July 2015 - Allocations-admins - mailman3.cels.anl.gov

New LCRC report submitted for Nek5000
by support＠lcrc.anl.gov 22 Jul '15

22 Jul '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=Nek5000

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 22 Jul '15

22 Jul '15

Hello, A change in allocation has been requested: Requester: sjklipp (Stephen Klippenstein) Project: Brewer_Kinetics Title: Estimation of Monomer Reactivity Ratios and Reaction Constants for Polymer Formation using Quantum Mechanics Description: In this project, DFT and ab initio electronic structure calculations will be used to calculate the reaction rate constants and monomer reaction ratios for the polymerization of Brewer materials. The details of this project, include using GAMESS and other appropriate electronic structure software to optimize monomer and transition state structures and determine the effects of solvent and molecular structure on activation energy and improve the quality of polymer materials. Target milestones are: M1: Geometry optimization using electronic structure calculations for copolymers formed by free radical polymerization M2: Transition state optimization and intrinsic reaction coordinate calculations M3: Investigation of the effect of chain length on activation energy and frequency factor M4: Investigation of solvent effects on reactivity ratios using a continuum solvent model (SMD) Current: undetermined amount Justification: Requested: 100000 A specific reason has been given: We have now passed the initial setup stages of our project and are generating meaningful electronic structure data. With John Low's help we are now making effective use of GAMESS on the cluster. The need to change from GAUSSIAN to GAMESS due to software licensing issues has resulted in somewhat increased CPU needs. As a result, our initial allotment of CPU has been used. At this time we would like to request an additional 100000 CPU hours for this non-proprietary stage of our project. We expect to use that CPU over the next 3 months. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 22 Jul '15

22 Jul '15

Additional 60k core hours granted. - JB On Tue, Jul 21, 2015 at 3:58 PM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: scarcell (Riccardo Scarcelli) > Project: FOA_dual_fuel > Title: Efficiency-Optimized Dual Fuel Engine with In-Cylinder Gasoline/CNG Blending > Description: The CFD activity is a crucial sub-task of this entire project and initially (Q1 and Q2) aims at fully characterizing the gaseous jets from DI gas injectors through comparison of numerical results against x-ray measurements carried out at APS. In the second half of FY2015 (Q3 and Q4), the comprehensive modeling of gaseous jets will be exploited to carry out investigations of the mixture formation process in a single-cylinder research engine when gasoline is introduced using port fuel injection (PFI) and compressed natural gas is directly injected (DI) into the cylinder. > > Simulations will be performed with the commercial code CONVERGE and computational grids of few million cells will require the use of 32-64 cores depending on mesh resolution (the RANS approach will be initially followed). The project is expected to have two members, with 2 or 3 cases run simultaneously on daily bases. With an average of 32 cores per run and 2 cases run in parallel, the expected amount of core-hrs needed for this project for each quarter is about: 32x24x90x2=138,240. > > There is not scalability data yet available for this project. However, similar engine simulations showed that with the CONVERGE software and with the expected grid resolution (few million cells) the runs should scale efficiently up to 3 nodes (48 cores). For reference please see the GDI_lean_burn project. > Current: undetermined amount > Justification: > > Requested: 60000 > > A specific reason has been given: > We would need additional 60,000 core-hrs for the project FOA_dual_fuel for Q4 in order to complete all our simulation tasks. In addition to continue our work to meet the deliverables, we are targeting a publication for the next SAE World Congress 2016 and most of the work for this publication needs to be done between August and September. We plan on running all our cases for this publication on 32-64 cores. Below please find the results from a scalability test: >> >> Simulation duration = 1.5e=5 sec >> Computational time on 1 node - 16 cores = 4700 s >> Computational time on 2 nodes - 32 cores = 2700 s --> 87% >> Computational time on 4 nodes - 64 cores = 1600 s --> 73% > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 22 Jul '15

22 Jul '15

Additional 50k core hours granted. - JB On Tue, Jul 21, 2015 at 3:17 PM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: wjiang (wei jiang) > Project: estrogen_namd > Title: Long-scale conformational activation in estrogen receptor with NAMD on GPU/CPU heterogeneous architecture > Description: Wei Jiang, Sunhwan Jo, Sichun Yang > Leadership Computing Facility, Argonne National Laboratory > Case Western Reserve University, School of Medicine > > Projection Description > > Figure 2 Simulations show large-scale dynamics near the H12 region. Four conformations (in yellow) obtained from all-atom NAMD simulations show the loop region near H12 is highly flexible. > > Figure 1 Two states of the LBD. The C-terminal helix (H12) adopts a completely different orientation. > Overall. The ligand-binding domain (LBD) of an estrogen receptor undergoes a large conformational switching from an inactive to active state in response to hormone stimuli (see Figure 1). The inactive conformation is preferred by therapeutic inhibitors such as tamoxifen, where a C-terminal helix H12 (marked in red and blue in Figure 1) blocks the receptor from recruiting co-activators. Once activated by estrogen binding, H12 is switched to a completely different position (marked in red) that covers up the hormone-binding pocket in the active conformation. These two well-defined conformations—active and inactive—have been revealed extensively by crystallographic studies. Very recently, a novel D538G mutant has been identified to be active in advanced breast cancer tumors. Despite being the key molecular target of breast cancer therapeutics, the LBD is a remarkable example of conformational switching, where molecular dynamics of LDB, especially the region near H12, from an > inactive to active conformation remains unclear. The first goal of this proposal is aimed at using high-performance molecular dynamics simulations to quantify the motion near the H12 region for structure-based drug discovery. The second goal is finding novel drug molecules against the receptor domain via accurate free energy calculations, based on those important sub-states identified in the first goal. > Preliminary findings on receptor dynamics simulations. Our published coarse-grained molecular dynamics shows such a transition could take at least in the order of 100 ns (Huang et al, JCTC, 10 (8) 2897–2900, 2014). While this information is highly informative, a key question remains, i.e., whether the mutation affects the active state only or sculpts the entire landscape, including both inactive and active states. More recently, supported by a LCRC award, we have begun to answer this question by simulating the receptor dynamics. Figure 2 shows our preliminary findings about a very diverse set of loop conformations near the H12, suggesting that the system is highly flexible and requires large-scale simulations for sufficient sampling. Note that the simulations were based on the active LBD conformations only. A full H12 transition from inactive to active can be quite challenging for atomic-level simulations using the standard CPU-based MD simulations, and obtaining such a com > plete set of loop/H12 conformations is highly promising for structure-based drug design. > To obtain better sampling and long-time MD trajectories, we propose to extend this study by using the GPU version (Nvidia CUDA) NAMD package on the Blues bigmem GPU/CPU nodes. NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. In this proposal, in addition to the brutal-force GPU/CPU work, we also explore AVX256 instruction set to optimize force kernel of NAMD for state-of-the-art Intel architecture. A fully vectorized force kernel with AVX256 also provides a better reasonable CPU performance reference for GPU. In this proposal we apply a total 50,000 core hours, including both long production run on GPU/CPU nodes and code development with AVX256. > > Figure 3 Accurate docking and binding affinity calculations. A set of four well-studied ligands were used in calculations. Their computed free energies are highly correlated with experimental measurements. > Preliminary findings on docking/binding affinity calculations. Identifying potent ligand-receptor binding is a primary objective of small molecule screening with regards to environmental safety and biological efficacy. During the past decades, computational docking and binding affinity calculations have benefited from improved force fields and sampling algorithms, as well as the advent of highly efficient parallel computing. Such developments have enabled free energy calculations to yield accurate binding affinity predictions, especially via a well-known method of free energy perturbation (FEP). Here, we will apply a docking-FEP protocol on receptor conformations identified from NAMD simulations to achieve the accuracy and reliability to influence lead optimization in a drug discovery setting. This computational method conducts a two-tier evaluation of all ligands: a high-speed docking evaluation by robust binding mode predictions and a high-performance binding affinity evalu > ation via accurate free energy calculations. To demonstrate how the calculations perform, we examined several ligands with four well-known experimental binding affinities to estrogen receptor (ER), supported by a recent LCRC award. Based on this set of ligands, we docked them into the hormone-binding site and applied free energy calculations to each docked ligand-receptor mode. We found a high-level accuracy across a broad range of free energies, with a remarkable agreement to their experimental binding data available in the literature. Figure 3 shows that we achieved a high level of accuracy by comparing the computed and experiential binding affinities of these ligands to the receptor. These highly consistent results from this pilot study are part of primary studies for this renewal for targeting a diverse set of receptor conformations that will be determined by large-scale NAMD simulations. > > 2015 allocation request: 100000 > > Q3: 50000 > Q4: 50000 > > Justification: The request for Q3 (July 1st to Sept 30) and Q4 (Oct 1st to Dec 31st) is based on our core-hour usage and achievement during Apr 1 and June 30rd. > > Current: undetermined amount > Justification: NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. > > Requested: 100000 > > A specific reason has been given: > High throughput drug screening based on the structural information obtained with previous MD/REST2 simulation on Blues/Fusion. > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 21 Jul '15

21 Jul '15

Hello, A change in allocation has been requested: Requester: scarcell (Riccardo Scarcelli) Project: FOA_dual_fuel Title: Efficiency-Optimized Dual Fuel Engine with In-Cylinder Gasoline/CNG Blending Description: The CFD activity is a crucial sub-task of this entire project and initially (Q1 and Q2) aims at fully characterizing the gaseous jets from DI gas injectors through comparison of numerical results against x-ray measurements carried out at APS. In the second half of FY2015 (Q3 and Q4), the comprehensive modeling of gaseous jets will be exploited to carry out investigations of the mixture formation process in a single-cylinder research engine when gasoline is introduced using port fuel injection (PFI) and compressed natural gas is directly injected (DI) into the cylinder. Simulations will be performed with the commercial code CONVERGE and computational grids of few million cells will require the use of 32-64 cores depending on mesh resolution (the RANS approach will be initially followed). The project is expected to have two members, with 2 or 3 cases run simultaneously on daily bases. With an average of 32 cores per run and 2 cases run in parallel, the expected amount of core-hrs needed for this project for each quarter is about: 32x24x90x2=138,240. There is not scalability data yet available for this project. However, similar engine simulations showed that with the CONVERGE software and with the expected grid resolution (few million cells) the runs should scale efficiently up to 3 nodes (48 cores). For reference please see the GDI_lean_burn project. Current: undetermined amount Justification: Requested: 60000 A specific reason has been given: We would need additional 60,000 core-hrs for the project FOA_dual_fuel for Q4 in order to complete all our simulation tasks. In addition to continue our work to meet the deliverables, we are targeting a publication for the next SAE World Congress 2016 and most of the work for this publication needs to be done between August and September. We plan on running all our cases for this publication on 32-64 cores. Below please find the results from a scalability test: > > Simulation duration = 1.5e=5 sec > Computational time on 1 node - 16 cores = 4700 s > Computational time on 2 nodes - 32 cores = 2700 s --> 87% > Computational time on 4 nodes - 64 cores = 1600 s --> 73% This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 21 Jul '15

21 Jul '15

Hello, A change in allocation has been requested: Requester: wjiang (wei jiang) Project: estrogen_namd Title: Long-scale conformational activation in estrogen receptor with NAMD on GPU/CPU heterogeneous architecture Description: Wei Jiang, Sunhwan Jo, Sichun Yang Leadership Computing Facility, Argonne National Laboratory Case Western Reserve University, School of Medicine Projection Description Figure 2 Simulations show large-scale dynamics near the H12 region. Four conformations (in yellow) obtained from all-atom NAMD simulations show the loop region near H12 is highly flexible. Figure 1 Two states of the LBD. The C-terminal helix (H12) adopts a completely different orientation. Overall. The ligand-binding domain (LBD) of an estrogen receptor undergoes a large conformational switching from an inactive to active state in response to hormone stimuli (see Figure 1). The inactive conformation is preferred by therapeutic inhibitors such as tamoxifen, where a C-terminal helix H12 (marked in red and blue in Figure 1) blocks the receptor from recruiting co-activators. Once activated by estrogen binding, H12 is switched to a completely different position (marked in red) that covers up the hormone-binding pocket in the active conformation. These two well-defined conformations—active and inactive—have been revealed extensively by crystallographic studies. Very recently, a novel D538G mutant has been identified to be active in advanced breast cancer tumors. Despite being the key molecular target of breast cancer therapeutics, the LBD is a remarkable example of conformational switching, where molecular dynamics of LDB, especially the region near H12, from an inactive to active conformation remains unclear. The first goal of this proposal is aimed at using high-performance molecular dynamics simulations to quantify the motion near the H12 region for structure-based drug discovery. The second goal is finding novel drug molecules against the receptor domain via accurate free energy calculations, based on those important sub-states identified in the first goal. Preliminary findings on receptor dynamics simulations. Our published coarse-grained molecular dynamics shows such a transition could take at least in the order of 100 ns (Huang et al, JCTC, 10 (8) 2897–2900, 2014). While this information is highly informative, a key question remains, i.e., whether the mutation affects the active state only or sculpts the entire landscape, including both inactive and active states. More recently, supported by a LCRC award, we have begun to answer this question by simulating the receptor dynamics. Figure 2 shows our preliminary findings about a very diverse set of loop conformations near the H12, suggesting that the system is highly flexible and requires large-scale simulations for sufficient sampling. Note that the simulations were based on the active LBD conformations only. A full H12 transition from inactive to active can be quite challenging for atomic-level simulations using the standard CPU-based MD simulations, and obtaining such a com plete set of loop/H12 conformations is highly promising for structure-based drug design. To obtain better sampling and long-time MD trajectories, we propose to extend this study by using the GPU version (Nvidia CUDA) NAMD package on the Blues bigmem GPU/CPU nodes. NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. In this proposal, in addition to the brutal-force GPU/CPU work, we also explore AVX256 instruction set to optimize force kernel of NAMD for state-of-the-art Intel architecture. A fully vectorized force kernel with AVX256 also provides a better reasonable CPU performance reference for GPU. In this proposal we apply a total 50,000 core hours, including both long production run on GPU/CPU nodes and code development with AVX256. Figure 3 Accurate docking and binding affinity calculations. A set of four well-studied ligands were used in calculations. Their computed free energies are highly correlated with experimental measurements. Preliminary findings on docking/binding affinity calculations. Identifying potent ligand-receptor binding is a primary objective of small molecule screening with regards to environmental safety and biological efficacy. During the past decades, computational docking and binding affinity calculations have benefited from improved force fields and sampling algorithms, as well as the advent of highly efficient parallel computing. Such developments have enabled free energy calculations to yield accurate binding affinity predictions, especially via a well-known method of free energy perturbation (FEP). Here, we will apply a docking-FEP protocol on receptor conformations identified from NAMD simulations to achieve the accuracy and reliability to influence lead optimization in a drug discovery setting. This computational method conducts a two-tier evaluation of all ligands: a high-speed docking evaluation by robust binding mode predictions and a high-performance binding affinity evalu ation via accurate free energy calculations. To demonstrate how the calculations perform, we examined several ligands with four well-known experimental binding affinities to estrogen receptor (ER), supported by a recent LCRC award. Based on this set of ligands, we docked them into the hormone-binding site and applied free energy calculations to each docked ligand-receptor mode. We found a high-level accuracy across a broad range of free energies, with a remarkable agreement to their experimental binding data available in the literature. Figure 3 shows that we achieved a high level of accuracy by comparing the computed and experiential binding affinities of these ligands to the receptor. These highly consistent results from this pilot study are part of primary studies for this renewal for targeting a diverse set of receptor conformations that will be determined by large-scale NAMD simulations. 2015 allocation request: 100000 Q3: 50000 Q4: 50000 Justification: The request for Q3 (July 1st to Sept 30) and Q4 (Oct 1st to Dec 31st) is based on our core-hour usage and achievement during Apr 1 and June 30rd. Current: undetermined amount Justification: NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. Requested: 100000 A specific reason has been given: High throughput drug screening based on the structural information obtained with previous MD/REST2 simulation on Blues/Fusion. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 08 Jul '15

08 Jul '15

Granted 150k to Fusion On Wed, Jul 1, 2015 at 3:49 PM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: coliu (Cong Liu) > Project: Bio_catalysis > Title: Biomass Catalysis for Energy > Description: In FY2014, we have completed two of the above aspects, “identifying suitable computational methods” and “reaction pathways”. In FY2015, we are going to focus on the catalysis of C-C coupling reactions. Detailed quantum mechanical calculations will be carried out as follows: > 1. To begin with, H-ZSM5 (zeolite catalyst) will be chosen as a potential catalyst for C-C coupling reactions associated with biomass conversion, based on its strong acidity and it ability to facilitate dehydration reactions. A set of C1-C6 compounds will then be selected from the products of biomass pyrolysis, as potential C-C coupling reactants. These compounds are mainly alcohols, aldehydes, ketones, alkenes, and furans. The interactions between these individual compounds and the catalyst (H-ZSM5) will be studied. Specifically, the binding energies of these compounds onto the acidic site of the catalyst will be calculated using DFT methods in VASP. > 2. Based on the binding energies, the most strong-binding compounds will be selected for C-C coupling reactions. A reaction network will be built among these selected compounds. Four types of C-C coupling reactions will be considered: Diels-Alder, Aldol, alkylation and Michael addition. In addition, dehydration and deoxygenation reactions will also be taken into account. > For example, H-ZSM5 catalyzed C-C coupling reactions furan interacting with acetaldehyde will be investigated with respect to three major reactions: a. furan + furan (Diels-Alder reactions and dehydration), b. furan + acetaldehyde (Diels-Alder reactions and alkylation) and c. acetaldehyde + acetaldehyde (Aldol condensation and dehydration). Reaction energies and barriers will be calculated. All possible reaction pathways will be mapped out and the most important reactions will be identified. These calculations will be carried out using DFT methods in VASP. > 3. The calculations of zeolite catalyzed C-C coupling reactions will then be extended to other C1-C5 compounds from biomass pyrolysis. The catalytic properties of the zeolite catalyst will be analyzed, and the correlations of C-C coupling reactions to the acidity of the catalyst will be identified and used as guidance to develop more efficient C-C coupling catalysts. > > Current: undetermined amount > Justification: > > Requested: 480000 > > A specific reason has been given: > The later stage of the project requires more allocation for the catalyst calculations. > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 08 Jul '15

08 Jul '15

Granted 150k to Fusion On Wed, Jul 1, 2015 at 3:48 PM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: coliu (Cong Liu) > Project: Hetero_Catalysis > Title: Development and Application of Accurate Theoretical Models for Calculating the Thermodynamics of Chemical Bonds for Heterogeneous Catalysis > Description: We will model the reaction mechanisms of the electrocatalysis of CO2 conversion to hydrocarbons using subnanometer Cu clusters supported by CNTs, graphene and aluminum oxide. The electronic and catalytic properties of the nanomaterials, metal-dependence, possible intermediates and transition states of the catalysis will be studied. These studies will provide crucial information for molecular insight into chemical reduction of CO2 and result in significant advancements in the development of novel efficient nanocatalysts. > The following calculations will be performed for FY2015: > > a. The catalytic properties of materials supported metal clusters will be explored. CNTs, graphene and aluminum oxide will be considered as support materials. Interactions between the support materials and metal clusters and the effect of defects on CNTs and graphene will be calculated using DFT methods within VASP package. The simulation of defects on CNTs will begin with a two-dimensional graphene model, with replacements of carbon atoms by N and O. The partial charges of surrounding carbon atoms will be determined as a parameter to measure the charge transfer interactions. Then the interaction between the Cu clusters and CNTs will be studied. The interaction between the Cu clusters and aluminum oxide surfaces (hydroxylated) will be focused on the electron transfer interaction and the effect of the hydroxyl groups on the surface. > b. Based on the results in parts b and c, the favorable reaction mechanism will be identified for catalytic CO2 reduction on supported Cu clusters. This will help the experimentalists better understand the details of the catalytic reaction and the role of the catalyst. Furthermore, insights to the effects of cluster size and support materials will be provided to guide experimental study by our collaborators. Based on this reaction mechanism, future computational studies will be carried out on different metal clusters (e.g., Co and Pt clusters) and metal alloy clusters. > An assessment of the necessary calculations indicates that at least 480,000 core hours are necessary to complete this work. > > Current: undetermined amount > Justification: > > Requested: 200000 > > A specific reason has been given: > I have used up all the allocations, and need more core hours for transition states calculations > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System > _______________________________________________ > allocations-admins mailing list > allocations-admins(a)lcrc.anl.gov > https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 08 Jul '15

08 Jul '15

Correction below... >Cong agrees to run Bio_catalysis on Fusion, and revised his request to >150K for >FY2015. Lets approve. > >Ray > >----------------------------------------- >Ray Bair >Computing, Environment, and Life Sciences >Argonne National Laboratory > and the University of Chicago >TCS Building 240, Room 4122 >9700 South Cass Avenue >Argonne, IL 60439 >email: rbair(at)anl.gov >Phone: (630)252-5751 > > > > > >On 7/1/15, 3:49 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of >accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf >of accounts(a)lcrc.anl.gov> wrote: > >>Hello, >> >>A change in allocation has been requested: >> >> Requester: coliu (Cong Liu) >> Project: Bio_catalysis >> Title: Biomass Catalysis for Energy >> Description: In FY2014, we have completed two of the above aspects, >>³identifying suitable computational methods² and ³reaction pathways². In >>FY2015, we are going to focus on the catalysis of C-C coupling reactions. >>Detailed quantum mechanical calculations will be carried out as follows: >>1. To begin with, H-ZSM5 (zeolite catalyst) will be chosen as a potential >>catalyst for C-C coupling reactions associated with biomass conversion, >>based on its strong acidity and it ability to facilitate dehydration >>reactions. A set of C1-C6 compounds will then be selected from the >>products of biomass pyrolysis, as potential C-C coupling reactants. These >>compounds are mainly alcohols, aldehydes, ketones, alkenes, and furans. >>The interactions between these individual compounds and the catalyst >>(H-ZSM5) will be studied. Specifically, the binding energies of these >>compounds onto the acidic site of the catalyst will be calculated using >>DFT methods in VASP. >>2. Based on the binding energies, the most strong-binding compounds will >>be selected for C-C coupling reactions. A reaction network will be built >>among these selected compounds. Four types of C-C coupling reactions will >>be considered: Diels-Alder, Aldol, alkylation and Michael addition. In >>addition, dehydration and deoxygenation reactions will also be taken into >>account. >>For example, H-ZSM5 catalyzed C-C coupling reactions furan interacting >>with acetaldehyde will be investigated with respect to three major >>reactions: a. furan + furan (Diels-Alder reactions and dehydration), b. >>furan + acetaldehyde (Diels-Alder reactions and alkylation) and c. >>acetaldehyde + acetaldehyde (Aldol condensation and dehydration). >>Reaction energies and barriers will be calculated. All possible reaction >>pathways will be mapped out and the most important reactions will be >>identified. These calculations will be carried out using DFT methods in >>VASP. >>3. The calculations of zeolite catalyzed C-C coupling reactions will then >>be extended to other C1-C5 compounds from biomass pyrolysis. The >>catalytic properties of the zeolite catalyst will be analyzed, and the >>correlations of C-C coupling reactions to the acidity of the catalyst >>will be identified and used as guidance to develop more efficient C-C >>coupling catalysts. >> >> Current: undetermined amount >>Justification: >> >> Requested: 480000 >> >>A specific reason has been given: >>The later stage of the project requires more allocation for the catalyst >>calculations. >> >>This needs to be approved and the final allocation amount decided upon. >> >>Thank You, >>The LCRC Accounts System > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0

Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 08 Jul '15

08 Jul '15

Cong agrees to run Hetero_Catalysis on Fusion, and revised his request to 150K for FY2015. Lets approve. Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 7/1/15, 3:48 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: coliu (Cong Liu) > Project: Hetero_Catalysis > Title: Development and Application of Accurate Theoretical Models >for Calculating the Thermodynamics of Chemical Bonds for Heterogeneous >Catalysis > Description: We will model the reaction mechanisms of the >electrocatalysis of CO2 conversion to hydrocarbons using subnanometer Cu >clusters supported by CNTs, graphene and aluminum oxide. The electronic >and catalytic properties of the nanomaterials, metal-dependence, possible >intermediates and transition states of the catalysis will be studied. >These studies will provide crucial information for molecular insight into >chemical reduction of CO2 and result in significant advancements in the >development of novel efficient nanocatalysts. >The following calculations will be performed for FY2015: > >a. The catalytic properties of materials supported metal clusters will be >explored. CNTs, graphene and aluminum oxide will be considered as support >materials. Interactions between the support materials and metal clusters >and the effect of defects on CNTs and graphene will be calculated using >DFT methods within VASP package. The simulation of defects on CNTs will >begin with a two-dimensional graphene model, with replacements of carbon >atoms by N and O. The partial charges of surrounding carbon atoms will be >determined as a parameter to measure the charge transfer interactions. >Then the interaction between the Cu clusters and CNTs will be studied. >The interaction between the Cu clusters and aluminum oxide surfaces >(hydroxylated) will be focused on the electron transfer interaction and >the effect of the hydroxyl groups on the surface. >b. Based on the results in parts b and c, the favorable reaction >mechanism will be identified for catalytic CO2 reduction on supported Cu >clusters. This will help the experimentalists better understand the >details of the catalytic reaction and the role of the catalyst. >Furthermore, insights to the effects of cluster size and support >materials will be provided to guide experimental study by our >collaborators. Based on this reaction mechanism, future computational >studies will be carried out on different metal clusters (e.g., Co and Pt >clusters) and metal alloy clusters. >An assessment of the necessary calculations indicates that at least >480,000 core hours are necessary to complete this work. > > Current: undetermined amount >Justification: > > Requested: 200000 > >A specific reason has been given: >I have used up all the allocations, and need more core hours for >transition states calculations > >This needs to be approved and the final allocation amount decided upon. > >Thank You, >The LCRC Accounts System >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

1 0