<i>Faunus</i>– a flexible framework for Monte Carlo simulation

Stenqvist, Björn; Thuresson, Axel; Kurut, Anıl; Vácha, Robert; Lund, Mikael

doi:10.1080/08927022.2013.828207

Cited by 48 publications

(42 citation statements)

References 37 publications

(35 reference statements)

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“…Calculations were performed with the Faunus biomolecular simulation package, 49 where the fast titration scheme was already implemented. The same condition was followed by the full model and cases a, b and c. From this function, the angularly averaged potential of mean force [bw(r) = Àln g(r)] was obtained with low noise, and used to estimate the free energy of the complexation at each physical chemistry condition.…”

Section: Monte Carlo Simulationsmentioning

confidence: 99%

Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin

et al. 2016

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Spider silk is a fascinating material combining mechanical properties such as maximum strength and high toughness comparable or better than man-made materials, with biocompatible degradability characteristics. Experimental measurements have shown that pH triggers the dimer formation of the N-terminal domain (NTD) of the major ampullate spidroin 1 (MaSp 1). A coarse-grained model accounting for electrostatics, van der Waals and pH-dependent charge-fluctuation interactions, by means of Monte Carlo simulations, gave us a more comprehensive view of the NTD dimerization process. A detailed analysis of the electrostatic properties and free energy derivatives for the NTD homoassociation was carried out at different pH values and salt concentrations for the protein wild type and for several mutants. We observed an enhancement of dipole-dipole interactions at pH 6 due to the ionization of key amino acids, a process identified as the main driving force for dimerization. Analytical estimates based on the DVLO theory framework corroborate our findings. Molecular dynamics simulations using the OPEP coarse-grained force field for proteins show that the mutant E17Q is subject to larger structural fluctuations when compared to the wild type. Estimates of the association rate constants for this mutant were evaluated by the Debye-Smoluchowski theory and are in agreement with the experimental data when thermally relaxed structures are used instead of the crystallographic data. Our results can contribute to the design of new mutants with specific association properties.

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Section: Monte Carlo Simulationsmentioning

confidence: 99%

Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin

et al. 2016

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“…Thus, the salt was allowed to exchange with a bulk reservoir with a set chemical potential. All simulations were performed using Faunus (Stenqvist et al 2013) and the temperature was set to 300 K. The free energy between the two parallel rods, WðrÞ, was calculated as a function of the center of mass distance, r, by integrating the mean force The interaction between the rods was investigated for different surface charge densities, salt concentrations, and cation valences. In the model described above there are two fitting parameters: (1) the rod surface charge density, and (2) the non-electrostatic LJ-parameter between the rod sites.…”

Section: Monte Carlo Simulationsmentioning

confidence: 99%

Aggregation behavior of aqueous cellulose nanocrystals: the effect of inorganic salts

et al. 2016

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Natural anisotropic building-blocks such as cellulose nanocrystals (CNCs) have attracted considerable attention due to their biodegradability and nanometer-size. In this work the colloidal behavior of CNCs, obtained from sulfuric acid hydrolysis of microcrystalline cellulose, has been studied in presence of salts of different valences. The influence on the colloidal stability and nature of aggregates has been investigated for monovalent salts (LiCl, NaCl, KCl, CsCl), divalent salts (CaCl 2 and MgCl 2 ), and a trivalent salt (AlCl 3 ), both experimentally by means of turbidity and small angle X-ray scattering (SAXS) measurements, as well as by Monte Carlo simulations using a simple coarse-grained model. For the entire salt series, a critical aggregation concentration (CAC) could be determined by turbidity measurements, as a result of the reduction of effective Coulomb repulsions due to the presence of sulfate groups on the CNC surface. The CACs also followed the Schulze-Hardy law, i.e. the critical aggregation concentration decreased with increasing counterion valence. For the monovalent ions, the CACs followed the trend, which could be rationalized in terms of matching affinities between the cation and the sulfate groups present at the surface of CNCs. From the SAXS measurements it was shown that the density of the aggregates increased with increasing salt concentration and ion valence. In addition, these findings were rationalized by means of simulation, which showed a good correlation with experimental data. The combination of the experimental techniques and the simulations offered insight into interactionaggregation relationship of CNC suspensions, which is of importance for their structural design applications.Electronic supplementary material The online version of this article

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“…43 The electronic Python Notebook (Jupyter) used for running the two-body simulations and construct the presented PMF plots is accessible at https://github.com/mlund/SI-proteins_in_ multivalent_electrolyte.…”

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Anomalous Protein–Protein Interactions in Multivalent Salt Solution

et al. 2017

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1 AbstractThe stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom Molecular Dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion,(ii) ion-ion correlation attraction, (iii) over-charge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly.Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.2

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Faunus– a flexible framework for Monte Carlo simulation

Cited by 48 publications

References 37 publications

Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin

Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin

Aggregation behavior of aqueous cellulose nanocrystals: the effect of inorganic salts

Anomalous Protein–Protein Interactions in Multivalent Salt Solution

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