Computer modelling & simulation group of Aatto Laaksonen

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MolSim - BioMod - CompMatSci - TheoChem
Division of Physical Chemistry - Arrhenius Laboratory
Stockholm University - Stockholm - Sweden

Computer modelling & simulations ...

- have been important tools at the PhysChem division more than three decades. It started in mid-70's with rigorous ab initio calculations of Nuclear Magnetic Resonance (NMR) parameters with the focus on nuclear spin-spin coupling constants and continued with Monte Carlo (MC) and classical Molecular Dynamics (MD) simulations - often carried out closely connected to solution-state NMR experiments to provide motional models and time scales to inter- and intra-molecular spin relaxation mechanisms and transport propertiesfor a great variety of systems from small organic molecules to nucleic acids. These types of computer simulations not only required an extensive model and method development work but also large programming efforts and invention of new algorithms and efficient parallellized computational schemes. The modeling and simulation now cover virtually all types of biomolecular systems, drug design, solutions, clusters and atmospheric icy particles, etc. The group now also participates in design of new functional porous materials.

Method development is still an important part of the work done in the group. Several innovative schemes for free-energy calculations, first-principles and hybrid QM/MM simulations, hierarchical coarse-graining/multi-scale modelling based on effective potentials, accurate treatment of long-ranged Coulombic interactions by an Ewald summation method using non-uniform fast FFTs, are just a few examples of these.

Modelling of human membrane proteins No crystal structures available for VGLUT1-3. Comparative modelling to a distant bacterial homologue with x-ray structure is validated with MD simulations providing a stable 3D model and a platform for docking trials. Read more ... >


MD simulations of DNA stretching MD simulations, to closely mimic a torsionally unconstrained single-molecule stretching experiment of dsDNA uncover three distinct force regimes, characterized by fast and slow elongation regions with a transition regime in between, where the α and γ backbone torsion angles of the elongated double-stranded DNA find rapidly new stationary values. In the slow elongation regime DNA gradually looses its twist, collectively breaks all base-pair H-bonds and develops a remarkable base-stacked structure with the bases strongly tilted, forming a zipper-like stack on the major groove side, stabilized by specific water interactions. Read more ... >

Solvation phenomena & preferential solvation Solubility, lack of solubility, and other solvation properties of atoms, molecules, and ions in aqueous solutions play an important role in very many areas and applications. Water is a unique solvent with a combination of superior solvation power for polar and ionic substances and a lack of it in the case of noble gas atoms and organic non-polar substances. Due to its small size and high mobility, water molecules are able to access and cover surface locations of solute molecules to form a hydration shell. It is possible for water molecules to participate in many arrangements of hydrogen bonds due to its double donor and acceptor ability. Solvent mixtures of water and a water-miscible organic solvent are important media in many areas of industrial and environmental processes. Read more ... >

Urocanic acid - an epidermal chromophore The cis-trans photoisomerization is a ubiquitous reaction for non-cyclic unsaturated chromophores in biological systems. It provides a unique way to transfer electromagnetic energy into permanent chemical energy via mechanical movement. Urocanic acid (4-imidazoleacrylic acid, is an epidermal soluble chromophore accumulating in the upper layer of the human skin where it is known to undergo a trans-cis photo-isomerization upon UV irradiation. However, the connection of this reaction to any biological effect is still largely unknown. Read more ... >

DNA damage & repair DNA is the only biomolecule which is repaired; all the other molecules are simply replaced. We have studied the damaged DNA called 8-oxoguanine, an endogenous mutagen contributing to transversion mutations G-C → T-A, and the most common somatic mutation in human cancers. One particular enzyme is capable to detect the mutated base and repair it is the human 8-oxoguanine DNA glycosylase, abbreviated hOGG1. Read more ... >

NlogN scaling robust and accurate Ewald based on non-uniform FFTs The electrostatic energies and forces in molecular computer simulations are the by far most time-consuming part due to their long-ranged interactions. We present a novel approach by combining the traditional Ewald summation technique with the non-uniform Fast Fourier transform. This method is both highly efficient, scaling as N log N and straight-forward to implement in existing simulation programs. We report an implementation where we utilize widely available libraries and demonstrate the speed and accuracy of our approach and the expected computational complexity. Read more ... >


Tight-binding-like approximate DFT A highly efficient ab initio tight-binding-like approximate density-functional quantum mechanical method is developed by us recently. In this method, the integrals related to the exchange-correlation part are obtained by higher order many-center expansions and all the integrals can be obtained by the interpolation of the look-up tables. The speed of the calculation is also enhanced by using a better way to choose the integrals in the look-up tables. It is shown that the calculated molecular equilibrium geometries and the reaction energies for hydrogenation reactions are very close to those from the usual density functional theory calculations. Read more ... >

Extended NDDO model for semi-empirical MO calculations The major advantage of the semi-empirical MO methods is their great simplicity. They can be used in the study of large molecular systems with very limited computer resources. However, the neglect (or partial neglect) of the explicit treatment of the electron-electron interactions makes these methods unable to study many important systems, We have recently developed a new quantum chemistry model which we call for ENDDO (Extended NDDO). It is based on a novel theoretical derivation starting from the ab initio molecular orbital (MO) model keeping as much of the interactions as possible as well as a proper balance in the treatment of the possible approximations in the derivation. Read more ... >

Self-consistent QM/MM approach A novel, self-consistent approach, applicable both for ground and excited electronic states, is introduced to calculate molecular properties in clusters and liquids. Using the method, carried out here at the second-order Mùller±Plesset perturbation theory (MP2) level, we obtain an average dipole moment of 2.65 D for water in liquid. Significant changes in quadrupole moment and polarizability, due to surrounding molecules, are also found along the water plane in the direction perpendicular to the axis bisecting the H-O-H bond angle. Read more ... >


QM/MM simulation of water The combined QM/MM calculations are a natural further development from the continuum solvation models where the microscopic environment is introduced into the quantum chemical calculations togteher with temperature and entropy. In MD simulations the dynamical behavior of the system as a function of time can then be incorporated. We have investigated the QM/MM coupling in simulations of liquid water. Read more ... >


Phase transitions in water clusters Freezing and melting are very much asymmetric as phase transitions in such that freezing occurs below the melting. Theoretical modelling and simulations are highly useful to gain more insight into the molecular physics and chemistry of atmospheric processes. Clusters are intermediates between isolated molecules and condensed bulk phases. Read more ... >

 

On the calculations of partial charges a detailed theoretical derivation based on quantum mechanics is presented to find the atomic charges appropriate for the MM force fields. In the derivation, only the Coulomb interaction of a molecule with its surrounding molecules is considered and the main focus is on the net Coulomb interaction. The derivation uses the variational principle and especially the perturbation technique. The final expression for the net Coulomb interaction is approximated as the Coulomb interaction between the effective point charges centered on the atomic sites. Read more ... >


Atmospheric water clusters We have carried out classical Molecular Dynamics computer simulations of local  structural, dynamical, electrical and thermodynamical properties of pure and ion-containing water clusters in atmospheric conditions. Read more ... >

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Adaptive Expanded Ensemble MD method This is an accurate method to compute absolute solvation free energies in one single MD simulation run. It is a hybrid where a Monte Carlo scheme is used for a continuous insertion/deletion of molecules along solvation coordinates. It has been automated recently to avoid the initial and often lengthy determination of the balancing factors.  [Åberg, Lyubartsev, Jacobsson, & Laaksonen, J. Chem. Phys., 120, 3770 (2004)].

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