Numerical estimation of entropy loss on dimerization: improved prediction of the quaternary structure of the GCN4 leucine zipper

A lattice based model of a protein is used to study the dimerization equilibrium of the GCN4 leucine zipper. Replica exchange Monte Carlo is used to determine the free energy of both the monomeric and dimeric forms as a function of temperature. The method of coincidences is then introduced to explicitly calculate the entropy loss associated with dimerization, and from it the free energy difference between monomer and dimer, as well as the corresponding equilibrium reaction constant. We find that the entropy loss of dimerization is a strong function of energy (or temperature), and that it is much larger than previously estimated, especially for high energy states. The results confirm that it is possible to study the dimerization equilibrium of GCN4 at physiological concentrations within the reduced representation of the protein employed

Computational studies of biomembrane systems: Theoretical considerations, simulation models, and applications

This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated interactions, attraction between transmembrane proteins, and aggregation in biomembranes leading to large superstructures such as the light harvesting complex of green plants. After a general overview of theoretical considerations and continuum theory of lipid membranes we introduce different options for simulations of biomembrane systems, addressing questions such as: What can be learned from generic models? When is it expedient to go beyond them? And what are the merits and challenges for systematic coarse graining and quasi-atomistic coarse grained models that ensure a certain chemical specificity

The arrow of time and the nature of spacetime

This paper extends the work of a previous paper [arXiv:1208.2611] on the flow of time, to consider the origin of the arrow of time. It proposes that a `past condition' cascades down from cosmological to micro scales, being realized in many microstructures and setting the arrow of time at the quantum level by top-down causation. This physics arrow of time then propagates up, through underlying emergence of higher level structures, to geology, astronomy, engineering, and biology. The appropriate space-time picture to view all this is an emergent block universe (`EBU'), that recognizes the way the present is different from both the past and the future. This essential difference is the ultimate reason the arrow of time has to be the way it is.Comment: 56 pages, 7 figure

Extending the Modern Synthesis: The evolution of ecosystems

The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis

Coarse grained force field for the molecular simulation of natural gases and condensates

AbstractThe atomistically-detailed molecular modelling of petroleum fluids is challenging, amongst other aspects, due to the very diverse multicomponent and asymmetric nature of the mixtures in question. Complicating matters further, the time scales for many important processes can be much larger than the current and foreseeable capacity of modern computers running fully-atomistic models. To overcome these limitations, a coarse grained (CG) model is proposed where some of the less-important degrees of freedom are safely integrated out, leaving as key parameters the average energy levels, the molecular conformations and the range of the Mie intermolecular potentials employed as the basis of the model. The parametrization is performed by using an analytical equation of state of the statistical associating fluid theory (SAFT) family to link the potential parameters to macroscopically observed thermophysical properties. The parameters found through this top-down approach are used directly in molecular dynamics simulations of multi-component multi-phase systems. The procedure is exemplified by calculating the phase envelope of the methane–decane binary and of two synthetic light condensate mixtures. A methodology based on the discrete expansion of a mixture is used to determine the bubble points of these latter mixtures, with an excellent agreement to experimental data. The model presented is entirely predictive and an abridged table of parameters for some fluids of interest is provided

Multiscale photosynthetic exciton transfer

Photosynthetic light harvesting provides a natural blueprint for bioengineered and biomimetic solar energy and light detection technologies. Recent evidence suggests some individual light harvesting protein complexes (LHCs) and LHC subunits efficiently transfer excitons towards chemical reaction centers (RCs) via an interplay between excitonic quantum coherence, resonant protein vibrations, and thermal decoherence. The role of coherence in vivo is unclear however, where excitons are transferred through multi-LHC/RC aggregates over distances typically large compared with intra-LHC scales. Here we assess the possibility of long-range coherent transfer in a simple chromophore network with disordered site and transfer coupling energies. Through renormalization we find that, surprisingly, decoherence is diminished at larger scales, and long-range coherence is facilitated by chromophoric clustering. Conversely, static disorder in the site energies grows with length scale, forcing localization. Our results suggest sustained coherent exciton transfer may be possible over distances large compared with nearest-neighbour (n-n) chromophore separations, at physiological temperatures, in a clustered network with small static disorder. This may support findings suggesting long-range coherence in algal chloroplasts, and provides a framework for engineering large chromophore or quantum dot high-temperature exciton transfer networks.Comment: 9 pages, 6 figures. A significantly updated version is now published online by Nature Physics (2012