Molecular Simulation (MOL SIMULAT)

Publisher: Taylor & Francis

Journal description

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.

Current impact factor: 1.13

Impact Factor Rankings

2016 Impact Factor Available summer 2017
2014 / 2015 Impact Factor 1.133
2013 Impact Factor 1.119
2012 Impact Factor 1.056
2011 Impact Factor 1.328
2010 Impact Factor 1.215
2009 Impact Factor 1.028
2008 Impact Factor 1.325
2007 Impact Factor 1.133
2006 Impact Factor 1.084
2005 Impact Factor 1.345
2004 Impact Factor 1.241
2003 Impact Factor 0.721
2002 Impact Factor 0.946
2001 Impact Factor 0.571
2000 Impact Factor 0.646
1999 Impact Factor 0.896
1998 Impact Factor 0.916
1997 Impact Factor 0.824
1996 Impact Factor 1.162
1995 Impact Factor 1.483
1994 Impact Factor 1.379

Impact factor over time

Impact factor
Year

Additional details

5-year impact 1.08
Cited half-life 7.60
Immediacy index 0.62
Eigenfactor 0.00
Article influence 0.31
Website Molecular Simulation website
Other titles Molecular simulation (Online)
ISSN 0892-7022
OCLC 50166441
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Taylor & Francis

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Some individual journals may have policies prohibiting pre-print archiving
    • On author's personal website or departmental website immediately
    • On institutional repository or subject-based repository after either 12 months embargo
    • Publisher's version/PDF cannot be used
    • On a non-profit server
    • Published source must be acknowledged
    • Must link to publisher version
    • Set statements to accompany deposits (see policy)
    • The publisher will deposit in on behalf of authors to a designated institutional repository including PubMed Central, where a deposit agreement exists with the repository
    • STM: Science, Technology and Medicine
    • Publisher last contacted on 25/03/2014
    • This policy is an exception to the default policies of 'Taylor & Francis'
  • Classification
    green

Publications in this journal


  • No preview · Article · Feb 2016 · Molecular Simulation

  • No preview · Article · Feb 2016 · Molecular Simulation
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    ABSTRACT: Innate immunity is an important part of immune system, providing immediate defence for the host against various infections through phagocytes. Toll-like receptors (TLRs) are major proteins expressed on the cell membrane known as pattern recognition receptors (PRR) that recognise non-self molecules (pathogen-associated molecular patterns (PAMPs)). Because TLRs have been implicated in many inflammatory diseases and cancer, TLRs targeted therapeutics have drawn great attention in clinical application in wide range of conditions. Many of them are undergoing evaluation in clinical trials. Chitin is the second most abundant polysaccharide detected in many insects and fungi. Studies have shown that chitin, as major PAMPs in host-infection, can activate TLR2-dependent innate immunity pathway. Therefore, chitin has potential use as an important agonist or antagonist to control key processes in innate immunity. However, no direct evidence has shown that chitin is the direct target of TLR2. This study first demonstrates a binding model of chitin and TLR2 and then confirmed its stability by molecular dynamic simulation and MM/PBSA (molecular mechanics/Poisson−Boltzmann surface area) calculations. The binding between chitin and TLR2 was taken place inside the binding pocket. Two hydrogen bonds were formed between chitin and TLR2, including Ser320 and Lys321. The van der Waals interaction has the major contribution in stabilising the binding of the chitin molecule with the protein. This study also suggests six hot-spots for specific binding of chitin in the binding site of TLR2, namely, Phe296, Phe299, Leu302, Thr309, Ser320 and Val322. Molecular dynamics simulation demonstrates that the complex of chitin and TLR2 is very stable with a total binding affinity of −27.2 kcal/mol from MM/PBSA calculation.
    No preview · Article · Feb 2016 · Molecular Simulation
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    ABSTRACT: Synaptotagmin 1 (Syt1) is a Ca2+ sensor in the membrane of pre-synaptic axon terminal, which functions as an essential regulator of neurotransmitter release and hormone secretion and plays an important role in learning, memory and thinking. The sevoflurane, a general anaesthetics used widely in surgery, has been reported to modulate intracellular calcium flux and downstream neural events by targeting Syt1 C2A domain, exhibiting potential to reshape cognition. In order to explore the binding sites of sevoflurane in Syt1 C2A domain, we herein conducted a systematic computational investigation that integrated ligand pocket mapping, molecular docking calculations and molecular dynamics simulations to perform conformational sampling in the interaction space of sevoflurane with the domain. With the protocol, we were able to identify a number of ‘hotspots’ where sevoflurane can potentially bind to the domain. Subsequently, the location, geometry and physicochemical property of these putative binding sites were examined in detail using a variety of bioinformatics tools, from which three promising candidates were selected and investigated in vitro. Consequently, one was confirmed as specific binding site that can be bound tightly by sevoflurane ligand, while another was suggested to form a relatively weak, non-specific interaction with the ligand. This work would help to understand the molecular mechanism and biological implication underlying Syt1-sevoflurane recognition, and to design molecular aptamers to intervene with cognitive behaviour.
    No preview · Article · Jan 2016 · Molecular Simulation
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    ABSTRACT: This work, to celebrate the distinguished scientific career of Professor Ian K. Snook, presents a derivation of the cable equation of Hodgkin and Huxley for the membrane potential (Formula presented.) from the principles of electrodiffusion to obtain(Formula presented.) where C is the membrane capacitance, (Formula presented.) the Debye parameter of the aqueous regions, a the radius of the axon, D is the average diffusion equation of mobile ions, (Formula presented.) the dielectric constant of water and (Formula presented.) the permittivity of free space.
    No preview · Article · Dec 2015 · Molecular Simulation
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    ABSTRACT: The miscibility and mechanical properties of poly vinyl alcohol (PVA) and poly acrylic acid (PAA)-composited membranes were studied with molecular simulation. The Flory–Huggins parameters (δ) were calculated to prove the good miscibility of PVA and PAA. The radial distribution functions of hydroxyl and carboxyl atoms and the average number of H-bonds were observed to indicate the degree of physical cross-linking between PVA and PAA. The influences of intermolecular physical cross-linking on the glass transition temperature and mechanical properties were estimated. The results revealed that the PVA/PAA membrane with a composition of 2:3 has the best plastic properties, which exhibits a good application value. All of the simulated results showed good agreement with the experimental data. It indicates that the method presented in this work has a promising application prospect.
    No preview · Article · Dec 2015 · Molecular Simulation
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    ABSTRACT: The conformational structure of dilute atactic-poly(methacrylic acid) (PMA) solution in binary water–ethanol mixture was investigated by molecular dynamics simulations, over 0–0.9 ethanol (co-solvent) fraction. The radius of gyration 〈Rg〉, torsion angle distribution, intra-chain hydrogen bonds (H-bonds), and H-bonds for PMA–water, PMA–ethanol and water–ethanol, atom–atom and atom–group pair radial distribution functions were analysed. An increase in the ethanol fraction leads to chain expansion. The non-monotonic variation of 〈Rg〉, commensurate with the experimentally observed behaviour of intrinsic viscosity [η], takes place by H-bonding effects between PMA, water and ethanol, as driven by the differences in the chemical structure of water and ethanol. The PMA repeat units are closer to the CH2 groups as compared with CH3 groups of ethanol, in the nearest coordination shell. Water as compared with ethanol is able to coordinate closer to the PMA repeat unit centre of mass. Intra-chain H-bonding depreciates with an increase in the ethanol content in solution. The changes, across the ethanol fraction range, in chain dimensions and of predicted intrinsic viscosity by the simulations, compare well with experimental results in the literature.
    No preview · Article · Dec 2015 · Molecular Simulation
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    ABSTRACT: Interactions between transmembrane (TM) peptides are important in biophysical chemistry, but there are few studies assessing atomistic simulation parameters concerning the energetics of interactions of TM helical peptides. Our potential of mean force analysis using OPLS-AA protein/Berger lipid force fields (FFs) shows that the dimerisation energy of (AALALAA)3 helical peptides in the dioleoylphosphatidylcholine bilayer is −4.4 kJ/mol, which was much smaller than the reported experimental value (−12.7 kJ/mol), thus calling for improvement of parameters of the combined FFs. As each of the FFs has been independently developed, we then tested the effects of downscaling the Lennard-Jones (LJ) energy terms between the OPLS-AA atoms and Berger lipid atoms, preserving the parameters within each FF. A 0.9-fold rescaling of the LJ energies was found to render the dimerisation energy close to the experimental value. Solvation of backbone atoms as well as side chain atoms in lipids is crucial for the TM helix interaction. In similar analyses, GROMOS 53A6 FF exhibited as weak dimerisation propensity (~−5.2 kJ/mol) as OPLS-AA/Berger, but CHARMM36 showed relatively accurate propensity (~−9.9 kJ/mol). Challenges and strategies in rendering the TM interaction energy realistic within the framework of current FFs are discussed.
    No preview · Article · Nov 2015 · Molecular Simulation
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    Preview · Article · Nov 2015 · Molecular Simulation
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    ABSTRACT: Responsive surfaces have been suggested to enhance longevity and antifouling performance of materials in many applications from industrial coatings to tissue engineering and drug delivery. We present a molecular dynamics study investigating de-swelling and swelling of some of the most commonly used responsive materials – PEG-functionalised silica and polymer surfaces – as a function of hydration and temperature. We show that PEG chains grafted onto the hard silica substrates exhibit a dehydration-induced collapse that is far more pronounced compared to chains grafted onto the soft polyester surface. The difference between the hard and soft substrates is particularly notable at low coverage densities where the chains are sufficiently separated from one another. We also show that inter-molecular hydrogen bonding responsible for the conformational state of the tethered chains in water can be temperature controlled. It can be suggested that the hard substrates with the intermediate-to-high coverage densities of low molecular weight hydrophilic grafts may be more appropriate for anti-fouling applications due to their ability to trap greater amount of water molecules. Soft substrates may be detrimental for the efficient response of the functionalised surfaces to changes in hydration and enhancement of the surface hardness must be considered when designing responsive surfaces for solution-based applications, such as antimicrobial coatings for industry and biomedicine.
    No preview · Article · Oct 2015 · Molecular Simulation
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    ABSTRACT: The functional cycle of heat shock protein 90 (Hsp90) is driven and inhibited by the association/dissociation of ligand molecules. In order to understand the molecular mechanism of the association of N-terminal domain of Hsp90 (N-Hsp90) and its ligand molecule, it is necessary to investigate which part in the target system promotes or inhibits the association of N-Hsp90 and its ligand molecule. We apply the decomposition analysis for the association free energy of N-Hsp90 and ADP. The mean force calculated by thermodynamic integration method combined with molecular dynamic simulations is divided into the contributions from molecules in the target system. Van der Waals interaction of the solvent water molecules strongly stabilises the association. Three lysine residues on the surface of the N-Hsp90 pull ADP toward the binding pocket of N-Hsp90. This study elucidates the association process of ADP from the bulk region to the binding pocket of the N-terminal domain Hsp90. This approach is applicable to elucidate the association process of biomolecules.
    No preview · Article · Oct 2015 · Molecular Simulation
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    ABSTRACT: To investigate the behaviour of poly(propylene imine) dendrimers – and urea–adamantyl functionalised ones – in solution using molecular dynamics simulations, we developed a coarse-grained model to tackle the relatively large system sizes and time scales needed. Harmonic bond and angle potentials were derived from atomistic simulations using an iterative Boltzmann inversion scheme, modified to incorporate Gaussian fits of the bond and angle distributions. With the coarse-grained model and accompanying force field simulations of generations 1–7 of both dendrimer types in water were performed. They compare favourably with atomistic simulations and experimental results on the basis of size, shape, monomer density, spacer back-folding and atomic form factor measurements. These results show that the structural dynamics of these dendrimers originate from flexible chains constrained by configurational and spatial requirements. Large dendrimers are more rigid and spherical, while small ones are flexible, alternatively rod-like and globular.
    No preview · Article · Oct 2015 · Molecular Simulation
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    ABSTRACT: Elucidating structural determinants in the functional regions of toxins can provide useful knowledge for designing novel analgesic peptides. A series of 100 ns MD simulations were performed on the scorpion toxin BmK AGAP in native and disulphide bond broken states. The comparison of disulphide bond broken states with the native state showed the α-helix was found to be the key to the analgesic activity. Furthermore, our results revealed disulphide bonds have considerable influence on the functionally important essential modes of motions and the correlations between the motions of the Core domain and the C-terminal region which are involved in the analgesic activity. Therefore, we can conclude that disulphide bonds have a crucial role in modulating the function via adjusting the dynamics of scorpion toxin BmK AGAP molecule.
    No preview · Article · Oct 2015 · Molecular Simulation