This looks like a solid request. Lets go ahead with 100K for the first half, hoping that John can use at least 50K by December 31st. Ray On 11/16/10 3:57 PM, "John Valdes" <[email protected]> wrote:

We haven't made a decision on this new project request. By that, are we saying that this person doesn't know what he's talking about? :)

John

On Fri, Oct 29, 2010 at 02:45:38PM -0500, [email protected] wrote:

...

Hello,

A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee.

Applicant's name: John J. Low Applicant's institution: ANL Applicant's division: MCS Project Name: aimd_catalysis Project title: Ab Initio Molecular Dynamics for Catalysis of Biomass to Fuels Associated funding: Department of Energy, Office of Science, and Office of Basic Energy Sciences Other Systems: None Science: Since the catalytic conversion of biomass occurs in the aqueous phases, water will be intimately involved with the reaction mechanisms. Ab Initio Molecular Dynamics allows for the quantum mechanical simulation of reaction mechanisms in aqueous phases under reaction conditions such as low pH and high temperature (~500K). Metadynamics accelerates the molecular dynamics along collective variables and enables the mapping of the free energy surfaces from reactants to products with trajectories covering several picoseconds. These trajectories reveal the reaction mechanism and estimate the free energies of activation for competing pathways. This project will model the acid catalyzed decomposition of glucose to hydroxy-methyl furfural (HMF) in water. HMF is precursor to transportation fuels and industrial chemicals. The AIMD of reactions with explicit water molecules is more realistic than the self consistent reaction fields used to predict thermodyn am ics in solutions with quantum chemistry because clusters of water hydrogen bond strongly to glucose and mediates hydrogen transfer reactions in aqueous phases. The results of the AIMD will be used to model the effects of mixed solvents on the glucose decomposition reaction and improved yields of fuel from glucose.

Supported nanoparticles of metals are used to selectively reduce oxygen content of biomass. The plethora of metastable geometries of these clusters makes it difficult to model the lowest energy reaction pathways on these metal clusters. Metadynamics provides a method to quickly sample the lowest energy geometries of metal clusters and discover the equilibrium geometry automatically. Metadynamics will be used to predict the lowest energy structures of multimetallic nanoparticles with adsorbates. These structures will be the basis of higher level calculations to predict chemistry on these particles. These calculations will lead to improved catalysts for converting biomass to fuel.

Project description: We will use CPMD to model reactions in aqueous phases. This program has the very efficient Carr-Parinello algorithm for AIMD and several different methods for thermodynamics sampling including metadynamics, umbrella sampling and the Blue-Moon ensemble. CPMD is an excellent tool for modeling reactions in liquids and sampling phase space.

The parallel performance of CPMD is fair. The unit cell for our model of glucose in sulfuric acid contains 230 atoms and a unit cell volume of 2500 ??3. The MPI version of CPMD had a parallel efficiency of 70% on 160 processors for this model. The number of planes in the real space grid limits the number of processors which can be used efficiently by CPMD. We plan to implement a hybrid (MPI/OPENMP) version of CPMD of version which should increase the parallel efficiency of CPMD significantly by allowing multiple processors (up to eight on Fusion) to work on each plane of the real space grid and reducing the overhead from MPI All_to_All communication. A metadynamics run of 10ps is adequate to model a step in the glucose decomposition reaction. Ten picoseconds require 7.3 kilocore-hours. We plan to model 20 reaction pathways in the glucose to HMF reaction mechanism. This work will require approximately 150 kilocore-hours.

Simulation time of 10ps will be required to sample the phase space of bimetallic metal clusters. We estimate that each of trajectories will require a kilocore-hour. We plan to model the geometry of ten different metal alloy clusters. We will also simulate these clusters with chemisorbed hydrogen and oxygen. This work will require 50 metadynamics runs or 50 kilocore-hours.

Project URL: Requested allocation: 200000 Justification:

The requester has used 0 hours of their initial startup project.

In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see:

https://wiki.lcrc.anl.gov/wiki/Processes/Categories

Once the Allocation committee has approved the project, please go to the Project Management page to create it:

https://accounts.lcrc.anl.gov/projects.php

Thank You, The LCRC Accounts System

...

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----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4126 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751