5 research outputs found

    Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package

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    The three-dimensional reference interaction site model with the closure relation by Kovalenko and Hirata (3D-RISM-KH) in combination with the density functional theory (DFT) method has been implemented in the Amsterdam density functional (ADF) software package. The analytical first derivatives of the free energy with respect to displacements of the solute nuclear coordinates have also been developed. This enables study of chemical reactions, including reaction coordinates and transition state search, with the molecular solvation described from the first principles. The method yields all of the features available by using other solvation approaches, for instance infrared spectra of solvated molecules. To evaluate the accuracy of the present method, test calculations have been carried out for a number of small molecules, including four glycine conformers, a set of small organic compounds, and carbon nanotubes of various lengths in aqueous solution. Our predictions for the solvation free energy agree well with other approaches as well as experiment. This new development makes it possible to calculate at modest computational cost the electronic properties and molecular solvation structure of a solute molecule in a given molecular liquid or mixture from the first principles.Peer reviewed: YesNRC publication: Ye

    Self-Consistent Combination of the Three-Dimensional RISM Theory of Molecular Solvation with Analytical Gradients and the Amsterdam Density Functional Package

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    Development and Application of Numerical Methods in Biomolecular Solvation

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    This work addresses the development of fast summation methods for long range particle interactions and their application to problems in biomolecular solvation, which describes the interaction of proteins or other biomolecules with their solvent environment. At the core of this work are treecodes, tree-based fast summation methods which, for N particles, reduce the cost of computing particle interactions from O(N^2) to O(N log N). Background on fast summation methods and treecodes in particular, as well as several treecode improvements developed in the early stages of this work, are presented. Building on treecodes, dual tree traversal (DTT) methods are another class of tree-based fast summation methods which reduce the cost of computing particle interactions for N particles to O(N). The primary result of this work is the development of an O(N) dual tree traversal fast summation method based on barycentric Lagrange polynomial interpolation (BLDTT). This method is implemented to run across multiple GPU compute nodes in the software package BaryTree. Across different problem sizes, particle distributions, geometries, and interaction kernels, the BLDTT shows consistently better performance than the previously developed barycentric Lagrange treecode (BLTC). The first major biomolecular solvation application of fast summation methods presented is to the Poissonā€“Boltzmann implicit solvent model, and in particular, the treecode-accelerated boundary integral Poissonā€“Boltzmann solver (TABI-PB). The work on TABI-PB consists of three primary projects and an application. The first project investigates the impact of various biomolecular surface meshing codes on TABI-PB, and integrated the NanoShaper software into the package, resulting in significantly better performance. Second, a node patch method for discretizing the system of integral equations is introduced to replace the previous centroid collocation scheme, resulting in faster convergence of solvation energies. Third, a new version of TABI-PB with GPU acceleration based on the BLDTT is developed, resulting in even more scalability. An application investigating the binding of biomolecular complexes is undertaken using the previous Taylor treecode-based version of TABI-PB. In addition to these projects, work performed over the course of this thesis integrated TABI-PB into the popular Adaptive Poissonā€“Boltzmann Solver (APBS) developed at Pacific Northwest National Laboratory. The second major application of fast summation methods is to the 3D reference interaction site model (3D-RISM), a statistical-mechanics based continuum solvation model. This work applies cluster-particle Taylor expansion treecodes to treat long-range asymptotic Coulomb-like potentials in 3D-RISM, and results in significant speedups and improved scalability to the 3D-RISM package implemented in AmberTools. Additionally, preliminary work on specialized GPU-accelerated treecodes based on BaryTree for 3D-RISM long-range asymptotic functions is presented.PHDApplied and Interdisciplinary MathematicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/168120/1/lwwilson_1.pd

    Predictive multiscale modeling of properties and interaction of macro/bio molecules in solvents and mixtures

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    Over the past few decades nanoscience and molecular biology has shown a strong growth worldwide in many areas of research and proved their significance in todays Ģ competitive environment. However, there still remains an enormous potential for further development which could revolutionize every area of human life. Unfortunately, in some cases, that potential is screened out by complexity and multilevel character of systems and processes at a nanometer scale. The success of future applications in a high-tech industry requires deep understanding of fundamental mechanisms on different levels of description and their communication. That could be provided only by appropriate combination of experimental study with predictive theoretical modeling. Nowadays, more and more scientists in different fields of chemistry and biology are using computational modeling methods in their research, either as a technique per se, or as a complement to experimental work. However, despite the in- creasing attention to computational nanoscience and biology the specificity of application of standard theoretical and computational modeling in nanotechnology and bioscience is complicated due to complexity of the systems of interest and needs to be discussed separately, especially in the view of multilevel representation of systems and pro- cesses on nanoscale. One of most important and demanding applications in computational chemistry is multiscale modeling of properties and interaction of macro/bio molecules in solvents and mixtures. The presentation will address different aspects of theoretical and computational approaches and their combination at the different time and length scales to model impact of solvents on physicochemical properties of molecules as geometry, conforma- tional equilibria, reaction rates, as well as their UV-vis, IR, or NMR spectra. It will focus on the combination of statistical-mechanical molecular theory of liquids (3D reference interaction site model, known as 3D-RISM) with density functional theory (DFT) which provides the accurate and efficient way to predict the electronic properties of molecular system in different solvents and mixtures with high level of accuracy comparable with simulations but with less computational cost [1]. Similar to explicit solvent simulations, 3D-RISM properly accounts for chemical and physical activity of both solute and solvent molecules, such as hydrogen bonding and hydrophobic forces, by yielding the 3D site density distributions of the solvent. Moreover, it readily provides, via analytical expressions, the solvation thermodynamics, including the solvation free energy, its energetic and entropic decomposition, and partial molar volume and compressibility. Recently the number of new approaches and approximations was de- veloped in order to increase efficiency of 3D-RISM and DFT combination. They could be subdivided into two main groups focused on the optimization of 3D-RISM algorithm (memory optimization, parallelization, etc.) and methodology improvements [2]. I will present a review and analysis of latest achievements focused on improves of accuracy and applicability the combination. Some examples will be also discussed. References [1] GusarovS., ZieglerT., KovalenkoA., Self-Consistent Combination of the Three-Dimensional RISM Theory of Molecular Solvation with Analytical Gradients and the Amsterdam Density Functional Package, JPCA 110, 1, pp. 6083-6090 (2006). [2] Gusarov S., Bhalchandra P., Kovalenko A., Efficient treatment of solvation shells in 3D molecular theory of solvation, , J. Comp. Chem, 33, 1, pp. 1478-1494 (2012).Non UBCUnreviewedAuthor affiliation: National Institute for NanotechnologyFacult
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