Recent progress in adaptive multiscale molecular dynamics simulations of soft matter
Phys. Chem. Chem.
Phys. 12, 12401 - 12414 (2010)
Steven O. Nielsen, Rosa E. Bulo, Preston B. Moore and Bernd Ensing
Understanding mesoscopic phenomena in terms of the fundamental motions of atoms and electrons poses a severe challenge for molecular simulation. This challenge is being met by multiscale modeling techniques that aim to bridge between the microscopic and mesoscopic time and length scales. In such techniques different levels of theory are combined to describe a system at a number of scales or resolutions. Here we review recent advancements in adaptive hybrid simulations, in which the different levels are used in separate spatial domains and matter can diffuse from one region to another with an accompanying resolution change. We discuss what it means to simulate such a system, and how to enact the resolution changes. We show how to construct efficient adaptive hybrid quantum mechanics/molecular mechanics (QM/MM) and atomistic/coarse grain (AA/CG) molecular dynamics methods that use an intermediate healing region to smoothly couple the regions together. This coupling is formulated to use only the native forces inherent to each region. The total energy is conserved through the use of auxiliary bookkeeping terms. Error control, and the choice of time step and healing region width, is obtained by careful analysis of the energy flow between the different representations. We emphasize the CG → AA reverse mapping problem and show how this problem is resolved through the use of rigid atomistic fragments located within each CG particle whose orientation is preconditioned for a possible resolution change through a rotational dynamics scheme. These advancements are shown to enable the adaptive hybrid multiscale molecular dynamics simulation of macromolecular soft matter systems.
- Read the whole article here: dx.doi.org/10.1039/C004111D
Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein
Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. Likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as well as tentative transition states, without further simulation. We find that the unfolding of the α-helical region 43–51 is followed by sequential solvent exposure of both Glu46 and the chromophore. Which of these two residues is exposed first is correlated with the presence of a salt bridge that is part of the N-terminal domain. Additional molecular dynamics simulations indicate that the exposure of the chromophore does not result in a productive pathway. We discuss several possibilities for experimental validation of these predictions. Our results open the way for studying millisecond conformational changes in other medium-sized (signaling) proteins.
- Read the whole article here: PNAS paper
- Catching a protein in the act Commentary on this paper by Gerard Hummer.
- Review of this paper in Dutch
State-of-the-art models for the phase diagram of carbon and diamond nucleation
Physics 106, 2011 - 2038 (18 August 2008)
L. M. Ghiringhelli, C. Valeriani, J. H. Los, E. J. Meijer, A. Fasolino, D. Frenkel
We review recent developments in the modelling of the phase diagram and the kinetics of crystallization of carbon. In particular, we show that a particular class of bond-order potentials (the so-called LCBOP models) account well for many of the known structural and thermodynamic properties of carbon at high pressures and temperatures. We discuss the LCBOP models in some detail. In addition, we briefly review the 'history' of experimental and theoretical studies of the phase behaviour of carbon. Using a well-tested version of the LCBOP model (viz. LCBOPI+) we address some of the more controversial hypotheses concerning the phase behaviour of carbon, in particular: the suggestion that liquid carbon can exist in two phases separated by a first-order phase transition and the conjecture that diamonds could have formed by homogeneous nucleation in Uranus and Neptune.
- Read the whole article here: dx.doi.org/10.1080/00268970802077884
Towards a molecular understanding of shape selectivity
Nature 451, 671-678
(7 February 2008)
Berend Smit and Theo L. M. Maesen
Shape selectivity is a simple concept: the transformation of reactants into products depends on how the processed molecules fit the active site of the catalyst. Nature makes abundant use of this concept, in that enzymes usually process only very few molecules, which fit their active sites. Industry has also exploited shape selectivity in zeolite catalysis for almost 50 years, yet our mechanistic understanding remains rather limited. Here we review shape selectivity in zeolite catalysis, and argue that a simple thermodynamic analysis of the molecules adsorbed inside the zeolite pores can explain which products form and guide the identification of zeolite structures that are particularly suitable for desired catalytic applications.
- Read the whole article here: doi:10.1038/nature06552
See for complete publication lists, the webpages of the research group below:
- theoretical chemistry, VU University Amsterdam
- computational chemistry, University of Amsterdam
- computational biophysics, Amolf