on up to 32,768 MPI processes., Der Fokus dieser Arbeit liegt auf Code-Optimierungen und insbesondere Leistungsoptimierung auf Knoten-Ebene für die Simulationssoftware ls1-mardyn. Durch verbesserte Datenstrukturen, SIMD-Vektorisierung und vor allem OpenMP-Parallelisierung wurde die weltweit erste Petaflop-Simulation von 2*1013 Molekülen ermöglicht. Zur Simulation von langreichweitigen Wechselwirkungen wurde die Fast-Multipole-Methode in ls1-mardyn eingeführt. Sequenzielle, Shared- und Distributed-Memory-Optimierungen wurden angewandt und erlaubten eine Ausführung auf bis zu 32768 MPI-Prozessen.

We present the results of a molecular simulation study of fluid mixtures, where complex diffusion behavior has experimentally been found and offer an explanation based on the hydrodynamic and thermodynamic components of the Fick diffusion coefficient. Special attention is paid to mixtures near critical and demixing regions, where in many cases strong discrepancies between different measurements of the Fick diffusion coefficients are found. Also molecular simulations are challenging in these regions and require extensive sampling due the presence of pronounced density fluctuations.

We present the results of a molecular simulation study of fluid mixtures, where complex diffusion behavior has experimentally been found and offer an explanation based on the hydrodynamic and thermodynamic components of the Fick diffusion coefficient. Special attention is paid to mixtures near critical and demixing regions, where in many cases strong discrepancies between different measurements of the Fick diffusion coefficients are found. Also molecular simulations are challenging in these regions and require extensive sampling due the presence of pronounced density fluctuations.

We present the results of a molecular simulation study of fluid mixtures, where complex diffusion behavior has experimentally been found and offer an explanation based on the hydrodynamic and thermodynamic components of the Fick diffusion coefficient. Special attention is paid to mixtures near critical and demixing regions, where in many cases strong discrepancies between different measurements of the Fick diffusion coefficients are found. Also molecular simulations are challenging in these regions and require extensive sampling due the presence of pronounced density fluctuations.

We present the results of a molecular simulation study of fluid mixtures, where complex diffusion behavior has experimentally been found and offer an explanation based on the hydrodynamic and thermodynamic components of the Fick diffusion coefficient. Special attention is paid to mixtures near critical and demixing regions, where in many cases strong discrepancies between different measurements of the Fick diffusion coefficients are found. Also molecular simulations are challenging in these regions and require extensive sampling due the presence of pronounced density fluctuations.

Diffusion of methane diluted in supercritical carbon dioxide is studied by experiment and molecular simulation in the temperature range from 292.55 to 332.85 K along the isobars 9.0, 12.5 and 14.7 MPa. Measurements of the Fick diffusion coefficient are carried out with the Taylor dispersion technique. Molecular dynamics simulation and the Green-Kubo formalism are employed to obtain Fick, Maxwell-Stefan and intradiffusion coefficients as well as shear viscosity. The obtained diffusion coefficients are on the order of 10−8 m2/s. The composition, temperature and density dependence of diffusion is analyzed. The Fick diffusion coefficient of methane in carbon dioxide shows an anomaly in the near-critical region. This behavior can be attributed to the crossing of the so-called Widom line, where the supercritical fluid goes through a transition between liquid-like and gas-like states. Further, several classical equations are tested on their ability to predict this behavior and it is found that equations that explicitly include the density are better suited to predict the sharp variation of the diffusion coefficient near the critical region predicted by molecular simulation., SCOPUS: ar.j, info:eu-repo/semantics/published

Experimental data on Fick diffusion coefficients of ternary and higher mixtures depend on the reference frame; those which are in common use are associated with the average velocity either with respect to volume, mass or mole number. In this study, the dependence of diffusion coefficients on the reference frame is thoroughly analyzed for three ternary mixtures of different types. The first one, tetralin-isobutylbenzene-dodecane, can almost be considered as ideal, the second one, cyclohexane-toluene-methanol, exhibits liquid-liquid phase separation and the third one, water-ethanol-triethylene glycol, contains three associating species and is also strongly non-ideal. Experimental diffusion coefficient data sampled in the volume reference frame are transformed to the molar and mass reference frames. The required partial molar volumes are derived from present density measurements. Four additional mixtures are considered along a single or two composition paths. A highlight of this study is the existence of a strong similarity of the main diffusion coefficients in the volume and mass reference frames for all considered mixtures. When the excess volume is small, the coefficients in the molar reference frame are also similar. However, for the mixture with a large excess volume (containing water), the diffusion coefficients in the molar reference frame differ significantly, even indicating negative main diffusion coefficients. It is shown that negative main diffusion coefficients appear due to relatively large experimental uncertainties of cross diffusion coefficients, which are propagated and amplified by frame transformation., SCOPUS: ar.j, info:eu-repo/semantics/published

Aspects of isomorph theory, Rosenfeld-Tarazona temperature scaling, and thermodynamic geometry are comparatively discussed on the basis of the Lennard-Jones potential. The first two approaches approximate the high-density fluid state well when the repulsive interparticle interactions become dominant, which is typically the case close to the freezing line. However, previous studies of Rosenfeld-Tarazona scaling for the isochoric heat capacity and its relation to isomorph theory reveal deviations for the temperature dependence. It turns out that a definition of a state region in which repulsive interactions dominate is required for achieving consistent results. The Riemannian thermodynamic scalar curvature R allows for such a classification, indicating predominantly repulsive interactions by R > 0. An analysis of the isomorphic character of the freezing line and the validity of Rosenfeld-Tarazona temperature scaling show that these approaches are consistent only in a small state region.

Aspects of isomorph theory, Rosenfeld-Tarazona temperature scaling, and thermodynamic geometry are comparatively discussed on the basis of the Lennard-Jones potential. The first two approaches approximate the high-density fluid state well when the repulsive interparticle interactions become dominant, which is typically the case close to the freezing line. However, previous studies of Rosenfeld-Tarazona scaling for the isochoric heat capacity and its relation to isomorph theory reveal deviations for the temperature dependence. It turns out that a definition of a state region in which repulsive interactions dominate is required for achieving consistent results. The Riemannian thermodynamic scalar curvature R allows for such a classification, indicating predominantly repulsive interactions by R > 0. An analysis of the isomorphic character of the freezing line and the validity of Rosenfeld-Tarazona temperature scaling show that these approaches are consistent only in a small state region.

The Fick diffusion coefficient matrix of ternary mixtures containing benzene + acetone + three different alcohols, i.e. methanol, ethanol, and 2-propanol, is studied by molecular dynamics simulation and Taylor dispersion experiments. Aiming to identify common features of these mixtures, it is found that one of the main diffusion coefficients and the smaller eigenvalue do not depend on the type of alcohol along the studied composition path. Two mechanisms that are responsible for this invariant behavior are discussed in detail, i.e. the interplay between kinetic and thermodynamic contributions to Fick diffusion coefficients and the presence of microscopic heterogeneities caused by hydrogen bonding. Experimental work alone cannot explain these mechanisms, while present simulations on the molecular level indicate structural changes and uniform intermolecular interactions between benzene and acetone molecules in the three ternary mixtures. The main diffusion coefficients of these ternary mixtures exhibit similarities with their binary subsystems. Analyses of radial distribution functions and hydrogen bonding statistics quantitatively evidence alcohol self-association and cluster formation, as well as component segregation. Furthermore, the excess volume of the mixtures is analyzed in the light of intermolecular interactions, further demonstrating the benefits of the simultaneous use of experiment and simulation. The proposed framework for studying diffusion coefficients of a set of ternary mixtures, where only one component varies, opens the way for further investigations and a better understanding of multicomponent diffusion. The presented numerical results may also give an impulse to the development of predictive approaches for multicomponent diffusion., SCOPUS: ar.j, info:eu-repo/semantics/published

With laboratory and numerical work, we demonstrate that one of the main diffusion coefficients and the smaller eigenvalue of the Fick diffusion matrix are invariant to the number of methylene groups of the alcohol in ternary mixtures composed of an aromatic (benzene), a ketone (acetone) and one of three different alcohols (methanol, ethanol or 2-propanol). A critical analysis of the relationship between the kinetic and thermodynamic contributions to the diffusion coefficients allows us to explain this intriguing behaviour of this class of mixture. These findings are reflected by the diffusive behaviour of the according binary subsystems. Our approach provides a promising systematic framework for future investigations into the important and challenging problem of transport diffusion in multicomponent liquids., SCOPUS: ar.j, info:eu-repo/semantics/published

The Lennard-Jones potential is used to study the high density fluid and face centered cubic solid state region, including solid-fluid equilibria. Numerous thermodynamic properties are considered, elucidating the behavior of matter in this poorly studied region. The present molecular simulation results are extensively compared to the latest and most accurate equation of state models for fluid and solid phases. It is shown that current models do not cover the thermodynamics of the system adequately near the solid-fluid phase transition. Furthermore, thermodynamic stability is analyzed, indicating that published solid-fluid coexistence data may not be correct at high temperatures. Particular attention is paid to the premelting zone, a range of states close to the melting line, which is characterized by strong variations of several thermodynamic properties. Because the underlying microscopic mechanisms are not yet fully understood, it is hoped that these data may contribute to the development of a theoretical framework for describing premelting effects. Published by AIP Publishing.

The Lennard-Jones potential is used to study the high density fluid and face centered cubic solid state region, including solid-fluid equilibria. Numerous thermodynamic properties are considered, elucidating the behavior of matter in this poorly studied region. The present molecular simulation results are extensively compared to the latest and most accurate equation of state models for fluid and solid phases. It is shown that current models do not cover the thermodynamics of the system adequately near the solid-fluid phase transition. Furthermore, thermodynamic stability is analyzed, indicating that published solid-fluid coexistence data may not be correct at high temperatures. Particular attention is paid to the premelting zone, a range of states close to the melting line, which is characterized by strong variations of several thermodynamic properties. Because the underlying microscopic mechanisms are not yet fully understood, it is hoped that these data may contribute to the development of a theoretical framework for describing premelting effects. Published by AIP Publishing.

To gain an understanding of the transport and thermodynamic behavior of the highly non-ideal mixture methanol + cyclohexane, three complementary approaches, i.e. experiment, molecular simulation and predictive equations, are employed. The temperature and composition dependence of different diffusion coefficients is studied around the miscibility gap at ambient pressure. On the one hand Fick diffusion coefficients are measured experimentally by interferometric probing and on the other hand Maxwell-Stefan diffusion coefficients and intradiffusion coefficients are sampled by equilibrium molecular dynamics simulation at five temperatures below the upper critical temperature of ∼319 K. The spinodal curve is determined from extrapolation of the experimental Fick diffusion coefficient data and compared to predictions from excess Gibbs energy models. It is found that these models are not capable to correctly describe the activity coefficients over the whole composition range of the studied mixture. Thus, different parameter sets for a modified Wilson model are used for calculations of the thermodynamic factor, which is needed to transform Maxwell-Stefan into Fick diffusion coefficients and vice versa. Further, predictive equations for the Maxwell-Stefan diffusion coefficient, which are based on intradiffusion coefficients, are compared to simulation results. Using different approaches provides a clearer understanding of the relations between kinetic and thermodynamic properties contributing to the diffusion behavior of partially miscible mixtures., SCOPUS: ar.j, info:eu-repo/semantics/published

In spite of considerable research on the nature of aqueous alcohol mixtures that are characterized by microscopic inhomogeneity or incomplete mixing at the molecular level, transport properties have received little attention. We report the results of a study on diffusion in the ternary mixture of water with two alcohols, that is, water + methanol + ethanol, which is investigated on microscopic and macroscopic scales by means of molecular simulation and Taylor dispersion experiments. A novel protocol is developed for the comparison of mutual diffusion coefficients sampled by two fundamentally different approaches, which allows for their critical analysis. Because of complex intermolecular interactions, given by the presence of hydrogen bonding, the analysis of transport processes in this mixture is challenging for not only on the microscopic scale for simulation techniques but also on the macroscopic scale due to unfavorable optical properties. Binary limits of the Fick diffusion matrix are used for validation of the experimental ternary mixture results together with the verification of the validity of the phenomenological Onsager reciprocal relations. The Maxwell-Stefan diffusion coefficients and the thermodynamic factor are sampled by molecular simulation consistently on the basis of given force field models. The protocol for the comparison of the results from both approaches is also challenging because Fick diffusion coefficients of ternary mixtures depend on the frame of reference. Accordingly, the measured coefficients are transformed from the volume-averaged to the molar-averaged frame of reference, and it is demonstrated that both approaches provide not only similar qualitative behavior along two concentration paths but also strong quantitative agreement. This coordinated work using different approaches to study diffusion in multicomponent mixtures is expected to be a significant step forward for the accurate assessment of cross-diffusion. (Figure Presented)., SCOPUS: ar.j, info:eu-repo/semantics/published

A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation to achieve higher scalability. Furthermore, the formalism by Lustig [R. Lustig, Mol. Phys. 110 (2012) 3041] is implemented, allowing for a systematic sampling of Massieu potential derivatives in a single simulation run. Moreover, the Green-Kubo formalism is extended for the sampling of the electric conductivity and the residence time. To remove the restriction of the preceding version to electro-neutral molecules, Ewald summation is implemented to consider ionic long range interactions. Finally, the sampling of the radial distribution function is added.

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales which were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multi-center rigid potential models based on Lennard-Jones sites, point charges and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, e.g. for fluids at interfaces, as well as non-equilibrium molecular dynamics simulation of heat and mass transfer.

The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline of Computational Molecular Engineering (CME) which makes basic research in soft matter physics fruitful for industrial applications. Within the coming decade, major breakthroughs can be reached if a research focus is placed on processes at interfaces, combining aspects where an increase in the accessible length and time scales due to massively parallel high-performance computing will lead to particularly significant improvements.

Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and employed for the simulation of electrolytes in aqueous solution. The enzymatically catalysed hydroxylation of oleic acid is investigated by molecular dynamics simulation taking the internal degrees of freedom of the macromolecules into account. Thereby, Ewald summation methods are used to compute the long range electrostatic interactions. In systems with a phase boundary, the dispersive interaction, which is modelled by the Lennard-Jones potential here, has a more significant long range contribution than in homogeneous systems. This effect is accounted for by implementing the Janecek cutoff correction scheme. On this basis, the HPC infrastructure at the Steinbuch Centre for Computing was accessed and efficiently used, yielding new insights on the molecular systems under consideration.

We expect that systematic and seamless computational upscaling and downscaling for modeling, predicting, or optimizing material and system properties and behavior with atomistic resolution will eventually be sufficiently accurate and practical that it will transform the mode of development in the materials, chemical, catalysis, and Pharma industries. However, despite truly dramatic progress in methods, software, and hardware, this goal remains elusive, particularly for systems that exhibit inherently complex chemistry under normal or extreme conditions of temperature, pressure, radiation, and others. We describe here some of the significant progress towards solving these problems via a general multiscale, multiparadigm strategy based on first-principles quantum mechanics (QM), and the development of breakthrough methods for treating reaction processes, excited electronic states, and weak bonding effects on the conformational dynamics of large-scale molecular systems. These methods have resulted directly from filling in the physical and chemical gaps in existing theoretical and computational models, within the multiscale, multiparadigm strategy. To illustrate the procedure we demonstrate the application and transferability of such methods on an ample set of challenging problems that span multiple fields, system length- and timescales, and that lay beyond the realm of existing computational or, in some case, experimental approaches, including understanding the solvation effects on the reactivity of organic and organometallic structures, predicting transmembrane protein structures, understanding carbon nanotube nucleation and growth, understanding the effects of electronic excitations in materials subjected to extreme conditions of temperature and pressure, following the dynamics and energetics of long-term conformational evolution of DNA macromolecules, and predicting the long-term mechanisms involved in enhancing the mechanical response of polymer-based hydrogels.