Molecular Simulation (MOL SIMULAT)
Molecular Simulation covers all aspects of research related to, or of importance to, molecular modelling and simulation (including informatics, theoretical and experimental work). Molecular Simulation exists to bring together the most significant papers concerned with applications of simulation methods, and original contributions to the development of simulation methodology from biology and biochemistry, chemistry, chemical engineering, materials and nanomaterials, medicine, physics and information science. The aim is to provide a forum in which cross fertilization between application areas, methodologies, disciplines, as well as academic and industrial researchers can take place and new developments can be encouraged. Molecular Simulation is of interest to all researchers using or developing simulation methods (for example those based on statistical mechanics) and to those experimentalists, theorists and information scientists who wish to use simulation data or address a simulation audience. This journal is abstracted and indexed within the ISI science citation index. Current impact factor is 0.946.
Journal Impact: 1.20*
Journal impact history
|2016 Journal impact||Available summer 2017|
|2015 Journal impact||1.20|
|2014 Journal impact||1.23|
|2013 Journal impact||1.04|
|2012 Journal impact||0.98|
|2011 Journal impact||1.57|
|2010 Journal impact||1.26|
|2009 Journal impact||1.14|
|2008 Journal impact||1.34|
|2007 Journal impact||1.02|
|2006 Journal impact||1.13|
|2005 Journal impact||1.47|
|2004 Journal impact||1.20|
|2003 Journal impact||0.88|
|2002 Journal impact||0.77|
|2001 Journal impact||0.44|
|2000 Journal impact||0.38|
Journal impact over time
|Website||Molecular Simulation website|
|Other titles||Molecular simulation (Online)|
|Material type||Document, Periodical, Internet resource|
|Document type||Internet Resource, Computer File, Journal / Magazine / Newspaper|
Publications in this journal
- [Show abstract] [Hide abstract] ABSTRACT: Continuum methods are not accurate enough for flows at high Knudsen numbers, whereas rigorous molecular dynamics (MD) methods are too costly for simulations at practical dimensions. Hard-sphere (HS) model is a simplified MD method efficient for dilute gaseous flow but is of poor parallelism due to its event-driven nature, which sets a strong limitation to its large-scale applications. In this work, pseudo-particle modelling, a time-driven modelling approach is coupled with HS model to construct a scalable parallel method capable of simulating flows and transport processes at high Knudsen numbers without losing necessary molecular details in describing their macro-scale behaviours. The method is validated in several classical simulation cases and its performance is evaluated to be favourable. To demonstrate the potential applications of this method, we also simulate the diffusion of small molecules in multi-scale porous media which is related to catalysis, material preparation and micro chemical engineering in the long term.
- [Show abstract] [Hide abstract] ABSTRACT: Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.
- [Show abstract] [Hide abstract] ABSTRACT: Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here, we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g. replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g. hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyse two different approaches: the QM/MM–MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analysed here, both approaches seem productive although care needs to be exercised when analysing the perturbative corrections.
- [Show abstract] [Hide abstract] ABSTRACT: We studied the adsorption of Cyanuric fluoride (CF) and s-triazine (ST) molecules on the surface of pristine as well as Al-doped graphenes by using density functional theory calculations (DFT). Our results reveal low adsorption on the surface of pristine graphene; but by modification of surface using aluminum, resulted Al-doped graphene becomes more reactive towards both CF and ST molecules. We aimed to focus on the adsorption energy, electronic structure, charge analysis, density of state (DOS) and global indices of each system upon adsorption of CF and ST molecules on the above-mentioned surfaces. Our calculated adsorption energies for the most stable position configurations of CF and ST on Al-doped graphene were -76.53 kJ mol−1 (-57.45 kJ mol−1 BSSE corrected energy) and -115.55 kJ mol−1 (-86.87 kJ mol−1 BSSE corrected energy), respectively, which point to the chemisorption process. For each CF and ST molecule, upon adsorption on the surface of Al-doped graphene, the band gap of HOMO-LUMO was reduced considerably and it becomes a p-type semiconductor whereas there is no hybridization between the above-mentioned molecules and pristine graphene.
- [Show abstract] [Hide abstract] ABSTRACT: Electrostatic free energies play an essential role in numerous bimolecular processes occurring in solution. Difficulties arise when the long-range Coulomb interaction is computed for idealized infinite simulation models with periodic boundary conditions. To maintain a neutral simulation box and a finite per-box energy, a neutralizing charge density or `gellium' is commonly used, leading to a mean box potential that is constrained to be rigorously equal to zero at all times. Thus, in considering quantities such as ion solvation free energy, the potential drop to move from solvent into the usual, gas phase reference state is missing. In fact, for an infinite molecular system, the electrostatic potential itself is not uniquely defined, but takes the form of an infinite series that is only conditionally convergent. This leads to several possible computational conventions that give different values for the potential and field, all mathematically valid. For experimentally measurable quantities, however, unique results are obtained when sufficiently large simulation boxes are utilized. These concepts are detailed, as well as a fundamental, linear response theoretical framework that provides qualitative understanding of the physical processes involved, especially dielectric relaxation of the environment in response to a new solute charge. Illustrative applications to ligand binding and biomolecular electron transfer are described.
- [Show abstract] [Hide abstract] ABSTRACT: In this work, six Pt(II) complexes have been studied via density functional theory (DFT)/time-dependent DFT caculations to explore the influence of different ancillary ligand on electron structures, photophysical properties and radiative decay processes. Moreover, the self-consistent spin–orbit coupling TDDFT was used to calculate zero-field splitting, radiative rate and radiative lifetime to unveil the radiative deactivation processes for these complexes. The results indicated that [Pt(ppy)(ppz)] (ppy = 2-phenylpyridine and ppz = 5-(2-pyridyl)-pyrazole) has a higher radiative decay rate constant and a smaller nonradiative decayrate constant than that of [Pt(ppy)(acac)] (acac = acetylacetonate). Furthermore, complex 5, with dimesityboron added on the 3′-position of the pyrazole ring in [Pt(ppy)(ppz)], shows great potential to serve as an efficient blue-green light emitter in OLED.Better phosphorescent properties can be obtained from proper alteration or modification of the ancillary ligand in cyclometalated platinum complexes.
- [Show abstract] [Hide abstract] ABSTRACT: The effects of temperature and size on the welding of Au nanowires (NWs) into T junctions is studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. Simulation results show that when the top NW approaches the bottom one, it elongates towards the bottom one just before welding due to the interaction of the van der Waals attractive force. During welding, the bottom NW gradually reaches critical bend deformation through successive pressure applied from the top one, followed by buckling of the top NW. The structural order of NWs significantly decreases with increasing welding temperature or decreasing NW width. Welding at high temperatures (700 K or above) causes alignment difficulty due to an unstable NW geometry or even welding failure due to a decrease in NW length. Smaller NWs have larger stress during the welding process.
- [Show abstract] [Hide abstract] ABSTRACT: In the present work, we used molecular dynamic simulations of the equilibrium NPT ensemble to examine the effect of an external electric field on the three-phase coexistence temperature of methane gas, liquid water and methane hydrate. For these simulations, we used the TIP4P/Ice rigid water model and a single-site model for methane. The simulations were implemented at two pressures, 400 and 250 bar, over temperatures ranging from 285 to 320 K and from 280 to 315 K, respectively. The application of an external electric field in the range of 0.1–0.9 caused the effect of the thermal vibrations of the water molecules to become attenuated. This resulted in a shift of the three-phase coexistence temperature to higher temperatures. Electric fields below this range did not cause a difference in the coexistence temperature, and electric fields above this range enhanced the thermal effect. The shift had a magnitude of 22.5 K on average.
- [Show abstract] [Hide abstract] ABSTRACT: In this study, the binding of the enzyme chitinase A1 (afChiA1) from the plant-type Aspergillus fumigatus with four potent inhibitors, allosamidin (ASM), acetazolamide (AZM), 8-chloro-theophylline (CTP) and kinetin (KIT) is investigated by molecular docking, molecular dynamics simulation and binding free energy calculation. The results reveal that the electrostatic interactions play an important role in the stabilisation of the binding of afChiA1 with inhibitors. Based on the binding energy of afChiA1-ligands, the key residues (Gln37 and Trp312) in the active binding pocket of the complex systems are confirmed by molecular mechanics/Poisson–Boltzmann surface area method, and the active inhibitors, ASM and AZM, both could form strong interaction with Gln37 and Trp312, and the non-active ligands, CTP and KIT, could not interact with these two residues, which is consistent with the result of experimental report. Then, it is identified that Gln37 and Trp312 should be one of the important active site residues of afChiA1.
- [Show abstract] [Hide abstract] ABSTRACT: An algorithm based on dissipative particle dynamics (DPD) method is employed to simulate the structure of ferromagnetic fluids at thermodynamic equilibrium state. Two cases are considered. First, the effects of the magnetic particle–particle interaction strength on the structure of magnetic fluids are studied for the fixed-magnetic particle area fraction using the above DPD-based method. The obtained aggregate structures of magnetic particles agree well qualitatively with the corresponding simulation and experimental results in the literature. The radial distribution functions (RDFs) characterising quantitatively the internal structure of magnetic fluids are also calculated and analysed. As a result, the magnetic particle–particle interaction strength plays a crucial role in the formation of magnetic particle chain structure. Second, the influences of the magnetic particle area fraction φ on the structure of magnetic fluids are investigated for the fixed-magnetic particle–particle interaction strength using the above method. The simulated results are in qualitatively good agreement with simulation and experimental results in the literature. The influence of the size of periodic boundary on the height of the first peaks of RDFs is discussed and for the present system, the influence can be neglected. All the simulations and calculations show the employed DPD-based method is very effective. In a word, the present DPD-based method is indeed a powerful tool for simulating the structure of magnetic fluids.
- [Show abstract] [Hide abstract] ABSTRACT: We present a numerical study of droplets sliding across chemically heterogeneous surfaces formed by a periodic pattern of alternating hydrophobic and hydrophilic stripes, or topographically heterogeneous surfaces which are microgrooved. The numerical simulation performed by using a particle-based numerical method, Many-body Dissipative Particle Dynamics (MDPD), is adopted to observe the stick-slip motion of droplets driven by a constant body force. The fractions of two types of surfaces are varied from 0.3 to 0.7 to investigate their influence on stick-slip motion of droplets. The dynamic contact angles and the variation in distance Dfr between the front and the rear contact points are shown for different fractions. The jerky motion characterised by stick-slip motion can be found on chemically heterogeneous surfaces for all fractions we choose and the partial stick-slip motion can also be discovered on topographically heterogeneous surfaces except for fraction Φs = 0.3. The snapshots of droplet show that stick-slip motion is the consequence of the periodic deformation of droplet interface during crossing heterogeneous surfaces and can be controlled by fractions.
- [Show abstract] [Hide abstract] ABSTRACT: Silicene has been proven to be a promising material with attractive electronic properties. During the synthesis of silicene, structural defects such as edge crack are likely to be generated and such defects in silicene have impacts on its properties. Herein, molecular dynamics simulations were performed to investigate the mechanical properties of the armchair silicene nanoribbons (ASiNRs) with edge cracks. Our results showed that the mechanical properties of the ASiNRs decrease because of the existence of edge crack. Both the pristine ASiNRs and the ASiNRs with edge cracks show brittle fracture behaviours. The crack length plays an important role in determining the critical strain and fracture strength of the ASiNRs. Moreover, we investigated the effects of strain rate and temperature on the mechanical properties of the ASiNRs with edge cracks. We observed that the increasing strain rate increases the critical strain and fracture strength while decreasing the Young’s modulus. Low-strain rates also changes the expanded directions of cracks in the ASiNRs. We also found that the increasing temperature could significantly decrease the mechanical properties of the ASiNRs with edge cracks.
- [Show abstract] [Hide abstract] ABSTRACT: Solvation structures of Na+–Cl− ion pair are investigated in acetonitrile (AN)–dimethylformamide (DMF) isodielectric mixtures. The potentials of mean force of Na+–Cl− in the five compositions of mixtures show minima corresponding to a contact ion pair (CIP) and a solvent-shared ion pair (SShIP). The solvent-separated ion pair minima are present in lower mole fractions of AN (xAN ≤ 0.50). CIPs are found to be more stable than the SShIPs. From a thermodynamic decomposition of the potentials of mean force, we find that the formation of the ion pair is entropically driven in these compositions. The most stable CIP is in pure AN. The local solvation structures around the ion pair are analysed through the running coordination numbers, excess coordination numbers, solvent orientational distributions and density profiles. We find that both Na+ and Cl− are preferentially solvated by DMF.
- [Show abstract] [Hide abstract] ABSTRACT: A series of graphene (GR) pull-out simulations based on molecular dynamics (MD) were carried out to investigate the interfacial mechanical properties between GR and a polymer matrix (polyethylene: PE). The effects of pull-out velocity, number of vacancy defect in GR and temperature on the interfacial mechanical properties of a GR/PE nanocomposite system were explored. The obtained results showed that the pull-out velocity and the temperature have significant influences on the interfacial mechanical properties for a perfect GR. Moderate vacancy defects in GR can effectively enhance the interfacial mechanical properties in GR-based polymer nanocomposites.
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