Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers*Computation* **2018**, *6*(2), 27; doi:10.3390/computation6020027 (registering DOI) - 21 March 2018**Abstract **

►
Figures
In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical

[...] Read more.
In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables.
Full article

Recent Progress in First-Principles Methods for Computing the Electronic Structure of Correlated Materials*Computation* **2018**, *6*(1), 26; doi:10.3390/computation6010026 - 19 March 2018**Abstract **

►
Figures
Substantial progress has been achieved in the last couple of decades in computing the electronic structure of correlated materials from first principles. This progress has been driven by parallel development in theory and numerical algorithms. Theoretical development in combining ab initio approaches and

[...] Read more.
Substantial progress has been achieved in the last couple of decades in computing the electronic structure of correlated materials from first principles. This progress has been driven by parallel development in theory and numerical algorithms. Theoretical development in combining ab initio approaches and many-body methods is particularly promising. A crucial role is also played by a systematic method for deriving a low-energy model, which bridges the gap between real and model systems. In this article, an overview is given tracing the development from the LDA+U to the latest progress in combining the $GW$ method and (extended) dynamical mean-field theory ($GW$ +EDMFT). The emphasis is on conceptual and theoretical aspects rather than technical ones.
Full article

Dissipation Effects in Schrödinger and Quantal Density Functional Theories of Electrons in an Electromagnetic Field*Computation* **2018**, *6*(1), 25; doi:10.3390/computation6010025 - 6 March 2018**Abstract **

►
Figures
Dissipative effects arise in an electronic system when it interacts with a time-dependent environment. Here, the Schrödinger theory of electrons in an electromagnetic field including dissipative effects is described from a new perspective. Dissipation is accounted for via the effective Hamiltonian approach in

[...] Read more.
Dissipative effects arise in an electronic system when it interacts with a time-dependent environment. Here, the Schrödinger theory of electrons in an electromagnetic field including dissipative effects is described from a new perspective. Dissipation is accounted for via the effective Hamiltonian approach in which the electron mass is time-dependent. The perspective is that of the individual electron: the corresponding equation of motion for the electron or time-dependent differential virial theorem—the ‘Quantal Newtonian’ second law—is derived. According to the law, each electron experiences an external field comprised of a binding electric field, the Lorentz field, and the electromagnetic field. In addition, there is an internal field whose components are representative of electron correlations due to the Pauli exclusion principle and Coulomb repulsion, kinetic effects, and density. There is also an internal contribution due to the magnetic field. The response of the electron is governed by the current density field in which a damping coefficient appears. The law leads to further insights into Schrödinger theory, and in particular the intrinsic self-consistent nature of the Schrödinger equation. It is proved that in the presence of dissipative effects, the basic variables (gauge-invariant properties, knowledge of which determines the Hamiltonian) are the density and physical current density. Finally, a local effective potential theory of dissipative systems—quantal density functional theory (QDFT)—is developed. This constitutes the mapping from the interacting dissipative electronic system to one of noninteracting fermions possessing the same dissipation and basic variables. Attributes of QDFT are the separation of the electron correlations due to the Pauli exclusion principle and Coulomb repulsion, and the determination of the correlation contributions to the kinetic energy. Hence, Schrödinger theory in conjunction with QDFT leads to additional insights into the dissipative system.
Full article

A Review of Numerical Modelling of Multi-Scale Wind Turbines and Their Environment*Computation* **2018**, *6*(1), 24; doi:10.3390/computation6010024 - 5 March 2018**Abstract **

►
Figures
Global demand for energy continues to increase rapidly, due to economic and population growth, especially for increasing market economies. These lead to challenges and worries about energy security that can increase as more users need more energy resources. Also, higher consumption of fossil

[...] Read more.
Global demand for energy continues to increase rapidly, due to economic and population growth, especially for increasing market economies. These lead to challenges and worries about energy security that can increase as more users need more energy resources. Also, higher consumption of fossil fuels leads to more greenhouse gas emissions, which contribute to global warming. Moreover, there are still more people without access to electricity. Several studies have reported that one of the rapidly developing source of power is wind energy and with declining costs due to technology and manufacturing advancements and concerns over energy security and environmental issues, the trend is predicted to continue. As a result, tools and methods to simulate and optimize wind energy technologies must also continue to advance. This paper reviews the most recently published works in Computational Fluid Dynamic (CFD) simulations of micro to small wind turbines, building integrated with wind turbines, and wind turbines installed in wind farms. In addition, the existing limitations and complications included with the wind energy system modelling were examined and issues that needs further work are highlighted. This study investigated the current development of CFD modelling of wind energy systems. Studies on aerodynamic interaction among the atmospheric boundary layer or wind farm terrain and the turbine rotor and their wakes were investigated. Furthermore, CFD combined with other tools such as blade element momentum were examined.
Full article

Ionic Liquids Treated within the Grand Canonical Adaptive Resolution Molecular Dynamics Technique*Computation* **2018**, *6*(1), 23; doi:10.3390/computation6010023 - 28 February 2018**Abstract **

►
Figures
We use the Grand Canonical Adaptive Resolution Molecular Dynamics Technique (GC-AdResS) to examine the essential degrees of freedom necessary for reproducing the structural properties of the imidazolium class of ionic liquids. In this technique, the atomistic details are treated as an open sub-region

[...] Read more.
We use the Grand Canonical Adaptive Resolution Molecular Dynamics Technique (GC-AdResS) to examine the essential degrees of freedom necessary for reproducing the structural properties of the imidazolium class of ionic liquids. In this technique, the atomistic details are treated as an open sub-region of the system while the surrounding environment is modelled as a generic coarse-grained model. We systematically characterize the spatial quantities such as intramolecular, intermolecular radial distribution functions, other structural and orientational properties of ILs. The spatial quantities computed in an open sub-region of the system are in excellent agreement with the equivalent quantities calculated in a full atomistic simulation, suggesting that the atomistic degrees of freedom outside the sub-region are negligible. The size of the sub-region considered in this study is 2 nm, which is essentially the size of a few ions. Insight from the study suggests that a higher degree of spatial locality seems to play a crucial role in characterizing the properties of imidazolium based ionic liquids.
Full article

The Role of Conformational Entropy in the Determination of Structural-Kinetic Relationships for Helix-Coil Transitions*Computation* **2018**, *6*(1), 21; doi:10.3390/computation6010021 - 26 February 2018**Abstract **

►
Figures
Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of alanine residues, the structural and kinetic properties of a simulation

[...] Read more.
Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of alanine residues, the structural and kinetic properties of a simulation model are linked in a rather simple way, given a certain level of physics present in the model. In this work, we extend these findings to a longer peptide, for which the representation of configuration space in terms of a full enumeration of sequences of helical/coil states along the peptide backbone is impractical. We verify the structural-kinetic relationships by scanning the parameter space of a simple native-biased model and then employ a distinct transferable model to validate and generalize the conclusions. Our results further demonstrate the validity of the previous findings, while clarifying the role of conformational entropy in the determination of the structural-kinetic relationships. More specifically, while the global, long timescale kinetic properties of a particular class of models with varying energetic parameters but approximately fixed conformational entropy are determined by the overarching structural features of the ensemble, a shift in these kinetic observables occurs for models with a distinct representation of steric interactions. At the same time, the relationship between structure and more local, faster kinetic properties is not affected by varying the conformational entropy of the model.
Full article

Optimal Data-Driven Estimation of Generalized Markov State Models for Non-Equilibrium Dynamics*Computation* **2018**, *6*(1), 22; doi:10.3390/computation6010022 - 26 February 2018**Abstract **

►
Figures
There are multiple ways in which a stochastic system can be out of statistical equilibrium. It might be subject to time-varying forcing; or be in a transient phase on its way towards equilibrium; it might even be in equilibrium without us noticing it,

[...] Read more.
There are multiple ways in which a stochastic system can be out of statistical equilibrium. It might be subject to time-varying forcing; or be in a transient phase on its way towards equilibrium; it might even be in equilibrium without us noticing it, due to insufficient observations; and it even might be a system failing to admit an equilibrium distribution at all. We review some of the approaches that model the effective statistical behavior of equilibrium and non-equilibrium dynamical systems, and show that both cases can be considered under the unified framework of optimal low-rank approximation of so-called transfer operators. Particular attention is given to the connection between these methods, Markov state models, and the concept of metastability, further to the estimation of such reduced order models from finite simulation data. All these topics bear an important role in, e.g., molecular dynamics, where Markov state models are often and successfully utilized, and which is the main motivating application in this paper. We illustrate our considerations by numerical examples.
Full article

Implications of PCCA+ in Molecular Simulation*Computation* **2018**, *6*(1), 20; doi:10.3390/computation6010020 - 19 February 2018**Abstract **

►
Figures
Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ‘bound’ vs. ‘unbound’), although the process itself takes place in a continuous space. In

[...] Read more.
Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ‘bound’ vs. ‘unbound’), although the process itself takes place in a continuous space. In this context, the formula $\chi =X\mathcal{A}$ connects the micro-dynamics of the molecular system to its macro-dynamics. $\chi $ can be understood as a clustering of micro-states of a molecular system into a few macro-states. *X* is a basis of an invariant subspace of a transfer operator describing the micro-dynamics of the system. The formula claims that there is an unknown linear relation $\mathcal{A}$ between these two objects. With the aid of this formula we can understand rebinding effects, the electron flux in pericyclic reactions, and systematic changes of binding rates in kinetic ITC experiments. We can also analyze sequential spectroscopy experiments and rare event systems more easily. This article provides an explanation of the formula and an overview of some of its consequences.
Full article

Coefficients Calculation in Pascal Approximation for Passive Filter Design*Computation* **2018**, *6*(1), 18; doi:10.3390/computation6010018 - 14 February 2018**Abstract **

►
Figures
The recently modified Pascal function is further exploited in this paper in the design of passive analog filters. The Pascal approximation has non-equiripple magnitude, in contrast of the most well-known approximations, such as the Chebyshev approximation. A novelty of this work is the

[...] Read more.
The recently modified Pascal function is further exploited in this paper in the design of passive analog filters. The Pascal approximation has non-equiripple magnitude, in contrast of the most well-known approximations, such as the Chebyshev approximation. A novelty of this work is the introduction of a precise method that calculates the coefficients of the Pascal function. Two examples are presented for the passive design to illustrate the advantages and the disadvantages of the Pascal approximation. Moreover, the values of the passive elements can be taken from tables, which are created to define the normalized values of these elements for the Pascal approximation, as Zverev had done for the Chebyshev, Elliptic, and other approximations. Although Pascal approximation can be implemented to both passive and active filter designs, a passive filter design is addressed in this paper, and the benefits and shortcomings of Pascal approximation are presented and discussed.
Full article

Effect of Carbon Concentration on the Sputtering of Carbon-Rich SiC Bombarded by Helium Ions*Computation* **2018**, *6*(1), 19; doi:10.3390/computation6010019 - 14 February 2018**Abstract **

►
Figures
Silicon carbide (SiC) is considered as an important material for nuclear engineering due to its excellent properties. Changing the carbon content in SiC can regulate and control its elastic and thermodynamic properties, but a simulation study of the effect of carbon content on

[...] Read more.
Silicon carbide (SiC) is considered as an important material for nuclear engineering due to its excellent properties. Changing the carbon content in SiC can regulate and control its elastic and thermodynamic properties, but a simulation study of the effect of carbon content on the sputtering (caused by the helium ions) of SiC is still lacking. In this work, we used the Monte-Carlo and molecular dynamics simulation methods to study the effects of carbon concentration, incidence energy, incident angle, and target temperature on the sputtering yield of SiC. The results show that the incident ions’ energy and angle have a significant effect on sputtering yield of SiC when the carbon concentration in SiC is around 62 at %, while the target temperature has a little effect on the sputtering yield of SiC. Our work might provide theoretical support for the experimental research and engineering application of carbon fiber-reinforced SiC that be used as the plasma-facing material in tokamak fusion reactors.
Full article

A Localized Meshless Technique for Generating 3-D Wind Fields*Computation* **2018**, *6*(1), 17; doi:10.3390/computation6010017 - 8 February 2018**Abstract **

►
Figures
A localized meshless method is used to simulate 3-D atmospheric wind fields for wind energy assessment and emergency response. The meshless (or mesh-free) method with radial basis functions (RBFs) alleviates the need to create a mesh required by finite difference, finite volume, and

[...] Read more.
A localized meshless method is used to simulate 3-D atmospheric wind fields for wind energy assessment and emergency response. The meshless (or mesh-free) method with radial basis functions (RBFs) alleviates the need to create a mesh required by finite difference, finite volume, and finite element methods. The method produces a fast solution that converges with high accuracy, establishing 3-D wind estimates over complex terrain. The method does not require discretization of the domain or boundary and removes the need for domain integration. The meshless method converges exponentially for smooth boundary shapes and boundary data, and is insensitive to dimensional constraints. Coding of the method is very easy and can be done using MATLAB or MAPLE. By employing a localized RBF procedure, 3-D wind fields can be established from sparse meteorological data. The meshless method can be easily run on PCs and hand-held mobile devices. This article summarizes previous work where the meshless method has successfully simulated 3D wind fields over various environments, along with the equations used to obtain the simulations.
Full article

Analysis, Synchronization and Circuit Design of a 4D Hyperchaotic Hyperjerk System*Computation* **2018**, *6*(1), 14; doi:10.3390/computation6010014 - 6 February 2018**Abstract **

►
Figures
In this work, a 4D hyperchaotic hyperjerk system, with better results for its Lyapunov exponents and Kaplan–Yorke dimension regarding other systems of this family, as well as its circuit implementation, is presented. Hyperchaotic hyperjerk systems depict complex dynamical behavior in a high-dimensional phase

[...] Read more.
In this work, a 4D hyperchaotic hyperjerk system, with better results for its Lyapunov exponents and Kaplan–Yorke dimension regarding other systems of this family, as well as its circuit implementation, is presented. Hyperchaotic hyperjerk systems depict complex dynamical behavior in a high-dimensional phase space with *n* ≥ 4, offering robustness against many types of attacks in private communications. For this reason, an adaptive controller in order to achieve global chaos synchronization of coupled 4D hyperchaotic hyperjerk systems with unknown parameters is designed. The adaptive results in this work are proved using Lyapunov stability theory and the effectiveness of the proposed synchronization scheme is confirmed through the simulation results.
Full article

Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments*Computation* **2018**, *6*(1), 15; doi:10.3390/computation6010015 - 6 February 2018**Abstract **

►
Figures
Molecular dynamics (MD) simulations allow the investigation of the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields, it is becoming common to integrate MD simulations with

[...] Read more.
Molecular dynamics (MD) simulations allow the investigation of the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields, it is becoming common to integrate MD simulations with experimental data obtained from ensemble measurements. We review here the approaches that can be used to combine MD and experiment under the guidance of the maximum entropy principle. We mostly focus on methods based on Lagrangian multipliers, either implemented as reweighting of existing simulations or through an on-the-fly optimization. We discuss how errors in the experimental data can be modeled and accounted for. Finally, we use simple model systems to illustrate the typical difficulties arising when applying these methods.
Full article

Simulation and Optimization of Control of Selected Phases of Gyroplane Flight

*Computation* **2018**, *6*(1), 16; doi:10.3390/computation6010016 - 6 February 2018**Abstract **

►
Figures
Optimization methods are increasingly used to solve problems in aeronautical engineering. Typically, optimization methods are utilized in the design of an aircraft airframe or its structure. The presented study is focused on improvement of aircraft flight control procedures through numerical optimization. The optimization

[...] Read more.
Optimization methods are increasingly used to solve problems in aeronautical engineering. Typically, optimization methods are utilized in the design of an aircraft airframe or its structure. The presented study is focused on improvement of aircraft flight control procedures through numerical optimization. The optimization problems concern selected phases of flight of a light gyroplane—a rotorcraft using an unpowered rotor in autorotation to develop lift and an engine-powered propeller to provide thrust. An original methodology of computational simulation of rotorcraft flight was developed and implemented. In this approach the aircraft motion equations are solved step-by-step, simultaneously with the solution of the Unsteady Reynolds-Averaged Navier–Stokes equations, which is conducted to assess aerodynamic forces acting on the aircraft. As a numerical optimization method, the BFGS (Broyden–Fletcher–Goldfarb–Shanno) algorithm was adapted. The developed methodology was applied to optimize the flight control procedures in selected stages of gyroplane flight in direct proximity to the ground, where proper control of the aircraft is critical to ensure flight safety and performance. The results of conducted computational optimizations proved the qualitative correctness of the developed methodology. The research results can be helpful in the design of easy-to-control gyroplanes and also in the training of pilots for this type of rotorcraft.
Full article

Assessing Density-Functional Theory for Equation-Of-State*Computation* **2018**, *6*(1), 13; doi:10.3390/computation6010013 - 3 February 2018**Abstract **

►
Figures
The last decade has seen a continued development of better experimental techniques to measure equation-of-state (EOS) for various materials. These improvements of both static and shock-compression approaches have increased the accuracy of the EOS and challenged the complimentary theoretical modeling. The conventional modeling

[...] Read more.
The last decade has seen a continued development of better experimental techniques to measure equation-of-state (EOS) for various materials. These improvements of both static and shock-compression approaches have increased the accuracy of the EOS and challenged the complimentary theoretical modeling. The conventional modeling of EOS, at least at pressure and temperature conditions that are not too extreme, is founded on density-functional theory (DFT). Naturally, there is an increased interest in the accuracy of DFT as the measurements are becoming more refined and there is a particular interest in the robustness and validity of DFT at conditions where experimental data are not available. Here, we consider a broad and large set of 64 elemental solids from low atomic number Z up to the very high Z actinide metals. The intent is to compare DFT with experimental zero-temperature isotherms up to 1 Mbar (100 GPa) and draw conclusions regarding the theoretical (DFT) error and quantify a reasonable and defensible approach to define the theoretical uncertainty. We find that in all 64 cases the DFT error at high pressure is *smaller than or equal**to* the DFT error at lower pressures which thus provides an upper bound to the error at high compression.
Full article

A Microwave Reflectometry Technique for Profiling the Dielectric-Conductivity Properties of the Hagia Sophia Globe*Computation* **2018**, *6*(1), 12; doi:10.3390/computation6010012 - 2 February 2018**Abstract **

►
Figures
A microwave free space reflectometry technique with swept frequency measurements for the profiling of wall structures and the detection of hidden (covered) layers has been applied to the Hagia Sophia byzantine monument. Experimental measurement results are presented and compared with three-dimensional (3D) simulated

[...] Read more.
A microwave free space reflectometry technique with swept frequency measurements for the profiling of wall structures and the detection of hidden (covered) layers has been applied to the Hagia Sophia byzantine monument. Experimental measurement results are presented and compared with three-dimensional (3D) simulated results, exhibiting fair agreement in some (though not all) aspects. Based on the experimental results, the possibility of clear discrimination between regions with and without covered mosaic layers, and hence the detection of such layers, is demonstrated.
Full article

Seismic Response of Adjacent Unequal Buildings Subjected to Double Pounding Considering Soil-Structure Interaction*Computation* **2018**, *6*(1), 10; doi:10.3390/computation6010010 - 1 February 2018**Abstract **

►
Figures
Various cases of two adjacent multi-story buildings with different numbers of floors and equal or unequal foundation levels under earthquake loading and considering soil-structure interaction (SSI) are investigated. A two-dimensional model for each case of the two adjacent unequal buildings without separation distance

[...] Read more.
Various cases of two adjacent multi-story buildings with different numbers of floors and equal or unequal foundation levels under earthquake loading and considering soil-structure interaction (SSI) are investigated. A two-dimensional model for each case of the two adjacent unequal buildings without separation distance is used and a special arrangement of contact elements in the contact zone is employed to fulfil all possible deformation contact modes which take place under seismic loading. The soil is modelled by two-dimensional 4-node elements which are in contact with the foundations of the two adjacent buildings. This paper studies the earthquake-induced double pounding that takes place between the two adjacent unequal height buildings in some upper points at superstructure in the contact zone and also at foundation level, considering soil-structure interaction (SSI). The double pounding and the soil-structure interaction (SSI) effects should be taken into consideration in the seismic analysis of adjacent buildings especially those with different heights and different foundation levels.
Full article

Holonomic Constraints: A Case for Statistical Mechanics of Non-Hamiltonian Systems*Computation* **2018**, *6*(1), 11; doi:10.3390/computation6010011 - 1 February 2018**Abstract **

A dynamical system submitted to holonomic constraints is Hamiltonian only if considered in the reduced phase space of its generalized coordinates and momenta, which need to be defined *ad hoc* in each particular case. However, specially in molecular simulations, where the number of

[...] Read more.
A dynamical system submitted to holonomic constraints is Hamiltonian only if considered in the reduced phase space of its generalized coordinates and momenta, which need to be defined *ad hoc* in each particular case. However, specially in molecular simulations, where the number of degrees of freedom is exceedingly high, the representation in generalized coordinates is completely unsuitable, although conceptually unavoidable, to provide a rigorous description of its evolution and statistical properties. In this paper, we first review the state of the art of the numerical approach that defines the way to conserve exactly the constraint conditions (by an algorithm universally known as SHAKE) and permits integrating the equations of motion directly in the phase space of the natural Cartesian coordinates and momenta of the system. We then discuss in detail SHAKE numerical implementations in the notable cases of Verlet and velocity-Verlet algorithms. After discussing in the same framework how constraints modify the properties of the equilibrium ensemble, we show how, at the price of moving to a dynamical system no more (directly) Hamiltonian, it is possible to provide a direct interpretation of the dynamical system and so derive its Statistical Mechanics both at equilibrium and in non-equilibrium conditions. To achieve that, we generalize the statistical treatment to systems no longer conserving the phase space volume (equivalently, we introduce a non-Euclidean invariant measure in phase space) and derive a generalized Liouville equation describing the ensemble even out of equilibrium. As a result, we can extend the response theory of Kubo (linear and nonlinear) to systems subjected to constraints.
Full article

An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems*Computation* **2018**, *6*(1), 9; doi:10.3390/computation6010009 - 31 January 2018**Abstract **

►
Figures
Stochastic simulation has been widely used to model the dynamics of biochemical reaction networks. Several algorithms have been proposed that are exact solutions of the chemical master equation, following the work of Gillespie. These stochastic simulation approaches can be broadly classified into two

[...] Read more.
Stochastic simulation has been widely used to model the dynamics of biochemical reaction networks. Several algorithms have been proposed that are exact solutions of the chemical master equation, following the work of Gillespie. These stochastic simulation approaches can be broadly classified into two categories: network-based and -free simulation. The network-based approach requires that the full network of reactions be established at the start, while the network-free approach is based on reaction rules that encode classes of reactions, and by applying rule transformations, it generates reaction events as they are needed without ever having to derive the entire network. In this study, we compare the efficiency and limitations of several available implementations of these two approaches. The results allow for an informed selection of the implementation and methodology for specific biochemical modeling applications.
Full article

Solid-State Testing of a Van-Der-Waals-Corrected Exchange-Correlation Functional Based on the Semiclassical Atom Theory*Computation* **2018**, *6*(1), 7; doi:10.3390/computation6010007 - 25 January 2018**Abstract **

►
Figures
We extend the SG4 generalized gradient approximation, developed for covalent and ionic solids with a nonlocal van der Waals functional. The resulting SG4-rVV10m functional is tested, considering two possible parameterizations, for various kinds of bulk solids including layered materials and molecular crystals as

[...] Read more.
We extend the SG4 generalized gradient approximation, developed for covalent and ionic solids with a nonlocal van der Waals functional. The resulting SG4-rVV10m functional is tested, considering two possible parameterizations, for various kinds of bulk solids including layered materials and molecular crystals as well as regular bulk materials. The results are compared to those of similar methods, PBE + rVV10L and rVV10. In most cases, SG4-rVV10m yields a quite good description of systems (from iono-covalent to hydrogen-bond and dispersion interactions), being competitive with PBE + rVV10L and rVV10 for dispersion-dominated systems and slightly superior for iono-covalent ones. Thus, it shows a promising applicability for solid-state applications. In a few cases, however, overbinding is observed. This is analysed in terms of gradient contributions to the functional.
Full article